make --no-print-directory -C front-ends Rpwd
make -C ../../include -f Makefile.win version
make Rpwd.exe
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I../../include -DR_ARCH='"x64"'  -O3 -Wall -pedantic   -c rpwd.c -o rpwd.o
C:/Rtools/mingw_64/bin/windres  -DWN64  -i rcico.rc -o rcico.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -s  -o Rpwd.exe rpwd.o rcico.o  
cp front-ends/Rpwd.exe Rpwd.exe
-------- Building ../../../library/base/R/Rprofile from ../../library/profile/Common.R ../../library/profile/Rprofile.windows--------
mkdir -p ../../../library/base/R
cp -p html/rwin.html ../../../doc/html/index.html
cp -p ./etc/Makeconf ./etc/Rdevga ./etc/Rprofile.site ./etc/Rcmd_environ ./etc/Rconsole ./etc/rgb.txt ../../../etc
rm -f ../../../etc/Makeconf
mkdir -p ../../../etc//x64
sed -e 's/WIN = 32/WIN = 64/' \
  -e "s/-O3/-O2/" \
  -e "s/@EOPTS@/-mtune=generic/" \
  -e "s|BINPREF =|BINPREF ?= C:/Rtools/mingw_64/bin/|" \
  -e "s|COMPILED_BY =|COMPILED_BY = gcc-4.9.3|" \
  -e "s|IMPDIR = bin|IMPDIR = bin/x64|" \
  -e "s|LOCAL_SOFT =|LOCAL_SOFT = C:/projects/BUILD/R-source-win64/extsoft|" \
  -e "s|R_ARCH =|R_ARCH = /x64|" \
  -e "s|DT_ARCH =|DT_ARCH = |" \
  -e "s|RC_ARCH =|RC_ARCH = |" \
  -e "s|M_ARCH =|M_ARCH = |" \
  -e "s|@SYMPAT@|'s/^.* [BCDRT] / /p'|" \
  -e "s|(TCL_HOME)/bin|(TCL_HOME)/bin64|" \
  -e "s|@OPENMP@|-fopenmp|" \
  -e "s|@PTHREAD@|-pthread|" \
  -e "s@NM_FILTER =@NM_FILTER = | sed -e '/[.]refptr[.]/d' -e '/[.]weak[.]/d'@" \
  etc/Makeconf > ../../../etc/x64/Makeconf
sed -e "s+@BINDIR@+bin/x64+" Makeconf > ../../../Makeconf
cp -p ../CHANGES2 ../CHANGES0 ../CHANGES1 ../../../doc
make[5]: Nothing to be done for 'svnonly'.
installing C headers
make[6]: Nothing to be done for 'svnonly'.
installing C headers
make --no-print-directory -C ../extra/intl CFLAGS='-O3 -Wall -pedantic -mtune=generic' -f Makefile.win
sed -e 's,@''HAVE_POSIX_PRINTF''@,1,g' \
    -e 's,@''HAVE_ASPRINTF''@,0,g' \
    -e 's,@''HAVE_SNPRINTF''@,1,g' \
    -e 's,@''HAVE_WPRINTF''@,0,g' \
  < libgnuintl.h.in > libgnuintl.h
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -DIN_LIBINTL -DHAVE_CONFIG_H -I. -I../../include  -O3 -Wall -pedantic -mtune=generic   -c bindtextdom.c -o bindtextdom.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -DIN_LIBINTL -DHAVE_CONFIG_H -I. -I../../include  -O3 -Wall -pedantic -mtune=generic   -c dcgettext.c -o dcgettext.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -DIN_LIBINTL -DHAVE_CONFIG_H -I. -I../../include  -O3 -Wall -pedantic -mtune=generic   -c dgettext.c -o dgettext.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -DIN_LIBINTL -DHAVE_CONFIG_H -I. -I../../include  -O3 -Wall -pedantic -mtune=generic   -c gettext.c -o gettext.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -DIN_LIBINTL -DHAVE_CONFIG_H -I. -I../../include  -O3 -Wall -pedantic -mtune=generic   -c finddomain.c -o finddomain.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -DIN_LIBINTL -DHAVE_CONFIG_H -I. -I../../include  -O3 -Wall -pedantic -mtune=generic   -c loadmsgcat.c -o loadmsgcat.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -DIN_LIBINTL -DHAVE_CONFIG_H -I. -I../../include  -O3 -Wall -pedantic -mtune=generic   -c textdomain.c -o textdomain.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -DIN_LIBINTL -DHAVE_CONFIG_H -I. -I../../include  -O3 -Wall -pedantic -mtune=generic   -c l10nflist.c -o l10nflist.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -DIN_LIBINTL -DHAVE_CONFIG_H -I. -I../../include  -O3 -Wall -pedantic -mtune=generic   -c explodename.c -o explodename.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -DIN_LIBINTL -DHAVE_CONFIG_H -I. -I../../include -DLOCALEDIR=\"\" -O3 -Wall -pedantic -mtune=generic   -c dcigettext.c -o dcigettext.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -DIN_LIBINTL -DHAVE_CONFIG_H -I. -I../../include  -O3 -Wall -pedantic -mtune=generic   -c dcngettext.c -o dcngettext.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -DIN_LIBINTL -DHAVE_CONFIG_H -I. -I../../include  -O3 -Wall -pedantic -mtune=generic   -c dngettext.c -o dngettext.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -DIN_LIBINTL -DHAVE_CONFIG_H -I. -I../../include  -O3 -Wall -pedantic -mtune=generic   -c ngettext.c -o ngettext.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -DIN_LIBINTL -DHAVE_CONFIG_H -I. -I../../include  -O3 -Wall -pedantic -mtune=generic   -c plural.c -o plural.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -DIN_LIBINTL -DHAVE_CONFIG_H -I. -I../../include  -O3 -Wall -pedantic -mtune=generic   -c plural-exp.c -o plural-exp.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -DIN_LIBINTL -DHAVE_CONFIG_H -I. -I../../include  -O3 -Wall -pedantic -mtune=generic   -c langprefs.c -o langprefs.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -DIN_LIBINTL -DHAVE_CONFIG_H -I. -I../../include  -O3 -Wall -pedantic -mtune=generic   -c localcharset.c -o localcharset.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -DIN_LIBINTL -DHAVE_CONFIG_H -I. -I../../include  -O3 -Wall -pedantic -mtune=generic   -c localename.c -o localename.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -DIN_LIBINTL -DHAVE_CONFIG_H -I. -I../../include  -O3 -Wall -pedantic -mtune=generic   -c printf.c -o printf.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -DIN_LIBINTL -DHAVE_CONFIG_H -I. -I../../include  -O3 -Wall -pedantic -mtune=generic   -c osdep.c -o osdep.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -DIN_LIBINTL -DHAVE_CONFIG_H -I. -I../../include  -O3 -Wall -pedantic -mtune=generic   -c hash-string.c -o hash-string.o
C:/Rtools/mingw_64/bin/ar crs libintl.a bindtextdom.o dcgettext.o dgettext.o gettext.o finddomain.o loadmsgcat.o textdomain.o l10nflist.o explodename.o dcigettext.o dcngettext.o dngettext.o ngettext.o plural.o plural-exp.o langprefs.o localcharset.o localename.o printf.o osdep.o hash-string.o
cp libgnuintl.h libintl.h
make --no-print-directory -C ../appl CFLAGS='-O3 -Wall -pedantic -mtune=generic' FFLAGS='-O3 -mtune=generic' -f Makefile.win
making integrate.d from integrate.c
making interv.d from interv.c
making maxcol.d from maxcol.c
making optim.d from optim.c
making pretty.d from pretty.c
making uncmin.d from uncmin.c
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c integrate.c -o integrate.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c interv.c -o interv.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c maxcol.c -o maxcol.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c optim.c -o optim.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c pretty.c -o pretty.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c uncmin.c -o uncmin.o
C:/Rtools/mingw_64/bin/gfortran  -O3 -mtune=generic  -c dchdc.f -o dchdc.o
C:/Rtools/mingw_64/bin/gfortran  -O3 -mtune=generic  -c dpbfa.f -o dpbfa.o
C:/Rtools/mingw_64/bin/gfortran  -O3 -mtune=generic  -c dpbsl.f -o dpbsl.o
C:/Rtools/mingw_64/bin/gfortran  -O3 -mtune=generic  -c dpoco.f -o dpoco.o
C:/Rtools/mingw_64/bin/gfortran  -O3 -mtune=generic  -c dpodi.f -o dpodi.o
C:/Rtools/mingw_64/bin/gfortran  -O3 -mtune=generic  -c dpofa.f -o dpofa.o
C:/Rtools/mingw_64/bin/gfortran  -O3 -mtune=generic  -c dposl.f -o dposl.o
C:/Rtools/mingw_64/bin/gfortran  -O3 -mtune=generic  -c dqrdc.f -o dqrdc.o
C:/Rtools/mingw_64/bin/gfortran  -O3 -mtune=generic  -c dqrdc2.f -o dqrdc2.o
C:/Rtools/mingw_64/bin/gfortran  -O3 -mtune=generic  -c dqrls.f -o dqrls.o
C:/Rtools/mingw_64/bin/gfortran  -O3 -mtune=generic  -c dqrsl.f -o dqrsl.o
C:/Rtools/mingw_64/bin/gfortran  -O3 -mtune=generic  -c dqrutl.f -o dqrutl.o
C:/Rtools/mingw_64/bin/gfortran  -O3 -mtune=generic  -c dsvdc.f -o dsvdc.o
C:/Rtools/mingw_64/bin/gfortran  -O3 -mtune=generic  -c dtrco.f -o dtrco.o
C:/Rtools/mingw_64/bin/gfortran  -O3 -mtune=generic  -c dtrsl.f -o dtrsl.o
C:/Rtools/mingw_64/bin/ar crs libappl.a integrate.o interv.o maxcol.o optim.o pretty.o uncmin.o dchdc.o dpbfa.o dpbsl.o dpoco.o dpodi.o dpofa.o dposl.o dqrdc.o dqrdc2.o dqrls.o dqrsl.o dqrutl.o dsvdc.o dtrco.o dtrsl.o
make --no-print-directory -C ../nmath CFLAGS='-O3 -Wall -pedantic -mtune=generic' FFLAGS='-O3 -mtune=generic' -f Makefile.win
making mlutils.d from mlutils.c
making d1mach.d from d1mach.c
making i1mach.d from i1mach.c
making fmax2.d from fmax2.c
making fmin2.d from fmin2.c
making fprec.d from fprec.c
making fround.d from fround.c
making ftrunc.d from ftrunc.c
making sign.d from sign.c
making fsign.d from fsign.c
making imax2.d from imax2.c
making imin2.d from imin2.c
making chebyshev.d from chebyshev.c
making log1p.d from log1p.c
making lgammacor.d from lgammacor.c
making gammalims.d from gammalims.c
making stirlerr.d from stirlerr.c
making bd0.d from bd0.c
making gamma.d from gamma.c
making lgamma.d from lgamma.c
making gamma_cody.d from gamma_cody.c
making beta.d from beta.c
making lbeta.d from lbeta.c
making polygamma.d from polygamma.c
making cospi.d from cospi.c
making bessel_i.d from bessel_i.c
making bessel_j.d from bessel_j.c
making bessel_k.d from bessel_k.c
making bessel_y.d from bessel_y.c
making choose.d from choose.c
making snorm.d from snorm.c
making sexp.d from sexp.c
making dgamma.d from dgamma.c
making pgamma.d from pgamma.c
making qgamma.d from qgamma.c
making rgamma.d from rgamma.c
making dbeta.d from dbeta.c
making pbeta.d from pbeta.c
making qbeta.d from qbeta.c
making rbeta.d from rbeta.c
making dunif.d from dunif.c
making punif.d from punif.c
making qunif.d from qunif.c
making runif.d from runif.c
making dnorm.d from dnorm.c
making pnorm.d from pnorm.c
making qnorm.d from qnorm.c
making rnorm.d from rnorm.c
making dlnorm.d from dlnorm.c
making plnorm.d from plnorm.c
making qlnorm.d from qlnorm.c
making rlnorm.d from rlnorm.c
making df.d from df.c
making pf.d from pf.c
making qf.d from qf.c
making rf.d from rf.c
making dnf.d from dnf.c
making dt.d from dt.c
making pt.d from pt.c
making qt.d from qt.c
making rt.d from rt.c
making dnt.d from dnt.c
making dchisq.d from dchisq.c
making pchisq.d from pchisq.c
making qchisq.d from qchisq.c
making rchisq.d from rchisq.c
making rnchisq.d from rnchisq.c
making dbinom.d from dbinom.c
making pbinom.d from pbinom.c
making qbinom.d from qbinom.c
making rbinom.d from rbinom.c
making rmultinom.d from rmultinom.c
making dcauchy.d from dcauchy.c
making pcauchy.d from pcauchy.c
making qcauchy.d from qcauchy.c
making rcauchy.d from rcauchy.c
making dexp.d from dexp.c
making pexp.d from pexp.c
making qexp.d from qexp.c
making rexp.d from rexp.c
making dgeom.d from dgeom.c
making pgeom.d from pgeom.c
making qgeom.d from qgeom.c
making rgeom.d from rgeom.c
making dhyper.d from dhyper.c
making phyper.d from phyper.c
making qhyper.d from qhyper.c
making rhyper.d from rhyper.c
making dnbinom.d from dnbinom.c
making pnbinom.d from pnbinom.c
making qnbinom.d from qnbinom.c
making rnbinom.d from rnbinom.c
making dpois.d from dpois.c
making ppois.d from ppois.c
making qpois.d from qpois.c
making rpois.d from rpois.c
making dweibull.d from dweibull.c
making pweibull.d from pweibull.c
making qweibull.d from qweibull.c
making rweibull.d from rweibull.c
making dlogis.d from dlogis.c
making plogis.d from plogis.c
making qlogis.d from qlogis.c
making rlogis.d from rlogis.c
making dnchisq.d from dnchisq.c
making pnchisq.d from pnchisq.c
making qnchisq.d from qnchisq.c
making dnbeta.d from dnbeta.c
making pnbeta.d from pnbeta.c
making qnbeta.d from qnbeta.c
making pnf.d from pnf.c
making pnt.d from pnt.c
making qnf.d from qnf.c
making qnt.d from qnt.c
making ptukey.d from ptukey.c
making qtukey.d from qtukey.c
making toms708.d from toms708.c
making wilcox.d from wilcox.c
making signrank.d from signrank.c
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c mlutils.c -o mlutils.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c d1mach.c -o d1mach.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c i1mach.c -o i1mach.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c fmax2.c -o fmax2.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c fmin2.c -o fmin2.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c fprec.c -o fprec.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c fround.c -o fround.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c ftrunc.c -o ftrunc.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c sign.c -o sign.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c fsign.c -o fsign.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c imax2.c -o imax2.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c imin2.c -o imin2.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c chebyshev.c -o chebyshev.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c log1p.c -o log1p.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c lgammacor.c -o lgammacor.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c gammalims.c -o gammalims.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c stirlerr.c -o stirlerr.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c bd0.c -o bd0.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c gamma.c -o gamma.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c lgamma.c -o lgamma.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c gamma_cody.c -o gamma_cody.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c beta.c -o beta.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c lbeta.c -o lbeta.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c polygamma.c -o polygamma.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c cospi.c -o cospi.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c bessel_i.c -o bessel_i.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c bessel_j.c -o bessel_j.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c bessel_k.c -o bessel_k.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c bessel_y.c -o bessel_y.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c choose.c -o choose.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c snorm.c -o snorm.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c sexp.c -o sexp.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c dgamma.c -o dgamma.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c pgamma.c -o pgamma.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c qgamma.c -o qgamma.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c rgamma.c -o rgamma.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c dbeta.c -o dbeta.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c pbeta.c -o pbeta.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c qbeta.c -o qbeta.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c rbeta.c -o rbeta.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c dunif.c -o dunif.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c punif.c -o punif.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c qunif.c -o qunif.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c runif.c -o runif.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c dnorm.c -o dnorm.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c pnorm.c -o pnorm.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c qnorm.c -o qnorm.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c rnorm.c -o rnorm.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c dlnorm.c -o dlnorm.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c plnorm.c -o plnorm.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c qlnorm.c -o qlnorm.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c rlnorm.c -o rlnorm.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c df.c -o df.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c pf.c -o pf.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c qf.c -o qf.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c rf.c -o rf.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c dnf.c -o dnf.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c dt.c -o dt.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c pt.c -o pt.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c qt.c -o qt.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c rt.c -o rt.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c dnt.c -o dnt.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c dchisq.c -o dchisq.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c pchisq.c -o pchisq.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c qchisq.c -o qchisq.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c rchisq.c -o rchisq.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c rnchisq.c -o rnchisq.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c dbinom.c -o dbinom.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c pbinom.c -o pbinom.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c qbinom.c -o qbinom.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c rbinom.c -o rbinom.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c rmultinom.c -o rmultinom.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c dcauchy.c -o dcauchy.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c pcauchy.c -o pcauchy.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c qcauchy.c -o qcauchy.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c rcauchy.c -o rcauchy.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c dexp.c -o dexp.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c pexp.c -o pexp.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c qexp.c -o qexp.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c rexp.c -o rexp.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c dgeom.c -o dgeom.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c pgeom.c -o pgeom.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c qgeom.c -o qgeom.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c rgeom.c -o rgeom.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c dhyper.c -o dhyper.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c phyper.c -o phyper.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c qhyper.c -o qhyper.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c rhyper.c -o rhyper.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c dnbinom.c -o dnbinom.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c pnbinom.c -o pnbinom.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c qnbinom.c -o qnbinom.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c rnbinom.c -o rnbinom.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c dpois.c -o dpois.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c ppois.c -o ppois.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c qpois.c -o qpois.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c rpois.c -o rpois.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c dweibull.c -o dweibull.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c pweibull.c -o pweibull.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c qweibull.c -o qweibull.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c rweibull.c -o rweibull.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c dlogis.c -o dlogis.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c plogis.c -o plogis.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c qlogis.c -o qlogis.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c rlogis.c -o rlogis.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c dnchisq.c -o dnchisq.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c pnchisq.c -o pnchisq.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c qnchisq.c -o qnchisq.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c dnbeta.c -o dnbeta.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c pnbeta.c -o pnbeta.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c qnbeta.c -o qnbeta.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c pnf.c -o pnf.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c pnt.c -o pnt.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c qnf.c -o qnf.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c qnt.c -o qnt.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c ptukey.c -o ptukey.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c qtukey.c -o qtukey.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c toms708.c -o toms708.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c wilcox.c -o wilcox.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c signrank.c -o signrank.o
C:/Rtools/mingw_64/bin/ar crs libnmath.a mlutils.o d1mach.o i1mach.o fmax2.o fmin2.o fprec.o fround.o ftrunc.o sign.o fsign.o imax2.o imin2.o chebyshev.o log1p.o lgammacor.o gammalims.o stirlerr.o bd0.o gamma.o lgamma.o gamma_cody.o beta.o lbeta.o polygamma.o cospi.o bessel_i.o bessel_j.o bessel_k.o bessel_y.o choose.o snorm.o sexp.o dgamma.o pgamma.o qgamma.o rgamma.o dbeta.o pbeta.o qbeta.o rbeta.o dunif.o punif.o qunif.o runif.o dnorm.o pnorm.o qnorm.o rnorm.o dlnorm.o plnorm.o qlnorm.o rlnorm.o df.o pf.o qf.o rf.o dnf.o dt.o pt.o qt.o rt.o dnt.o dchisq.o pchisq.o qchisq.o rchisq.o rnchisq.o dbinom.o pbinom.o qbinom.o rbinom.o rmultinom.o dcauchy.o pcauchy.o qcauchy.o rcauchy.o dexp.o pexp.o qexp.o rexp.o dgeom.o pgeom.o qgeom.o rgeom.o dhyper.o phyper.o qhyper.o rhyper.o dnbinom.o pnbinom.o qnbinom.o rnbinom.o dpois.o ppois.o qpois.o rpois.o dweibull.o pweibull.o qweibull.o rweibull.o dlogis.o plogis.o qlogis.o rlogis.o dnchisq.o pnchisq.o qnchisq.o dnbeta.o pnbeta.o qnbeta.o pnf.o pnt.o qnf.o qnt.o ptukey.o qtukey.o toms708.o wilcox.o signrank.o
make --no-print-directory -C ../main CFLAGS='-O3 -Wall -pedantic -mtune=generic' FFLAGS='-O3 -mtune=generic' malloc-DEFS='' -f Makefile.win
making CommandLineArgs.d from CommandLineArgs.c
making Rdynload.d from Rdynload.c
making Renviron.d from Renviron.c
making RNG.d from RNG.c
making agrep.d from agrep.c
making altclasses.d from altclasses.c
making altrep.d from altrep.c
making apply.d from apply.c
making arithmetic.d from arithmetic.c
making array.d from array.c
making attrib.d from attrib.c
making bind.d from bind.c
making builtin.d from builtin.c
making character.d from character.c
making coerce.d from coerce.c
making colors.d from colors.c
making complex.d from complex.c
making connections.d from connections.c
making context.d from context.c
making cum.d from cum.c
making dcf.d from dcf.c
making datetime.d from datetime.c
making debug.d from debug.c
making deparse.d from deparse.c
making devices.d from devices.c
making dotcode.d from dotcode.c
making dounzip.d from dounzip.c
making dstruct.d from dstruct.c
making duplicate.d from duplicate.c
making edit.d from edit.c
making engine.d from engine.c
making envir.d from envir.c
making errors.d from errors.c
making eval.d from eval.c
making format.d from format.c
making gevents.d from gevents.c
making gram.d from gram.c
making gram-ex.d from gram-ex.c
making graphics.d from graphics.c
making grep.d from grep.c
making identical.d from identical.c
making inlined.d from inlined.c
making inspect.d from inspect.c
making internet.d from internet.c
making iosupport.d from iosupport.c
making lapack.d from lapack.c
making list.d from list.c
making localecharset.d from localecharset.c
making logic.d from logic.c
making main.d from main.c
making mapply.d from mapply.c
making match.d from match.c
making memory.d from memory.c
making mkdtemp.d from mkdtemp.c
making names.d from names.c
making objects.d from objects.c
making options.d from options.c
making paste.d from paste.c
making platform.d from platform.c
making plot.d from plot.c
making plot3d.d from plot3d.c
making plotmath.d from plotmath.c
making print.d from print.c
making printarray.d from printarray.c
making printvector.d from printvector.c
making printutils.d from printutils.c
making qsort.d from qsort.c
making radixsort.d from radixsort.c
making random.d from random.c
making raw.d from raw.c
making registration.d from registration.c
making relop.d from relop.c
making rlocale.d from rlocale.c
making saveload.d from saveload.c
making scan.d from scan.c
making seq.d from seq.c
making serialize.d from serialize.c
making sort.d from sort.c
making source.d from source.c
making split.d from split.c
making sprintf.d from sprintf.c
making startup.d from startup.c
making subassign.d from subassign.c
making subscript.d from subscript.c
making subset.d from subset.c
making summary.d from summary.c
making sysutils.d from sysutils.c
making times.d from times.c
making unique.d from unique.c
making util.d from util.c
making version.d from version.c
making g_alab_her.d from g_alab_her.c
making g_cntrlify.d from g_cntrlify.c
making g_fontdb.d from g_fontdb.c
making g_her_glyph.d from g_her_glyph.c
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c CommandLineArgs.c -o CommandLineArgs.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c Rdynload.c -o Rdynload.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c Renviron.c -o Renviron.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"' -I../nmath -O3 -Wall -pedantic -mtune=generic   -c RNG.c -o RNG.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"' -I../extra -O3 -Wall -pedantic -mtune=generic   -c agrep.c -o agrep.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c altclasses.c -o altclasses.o
altclasses.c:961:13: warning: 'make_mmap' defined but not used [-Wunused-function]
 static SEXP make_mmap(void *p, SEXP file, size_t size, int type,
             ^
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c altrep.c -o altrep.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c apply.c -o apply.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c arithmetic.c -o arithmetic.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c array.c -o array.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c attrib.c -o attrib.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c bind.c -o bind.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"' -I../gnuwin32 -O3 -Wall -pedantic -mtune=generic   -c builtin.c -o builtin.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c character.c -o character.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c coerce.c -o coerce.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c colors.c -o colors.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c complex.c -o complex.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"' -DLZMA_API_STATIC -I"C:/projects/BUILD/R-source-win64/extsoft"/include -DHAVE_CURL_CURL_H -DHAVE_LIBCURL -O3 -Wall -pedantic -mtune=generic   -c connections.c -o connections.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c context.c -o context.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c cum.c -o cum.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"' -I../extra -O3 -Wall -pedantic -mtune=generic   -c dcf.c -o dcf.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c datetime.c -o datetime.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c debug.c -o debug.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic -Wno-format  -c deparse.c -o deparse.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c devices.c -o devices.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c dotcode.c -o dotcode.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"' -IC:/projects/BUILD/R-source-win64/extsoft/include -O3 -Wall -pedantic -mtune=generic   -c dounzip.c -o dounzip.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c dstruct.c -o dstruct.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c duplicate.c -o duplicate.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"' -I../gnuwin32 -O3 -Wall -pedantic -mtune=generic   -c edit.c -o edit.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c engine.c -o engine.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c envir.c -o envir.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c errors.c -o errors.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c eval.c -o eval.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c format.c -o format.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c gevents.c -o gevents.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c gram.c -o gram.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c gram-ex.c -o gram-ex.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c graphics.c -o graphics.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"' -DPCRE_STATIC -I../extra -I../gnuwin32 -I"C:/projects/BUILD/R-source-win64/extsoft"/include -O3 -Wall -pedantic -mtune=generic   -c grep.c -o grep.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c identical.c -o identical.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c inlined.c -o inlined.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c inspect.c -o inspect.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c internet.c -o internet.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c iosupport.c -o iosupport.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c lapack.c -o lapack.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c list.c -o list.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c localecharset.c -o localecharset.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c logic.c -o logic.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c main.c -o main.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c mapply.c -o mapply.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c match.c -o match.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c memory.c -o memory.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c mkdtemp.c -o mkdtemp.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c names.c -o names.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c objects.c -o objects.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c options.c -o options.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c paste.c -o paste.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"' -I../gnuwin32 -I../extra -DPLATFORM_PKGTYPE='"win.binary"' -DPCRE_STATIC -DLZMA_API_STATIC -I"C:/projects/BUILD/R-source-win64/extsoft"/include -DUSE_ICU -I"C:/Rtools/mingw_libs"/include -DHAVE_CURL_CURL_H -DHAVE_LIBCURL -O3 -Wall -pedantic -mtune=generic   -c platform.c -o platform.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c plot.c -o plot.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c plot3d.c -o plot3d.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c plotmath.c -o plotmath.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c print.c -o print.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c printarray.c -o printarray.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c printvector.c -o printvector.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"' -I../gnuwin32 -O3 -Wall -pedantic -mtune=generic   -c printutils.c -o printutils.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c qsort.c -o qsort.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c radixsort.c -o radixsort.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c random.c -o random.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c raw.c -o raw.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c registration.c -o registration.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c relop.c -o relop.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c rlocale.c -o rlocale.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"' -I../extra/xdr -O3 -Wall -pedantic -mtune=generic   -c saveload.c -o saveload.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c scan.c -o scan.o
scan.c: In function 'scanVector':
scan.c:581:3: warning: unknown conversion type character 'l' in format [-Wformat=]
   sprintf(ConsolePrompt, "%lld: ", (long long) (n + 1));
   ^
scan.c:581:3: warning: too many arguments for format [-Wformat-extra-args]
scan.c: In function 'scanFrame':
scan.c:737:3: warning: unknown conversion type character 'l' in format [-Wformat=]
   sprintf(ConsolePrompt, "%lld: ", (long long) (n + 1));
   ^
scan.c:737:3: warning: too many arguments for format [-Wformat-extra-args]
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c seq.c -o seq.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"' -I../extra/xdr -O3 -Wall -pedantic -mtune=generic   -c serialize.c -o serialize.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c sort.c -o sort.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c source.c -o source.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c split.c -o split.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c sprintf.c -o sprintf.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c startup.c -o startup.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c subassign.c -o subassign.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c subscript.c -o subscript.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c subset.c -o subset.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c summary.c -o summary.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"' -I../gnuwin32 -O3 -Wall -pedantic -mtune=generic   -c sysutils.c -o sysutils.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c times.c -o times.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c unique.c -o unique.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"' -DLZMA_API_STATIC -I"C:/projects/BUILD/R-source-win64/extsoft"/include -DUSE_ICU -I"C:/Rtools/mingw_libs"/include -O3 -Wall -pedantic -mtune=generic   -c util.c -o util.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c version.c -o version.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c g_alab_her.c -o g_alab_her.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c g_cntrlify.c -o g_cntrlify.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c g_fontdb.c -o g_fontdb.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -DR_ARCH='"x64"'  -O3 -Wall -pedantic -mtune=generic   -c g_her_glyph.c -o g_her_glyph.o
C:/Rtools/mingw_64/bin/gfortran  -O3 -mtune=generic  -c xxxpr.f -o xxxpr.o
C:/Rtools/mingw_64/bin/ar crs libmain.a CommandLineArgs.o Rdynload.o Renviron.o RNG.o agrep.o altclasses.o altrep.o apply.o arithmetic.o array.o attrib.o bind.o builtin.o character.o coerce.o colors.o complex.o connections.o context.o cum.o dcf.o datetime.o debug.o deparse.o devices.o dotcode.o dounzip.o dstruct.o duplicate.o edit.o engine.o envir.o errors.o eval.o format.o gevents.o gram.o gram-ex.o graphics.o grep.o identical.o inlined.o inspect.o internet.o iosupport.o lapack.o list.o localecharset.o logic.o main.o mapply.o match.o memory.o mkdtemp.o names.o objects.o options.o paste.o platform.o plot.o plot3d.o plotmath.o print.o printarray.o printvector.o printutils.o qsort.o radixsort.o random.o raw.o registration.o relop.o rlocale.o saveload.o scan.o seq.o serialize.o sort.o source.o split.o sprintf.o startup.o subassign.o subscript.o subset.o summary.o sysutils.o times.o unique.o util.o version.o g_alab_her.o g_cntrlify.o g_fontdb.o g_her_glyph.o xxxpr.o
make --no-print-directory -C ./getline CFLAGS='-O3 -Wall -pedantic -mtune=generic'
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -DWin32 -I. -I../../include  -O3 -Wall -pedantic -mtune=generic   -c getline.c -o getline.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -DWin32 -I. -I../../include  -O3 -Wall -pedantic -mtune=generic   -c wc_history.c -o wc_history.o
C:/Rtools/mingw_64/bin/ar crs gl.a getline.o wc_history.o
making array.d from array.c
making cursors.d from cursors.c
making printer.d from printer.c
making strings.d from strings.c
making gimage.d from gimage.c
making menus.d from menus.c
making buttons.d from buttons.c
making stdimg.d from stdimg.c
making bitmaps.d from bitmaps.c
making status.d from status.c
making gdraw.d from gdraw.c
making fonts.d from fonts.c
making gbuttons.d from gbuttons.c
making context.d from context.c
making drawtext.d from drawtext.c
making windows.d from windows.c
making drawing.d from drawing.c
making dialogs.d from dialogs.c
making events.d from events.c
making objects.d from objects.c
making gmenus.d from gmenus.c
making init.d from init.c
making controls.d from controls.c
making arith.d from arith.c
making metafile.d from metafile.c
making rgb.d from rgb.c
making gif.d from gif.c
making image.d from image.c
making tooltips.d from tooltips.c
making clipboard.d from clipboard.c
C:/Rtools/mingw_64/bin/dlltool --as C:/Rtools/mingw_64/bin/as  -k  --dllname R.dll --input-def R.def --output-lib libR.dll.a
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../../gnuwin32 -I../../include -DGA_DLL_BUILD -DENABLE_NLS=1  -O3 -Wall -pedantic -mtune=generic   -c array.c -o array.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../../gnuwin32 -I../../include -DGA_DLL_BUILD -DENABLE_NLS=1  -O3 -Wall -pedantic -mtune=generic   -c cursors.c -o cursors.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../../gnuwin32 -I../../include -DGA_DLL_BUILD -DENABLE_NLS=1  -O3 -Wall -pedantic -mtune=generic   -c printer.c -o printer.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../../gnuwin32 -I../../include -DGA_DLL_BUILD -DENABLE_NLS=1  -O3 -Wall -pedantic -mtune=generic   -c strings.c -o strings.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../../gnuwin32 -I../../include -DGA_DLL_BUILD -DENABLE_NLS=1  -O3 -Wall -pedantic -mtune=generic   -c gimage.c -o gimage.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../../gnuwin32 -I../../include -DGA_DLL_BUILD -DENABLE_NLS=1  -O3 -Wall -pedantic -mtune=generic   -c menus.c -o menus.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../../gnuwin32 -I../../include -DGA_DLL_BUILD -DENABLE_NLS=1  -O3 -Wall -pedantic -mtune=generic   -c buttons.c -o buttons.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../../gnuwin32 -I../../include -DGA_DLL_BUILD -DENABLE_NLS=1  -O3 -Wall -pedantic -mtune=generic   -c stdimg.c -o stdimg.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../../gnuwin32 -I../../include -DGA_DLL_BUILD -DENABLE_NLS=1  -O3 -Wall -pedantic -mtune=generic   -c bitmaps.c -o bitmaps.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../../gnuwin32 -I../../include -DGA_DLL_BUILD -DENABLE_NLS=1  -O3 -Wall -pedantic -mtune=generic   -c status.c -o status.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../../gnuwin32 -I../../include -DGA_DLL_BUILD -DENABLE_NLS=1  -O3 -Wall -pedantic -mtune=generic   -c gdraw.c -o gdraw.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../../gnuwin32 -I../../include -DGA_DLL_BUILD -DENABLE_NLS=1  -O3 -Wall -pedantic -mtune=generic   -c fonts.c -o fonts.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../../gnuwin32 -I../../include -DGA_DLL_BUILD -DENABLE_NLS=1  -O3 -Wall -pedantic -mtune=generic   -c gbuttons.c -o gbuttons.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../../gnuwin32 -I../../include -DGA_DLL_BUILD -DENABLE_NLS=1  -O3 -Wall -pedantic -mtune=generic   -c context.c -o context.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../../gnuwin32 -I../../include -DGA_DLL_BUILD -DENABLE_NLS=1  -O3 -Wall -pedantic -mtune=generic   -c drawtext.c -o drawtext.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../../gnuwin32 -I../../include -DGA_DLL_BUILD -DENABLE_NLS=1  -O3 -Wall -pedantic -mtune=generic   -c windows.c -o windows.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../../gnuwin32 -I../../include -DGA_DLL_BUILD -DENABLE_NLS=1  -O3 -Wall -pedantic -mtune=generic   -c drawing.c -o drawing.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../../gnuwin32 -I../../include -DGA_DLL_BUILD -DENABLE_NLS=1  -O3 -Wall -pedantic -mtune=generic   -c dialogs.c -o dialogs.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../../gnuwin32 -I../../include -DGA_DLL_BUILD -DENABLE_NLS=1  -O3 -Wall -pedantic -mtune=generic   -c events.c -o events.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../../gnuwin32 -I../../include -DGA_DLL_BUILD -DENABLE_NLS=1  -O3 -Wall -pedantic -mtune=generic   -c objects.c -o objects.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../../gnuwin32 -I../../include -DGA_DLL_BUILD -DENABLE_NLS=1  -O3 -Wall -pedantic -mtune=generic   -c gmenus.c -o gmenus.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../../gnuwin32 -I../../include -DGA_DLL_BUILD -DENABLE_NLS=1  -O3 -Wall -pedantic -mtune=generic   -c init.c -o init.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../../gnuwin32 -I../../include -DGA_DLL_BUILD -DENABLE_NLS=1  -O3 -Wall -pedantic -mtune=generic   -c controls.c -o controls.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../../gnuwin32 -I../../include -DGA_DLL_BUILD -DENABLE_NLS=1  -O3 -Wall -pedantic -mtune=generic   -c arith.c -o arith.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../../gnuwin32 -I../../include -DGA_DLL_BUILD -DENABLE_NLS=1  -O3 -Wall -pedantic -mtune=generic   -c metafile.c -o metafile.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../../gnuwin32 -I../../include -DGA_DLL_BUILD -DENABLE_NLS=1  -O3 -Wall -pedantic -mtune=generic   -c rgb.c -o rgb.o
In file included from ga.h:29:0,
                 from rgb.c:32:
graphapp.h:43:23: note: previous declaration of 'GAbyte' was here
 typedef unsigned char GAbyte;
                       ^
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../../gnuwin32 -I../../include -DGA_DLL_BUILD -DENABLE_NLS=1  -O3 -Wall -pedantic -mtune=generic   -c gif.c -o gif.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../../gnuwin32 -I../../include -DGA_DLL_BUILD -DENABLE_NLS=1  -O3 -Wall -pedantic -mtune=generic   -c image.c -o image.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../../gnuwin32 -I../../include -DGA_DLL_BUILD -DENABLE_NLS=1  -O3 -Wall -pedantic -mtune=generic   -c tooltips.c -o tooltips.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../../gnuwin32 -I../../include -DGA_DLL_BUILD -DENABLE_NLS=1  -O3 -Wall -pedantic -mtune=generic   -c clipboard.c -o clipboard.o
C:/Rtools/mingw_64/bin/windres    -i dllversion.rc -o dllversion.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -shared -mwindows -o Rgraphapp.dll Rgraphapp.def array.o cursors.o printer.o strings.o gimage.o menus.o buttons.o stdimg.o bitmaps.o status.o gdraw.o fonts.o gbuttons.o context.o drawtext.o windows.o drawing.o dialogs.o events.o objects.o gmenus.o init.o controls.o arith.o metafile.o rgb.o gif.o image.o tooltips.o clipboard.o dllversion.o -L. -lR -lcomctl32 -limm32 -lmsimg32
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../../include -DWIN32 -DHAVE_CONFIG_H  -O3 -Wall -pedantic -mtune=generic   -c xdr.c -o xdr.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../../include -DWIN32 -DHAVE_CONFIG_H  -O3 -Wall -pedantic -mtune=generic   -c xdr_float.c -o xdr_float.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../../include -DWIN32 -DHAVE_CONFIG_H  -O3 -Wall -pedantic -mtune=generic   -c xdr_stdio.c -o xdr_stdio.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I. -I../../include -DWIN32 -DHAVE_CONFIG_H  -O3 -Wall -pedantic -mtune=generic   -c xdr_mem.c -o xdr_mem.o
C:/Rtools/mingw_64/bin/ar crs libxdr.a xdr.o xdr_float.o xdr_stdio.o xdr_mem.o
make -f Makefile.win makeMakedeps
making regcomp.d from regcomp.c
making regerror.d from regerror.c
making regexec.d from regexec.c
making tre-ast.d from tre-ast.c
making tre-compile.d from tre-compile.c
making tre-match-approx.d from tre-match-approx.c
making tre-match-backtrack.d from tre-match-backtrack.c
making tre-match-parallel.d from tre-match-parallel.c
making tre-mem.d from tre-mem.c
making tre-parse.d from tre-parse.c
making tre-stack.d from tre-stack.c
making xmalloc.d from xmalloc.c
make -f Makefile.win libtre.a
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I../../include -I. -DHAVE_CONFIG_H  -O3 -Wall -pedantic -mtune=generic   -c regcomp.c -o regcomp.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I../../include -I. -DHAVE_CONFIG_H  -O3 -Wall -pedantic -mtune=generic   -c regerror.c -o regerror.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I../../include -I. -DHAVE_CONFIG_H  -O3 -Wall -pedantic -mtune=generic   -c regexec.c -o regexec.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I../../include -I. -DHAVE_CONFIG_H  -O3 -Wall -pedantic -mtune=generic   -c tre-ast.c -o tre-ast.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I../../include -I. -DHAVE_CONFIG_H  -O3 -Wall -pedantic -mtune=generic   -c tre-compile.c -o tre-compile.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I../../include -I. -DHAVE_CONFIG_H  -O3 -Wall -pedantic -mtune=generic   -c tre-match-approx.c -o tre-match-approx.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I../../include -I. -DHAVE_CONFIG_H  -O3 -Wall -pedantic -mtune=generic   -c tre-match-backtrack.c -o tre-match-backtrack.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I../../include -I. -DHAVE_CONFIG_H  -O3 -Wall -pedantic -mtune=generic   -c tre-match-parallel.c -o tre-match-parallel.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I../../include -I. -DHAVE_CONFIG_H  -O3 -Wall -pedantic -mtune=generic   -c tre-mem.c -o tre-mem.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I../../include -I. -DHAVE_CONFIG_H  -O3 -Wall -pedantic -mtune=generic   -c tre-parse.c -o tre-parse.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I../../include -I. -DHAVE_CONFIG_H  -O3 -Wall -pedantic -mtune=generic   -c tre-stack.c -o tre-stack.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I../../include -I. -DHAVE_CONFIG_H  -O3 -Wall -pedantic -mtune=generic   -c xmalloc.c -o xmalloc.o
C:/Rtools/mingw_64/bin/ar crs libtre.a regcomp.o regerror.o regexec.o tre-ast.o tre-compile.o tre-match-approx.o tre-match-backtrack.o tre-match-parallel.o tre-mem.o tre-parse.o tre-stack.o xmalloc.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99    -O3 -Wall -pedantic -mtune=generic   -c compat.c -o compat.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99   -DTRIO_FEATURE_WIDECHAR=1 -O3 -Wall -pedantic -mtune=generic   -c trio.c -o trio.o
C:/Rtools/mingw_64/bin/ar crs libtrio.a compat.o trio.o
making localtime.d from localtime.c
making registryTZ.d from registryTZ.c
making strftime.d from strftime.c
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I../../include -I../../main  -O3 -Wall -pedantic -mtune=generic   -c localtime.c -o localtime.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I../../include -I../../main  -O3 -Wall -pedantic -mtune=generic   -c registryTZ.c -o registryTZ.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I../../include -I../../main  -O3 -Wall -pedantic -mtune=generic   -c strftime.c -o strftime.o
C:/Rtools/mingw_64/bin/ar crs libtz.a localtime.o registryTZ.o strftime.o
installing zoneinfo
making win_iconv.d from win_iconv.c
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I../../include  -O3 -Wall -pedantic -mtune=generic   -c win_iconv.c -o win_iconv.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -shared   -o Riconv.dll Riconv.def win_iconv.o  
making console.d from console.c
making dynload.d from dynload.c
making editor.d from editor.c
making embeddedR.d from embeddedR.c
making extra.d from extra.c
making malloc.d from malloc.c
making opt.d from opt.c
making pager.d from pager.c
making preferences.d from preferences.c
making psignal.d from psignal.c
making rhome.d from rhome.c
making rt_complete.d from rt_complete.c
making rui.d from rui.c
making run.d from run.c
making shext.d from shext.c
making sys-win32.d from sys-win32.c
making system.d from system.c
making dos_wglob.d from dos_wglob.c
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I../include -I. -I../extra -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c console.c -o console.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I../include -I. -I../extra -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c dynload.c -o dynload.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I../include -I. -I../extra -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c editor.c -o editor.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I../include -I. -I../extra -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c embeddedR.c -o embeddedR.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I../include -I. -I../extra -DHAVE_CONFIG_H -DR_DLL_BUILD -I../library/grDevices/src -O3 -Wall -pedantic -mtune=generic   -c extra.c -o extra.o
In file included from ../extra/graphapp/ga.h:29:0,
                 from extra.c:39:
../extra/graphapp/graphapp.h:43:23: note: previous declaration of 'GAbyte' was here
 typedef unsigned char GAbyte;
                       ^
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I../include -I. -I../extra -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c malloc.c -o malloc.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I../include -I. -I../extra -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c opt.c -o opt.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I../include -I. -I../extra -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c pager.c -o pager.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I../include -I. -I../extra -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c preferences.c -o preferences.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I../include -I. -I../extra -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c psignal.c -o psignal.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I../include -I. -I../extra -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c rhome.c -o rhome.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I../include -I. -I../extra -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c rt_complete.c -o rt_complete.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I../include -I. -I../extra -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c rui.c -o rui.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I../include -I. -I../extra -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c run.c -o run.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I../include -I. -I../extra -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c shext.c -o shext.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I../include -I. -I../extra -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c sys-win32.c -o sys-win32.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I../include -I. -I../extra -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c system.c -o system.o
In file included from ../extra/graphapp/ga.h:29:0,
                 from system.c:31:
../extra/graphapp/graphapp.h:43:23: note: previous declaration of 'GAbyte' was here
 typedef unsigned char GAbyte;
                       ^
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I../include -I. -I../extra -DHAVE_CONFIG_H -DR_DLL_BUILD  -O3 -Wall -pedantic -mtune=generic   -c dos_wglob.c -o dos_wglob.o
C:/Rtools/mingw_64/bin/windres   -I../include -i dllversion.rc -o dllversion.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -shared -s -mwindows -o R.dll R.def console.o dynload.o editor.o embeddedR.o extra.o malloc.o opt.o pager.o preferences.o psignal.o rhome.o rt_complete.o rui.o run.o shext.o sys-win32.o system.o dos_wglob.o dllversion.o ../main/libmain.a ../appl/libappl.a ../nmath/libnmath.a getline/gl.a ../extra/xdr/libxdr.a ../extra/intl/libintl.a ../extra/trio/libtrio.a ../extra/tzone/libtz.a ../extra/tre/libtre.a -fopenmp -L. -lgfortran -lquadmath -lRblas -L../../bin/x64 -lRgraphapp -lRiconv -lcomctl32 -lwinmm -lversion -L"C:/projects/BUILD/R-source-win64/extsoft"/lib/x64 -lpcre -lz -lbz2 -llzma -L"C:/Rtools/mingw_libs"/lib/x64 -lsicuin -lsicuuc -lsicudt -lstdc++ 
cp R.dll ../../bin/x64
C:/Rtools/mingw_64/bin/gfortran  -O3 -mtune=generic  -c blas.f -o blas.o
C:/Rtools/mingw_64/bin/gfortran  -O3 -mtune=generic  -c cmplxblas.f -o cmplxblas.o
-------- Building ../../../bin/x64/Rblas.dll --------
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -shared  -o ../../../bin/x64/Rblas.dll blas.o cmplxblas.o ../../gnuwin32/dllversion.o Rblas.def -L../../../bin/x64 -lR -lgfortran -lquadmath
make --no-print-directory -C front-ends
making rterm.d from rterm.c
making rgui.d from rgui.c
making Rfe.d from Rfe.c
making RSetReg.d from RSetReg.c
making graphappmain.d from graphappmain.c
making open.d from open.c
making rcmdfn.d from rcmdfn.c
making Renviron.d from Renviron.c
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I../../include -DR_ARCH='"x64"'  -O3 -Wall -pedantic   -c graphappmain.c -o graphappmain.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I../../include -DR_ARCH='"x64"' -DWin32 -O3 -Wall -pedantic   -c rgui.c -o rgui.o
C:/Rtools/mingw_64/bin/windres  -DWN64  -i rgico.rc -o rgico.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -s -mwindows  -Wl,--stack=0x4000000 -o Rgui.exe graphappmain.o rgui.o rgico.o -L../../../bin/x64 -lR -lRgraphapp 
mkdir -p ../../../bin/x64
cp Rgui.exe ../../../bin/x64/Rgui.exe
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I../../include -DR_ARCH='"x64"' -DWin32 -O3 -Wall -pedantic   -c rterm.c -o rterm.o
C:/Rtools/mingw_64/bin/windres  -DWN64  -i rtico.rc -o rtico.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -s  -Wl,--stack=0x4000000 -o Rterm.exe graphappmain.o rterm.o rtico.o -L../../../bin/x64 -lR -lRgraphapp 
mkdir -p ../../../bin/x64
cp Rterm.exe ../../../bin/x64/Rterm.exe	
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I../../include -DR_ARCH='"x64"'  -O3 -Wall -pedantic   -c rcmd.c -o rcmd.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I../../include -DR_ARCH='"x64"'  -O3 -Wall -pedantic -DBINDIR='"bin/x64"'  -c rcmdfn.c -o rcmdfn.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I../../include -DR_ARCH='"x64"'  -O3 -Wall -pedantic   -c Renviron.c -o Renviron.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -s  -o Rcmd.exe rcmd.o ../rhome.o ../shext.o rcico.o rcmdfn.o Renviron.o  
mkdir -p ../../../bin/x64
cp Rcmd.exe ../../../bin/x64/Rcmd.exe
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I../../include -DR_ARCH='"x64"'  -O3 -Wall -pedantic   -c RSetReg.c -o RSetReg.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -s  -o RSetReg.exe RSetReg.o ../rhome.o rcico.o  
mkdir -p ../../../bin/x64
cp RSetReg.exe ../../../bin/x64/RSetReg.exe
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I../../include -DR_ARCH='"x64"'  -O3 -Wall -pedantic   -c R.c -o R.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -s  -o R.exe R.o ../rhome.o ../shext.o rcico.o rcmdfn.o Renviron.o  
mkdir -p ../../../bin/x64
cp R.exe ../../../bin/x64/R.exe	
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -O3 -Wall -pedantic -DBINDIR='"bin/x64"' -I. -I../../include -DHAVE_CONFIG_H -c ../../unix/Rscript.c -o Rscript.o
C:/Rtools/mingw_64/bin/windres  -DWN64  -i rsico.rc -o rsico.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -s  -Wl,--stack=0x4000000 -o Rscript.exe Rscript.o rsico.o -L../../../bin/x64 -lR -lRgraphapp 
mkdir -p ../../../bin/x64
cp Rscript.exe ../../../bin/x64/Rscript.exe	
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I../../include -DR_ARCH='"x64"'  -O3 -Wall -pedantic   -c open.c -o open.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -s  -o open.exe open.o  
mkdir -p ../../../bin/x64
cp open.exe ../../../bin/x64/open.exe	
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I../../include -DR_ARCH='"x64"'  -O3 -Wall -pedantic   -c Rfe.c -o Rfe.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -s  -o Rfe.exe Rfe.o ../rhome.o rcico.o  
mkdir -p ../../../bin/x64
cp Rfe.exe ../../../bin/x64/Rfe.exe
mkdir -p ../../../bin
cp Rfe.exe ../../../bin/R.exe	
mkdir -p ../../../bin
cp Rfe.exe ../../../bin/Rscript.exe	
cat ../../doc/COPYRIGHTS COPYRIGHTS.win > COPYRIGHTS
make --no-print-directory -C ../modules -f Makefile.win \
  CFLAGS='-O3 -Wall -pedantic -mtune=generic' FFLAGS='-O3 -mtune=generic'
making internet.d from internet.c
making libcurl.d from libcurl.c
making nanoftp.d from nanoftp.c
making nanohttp.d from nanohttp.c
making sockconn.d from sockconn.c
making Rsock.d from Rsock.c
making sock.d from sock.c
making Rhttpd.d from Rhttpd.c
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I../../include -I../../extra/graphapp -DHAVE_CONFIG_H  -O3 -Wall -pedantic -mtune=generic   -c internet.c -o internet.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I../../include -I../../extra/graphapp -DHAVE_CONFIG_H -DHAVE_CURL_CURL_H -DHAVE_LIBCURL -DCURL_STATICLIB -I"C:/projects/BUILD/R-source-win64/libcurl"/include -O3 -Wall -pedantic -mtune=generic   -c libcurl.c -o libcurl.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I../../include -I../../extra/graphapp -DHAVE_CONFIG_H  -O3 -Wall -pedantic -mtune=generic   -c nanoftp.c -o nanoftp.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I../../include -I../../extra/graphapp -DHAVE_CONFIG_H  -O3 -Wall -pedantic -mtune=generic   -c nanohttp.c -o nanohttp.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I../../include -I../../extra/graphapp -DHAVE_CONFIG_H  -O3 -Wall -pedantic -mtune=generic   -c sockconn.c -o sockconn.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I../../include -I../../extra/graphapp -DHAVE_CONFIG_H  -O3 -Wall -pedantic -mtune=generic   -c Rhttpd.c -o Rhttpd.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I../../include -I../../extra/graphapp -DHAVE_CONFIG_H  -O3 -Wall -pedantic -mtune=generic   -c Rsock.c -o Rsock.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I../../include -I../../extra/graphapp -DHAVE_CONFIG_H  -O3 -Wall -pedantic -mtune=generic   -c sock.c -o sock.o
C:/Rtools/mingw_64/bin/windres    -i dllversion.rc -o dllversion.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -shared  -o ../../../modules/x64/internet.dll internet.o libcurl.o nanoftp.o nanohttp.o sockconn.o Rhttpd.o Rsock.o sock.o dllversion.o internet.def -L../../../bin/x64 -lR -lRgraphapp -lwininet -lws2_32 -L"C:/projects/BUILD/R-source-win64/libcurl"/lib/x64 -lcurl-dualssl -lssh2 -lz -lssl -lcrypto -lgdi32 -lws2_32 -lcrypt32 -lwldap32
making Lapack.d from Lapack.c
C:/Rtools/mingw_64/bin/gfortran  -O3 -mtune=generic -ffloat-store -c dlamch.f -o dlamch.o
C:/Rtools/mingw_64/bin/gfortran  -O3 -mtune=generic  -c dlapack.f -o dlapack.o
C:/Rtools/mingw_64/bin/gfortran  -O3 -mtune=generic  -c cmplx.f -o cmplx.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I../../include -DHAVE_CONFIG_H  -O3 -Wall -pedantic -mtune=generic   -c init_win.c -o init_win.o
C:/Rtools/mingw_64/bin/windres    -i Rlapackrc.rc -o Rlapackrc.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -shared -s -o ../../../bin/x64/Rlapack.dll dlamch.o dlapack.o cmplx.o init_win.o Rlapackrc.o -L../../../bin/x64 -lR -lRblas -lgfortran -lquadmath
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -I../../include -DHAVE_CONFIG_H  -O3 -Wall -pedantic -mtune=generic   -c Lapack.c -o Lapack.o
C:/Rtools/mingw_64/bin/windres    -i dllversion.rc -o dllversion.o
C:/Rtools/mingw_64/bin/gcc -std=gnu99  -shared -s  -o lapack.dll lapack.def Lapack.o dllversion.o -L../../../bin/x64 -lRlapack -lRblas -lR 
cp lapack.dll ../../../modules/x64/lapack.dll
building package 'base'
building package 'tools'
making text.d from text.c
making init.d from init.c
making Rmd5.d from Rmd5.c
making md5.d from md5.c
making signals.d from signals.c
making install.d from install.c
making getfmts.d from getfmts.c
making http.d from http.c
making gramLatex.d from gramLatex.c
making gramRd.d from gramRd.c
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c text.c -o text.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c init.c -o init.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c Rmd5.c -o Rmd5.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c md5.c -o md5.o
md5.c: In function 'md5_finish_ctx':
md5.c:102:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   *(md5_uint32 *) &ctx->buffer[bytes + pad] = SWAP (ctx->total[0] << 3);
   ^
md5.c:103:3: warning: dereferencing type-punned pointer will break strict-aliasing rules [-Wstrict-aliasing]
   *(md5_uint32 *) &ctx->buffer[bytes + pad + 4] = SWAP ((ctx->total[1] << 3) |
   ^
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c signals.c -o signals.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c install.c -o install.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c getfmts.c -o getfmts.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c http.c -o http.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c gramLatex.c -o gramLatex.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c gramRd.c -o gramRd.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o tools.dll tmp.def text.o init.o Rmd5.o md5.o signals.o install.o getfmts.o http.o gramLatex.o gramRd.o ../../../gnuwin32/dllversion.o -LC:/projects/BUILD/R-source-win64/extsoft/lib/x64 -LC:/projects/BUILD/R-source-win64/extsoft/lib -L../../../../bin/x64 -lR
installing 'sysdata.rda'
building package 'compiler'
byte-compiling package 'compiler'
byte-compiling package 'base'
byte-compiling package 'tools'
building package 'utils'
making init.d from init.c
making io.d from io.c
making size.d from size.c
making sock.d from sock.c
making stubs.d from stubs.c
making utils.d from utils.c
making windows/dataentry.d from windows/dataentry.c
making windows/dialogs.d from windows/dialogs.c
making windows/registry.d from windows/registry.c
making windows/util.d from windows/util.c
making windows/widgets.d from windows/widgets.c
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I../../../../src/gnuwin32 -I../../../../src/extra -I../../../../src/library/grDevices/src -DLZMA_API_STATIC -IC:/projects/BUILD/R-source-win64/extsoft/include    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c init.c -o init.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I../../../../src/gnuwin32 -I../../../../src/extra -I../../../../src/library/grDevices/src -DLZMA_API_STATIC -IC:/projects/BUILD/R-source-win64/extsoft/include    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c io.c -o io.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I../../../../src/gnuwin32 -I../../../../src/extra -I../../../../src/library/grDevices/src -DLZMA_API_STATIC -IC:/projects/BUILD/R-source-win64/extsoft/include    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c size.c -o size.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I../../../../src/gnuwin32 -I../../../../src/extra -I../../../../src/library/grDevices/src -DLZMA_API_STATIC -IC:/projects/BUILD/R-source-win64/extsoft/include    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c sock.c -o sock.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I../../../../src/gnuwin32 -I../../../../src/extra -I../../../../src/library/grDevices/src -DLZMA_API_STATIC -IC:/projects/BUILD/R-source-win64/extsoft/include    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c stubs.c -o stubs.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I../../../../src/gnuwin32 -I../../../../src/extra -I../../../../src/library/grDevices/src -DLZMA_API_STATIC -IC:/projects/BUILD/R-source-win64/extsoft/include    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c utils.c -o utils.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I../../../../src/gnuwin32 -I../../../../src/extra -I../../../../src/library/grDevices/src -DLZMA_API_STATIC -IC:/projects/BUILD/R-source-win64/extsoft/include    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c windows/dataentry.c -o windows/dataentry.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I../../../../src/gnuwin32 -I../../../../src/extra -I../../../../src/library/grDevices/src -DLZMA_API_STATIC -IC:/projects/BUILD/R-source-win64/extsoft/include    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c windows/dialogs.c -o windows/dialogs.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I../../../../src/gnuwin32 -I../../../../src/extra -I../../../../src/library/grDevices/src -DLZMA_API_STATIC -IC:/projects/BUILD/R-source-win64/extsoft/include    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c windows/registry.c -o windows/registry.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I../../../../src/gnuwin32 -I../../../../src/extra -I../../../../src/library/grDevices/src -DLZMA_API_STATIC -IC:/projects/BUILD/R-source-win64/extsoft/include    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c windows/util.c -o windows/util.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main -I../../../../src/gnuwin32 -I../../../../src/extra -I../../../../src/library/grDevices/src -DLZMA_API_STATIC -IC:/projects/BUILD/R-source-win64/extsoft/include    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c windows/widgets.c -o windows/widgets.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o utils.dll tmp.def init.o io.o size.o sock.o stubs.o utils.o windows/dataentry.o windows/dialogs.o windows/registry.o windows/util.o windows/widgets.o ../../../gnuwin32/dllversion.o -lRgraphapp -lVersion -LC:/projects/BUILD/R-source-win64/extsoft/lib/x64 -llzma -LC:/projects/BUILD/R-source-win64/extsoft/lib/x64 -LC:/projects/BUILD/R-source-win64/extsoft/lib -L../../../../bin/x64 -lR
installing 'sysdata.rda'
byte-compiling package 'utils'
building package 'grDevices'
making axis_scales.d from axis_scales.c
making chull.d from chull.c
making devices.d from devices.c
making init.d from init.c
making stubs.d from stubs.c
making colors.d from colors.c
making devPicTeX.d from devPicTeX.c
making devPS.d from devPS.c
making devWindows.d from devWindows.c
making winbitmap.d from winbitmap.c
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -I../../../../src/include -DHAVE_CONFIG_H    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c axis_scales.c -o axis_scales.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -I../../../../src/include -DHAVE_CONFIG_H    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c chull.c -o chull.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -I../../../../src/include -DHAVE_CONFIG_H    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c devices.c -o devices.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -I../../../../src/include -DHAVE_CONFIG_H    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c init.c -o init.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -I../../../../src/include -DHAVE_CONFIG_H    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c stubs.c -o stubs.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -I../../../../src/include -DHAVE_CONFIG_H    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c colors.c -o colors.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -I../../../../src/include -DHAVE_CONFIG_H    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c devPicTeX.c -o devPicTeX.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -I../../../../src/include -DHAVE_CONFIG_H   -I"C:/projects/BUILD/R-source-win64/extsoft" -I../../../../src/gnuwin32 -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c devPS.c -o devPS.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -I../../../../src/include -DHAVE_CONFIG_H   -I../../../../src/gnuwin32 -I../../../../src/extra -DR_ARCH='"x64"' -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c devWindows.c -o devWindows.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -I../../../../src/include -DHAVE_CONFIG_H   -DHAVE_PNG -DHAVE_JPEG -DHAVE_TIFF -I"C:/projects/BUILD/R-source-win64/extsoft" -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c winbitmap.c -o winbitmap.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o grDevices.dll tmp.def axis_scales.o chull.o devices.o init.o stubs.o colors.o devPicTeX.o devPS.o devWindows.o winbitmap.o ../../../gnuwin32/dllversion.o -LC:/projects/BUILD/R-source-win64/extsoft/lib/x64 -lRgraphapp -lpng -ltiff -ljpeg -lz -LC:/projects/BUILD/R-source-win64/extsoft/lib/x64 -LC:/projects/BUILD/R-source-win64/extsoft/lib -L../../../../bin/x64 -lR
byte-compiling package 'grDevices'
building package 'graphics'
making init.d from init.c
making base.d from base.c
making graphics.d from graphics.c
making par.d from par.c
making plot.d from plot.c
making plot3d.d from plot3d.c
making stem.d from stem.c
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c init.c -o init.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c base.c -o base.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c graphics.c -o graphics.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c par.c -o par.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c plot.c -o plot.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c plot3d.c -o plot3d.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -I../../../../src/include -DHAVE_CONFIG_H -I../../../../src/main    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c stem.c -o stem.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o graphics.dll tmp.def init.o base.o graphics.o par.o plot.o plot3d.o stem.o ../../../gnuwin32/dllversion.o -LC:/projects/BUILD/R-source-win64/extsoft/lib/x64 -LC:/projects/BUILD/R-source-win64/extsoft/lib -L../../../../bin/x64 -lR
byte-compiling package 'graphics'
building package 'stats'
making init.d from init.c
making kmeans.d from kmeans.c
making ansari.d from ansari.c
making bandwidths.d from bandwidths.c
making chisqsim.d from chisqsim.c
making d2x2xk.d from d2x2xk.c
making fexact.d from fexact.c
making kendall.d from kendall.c
making ks.d from ks.c
making line.d from line.c
making smooth.d from smooth.c
making prho.d from prho.c
making swilk.d from swilk.c
making ksmooth.d from ksmooth.c
making loessc.d from loessc.c
making monoSpl.d from monoSpl.c
making isoreg.d from isoreg.c
making Srunmed.d from Srunmed.c
making dblcen.d from dblcen.c
making distance.d from distance.c
making hclust-utils.d from hclust-utils.c
making nls.d from nls.c
making rWishart.d from rWishart.c
making HoltWinters.d from HoltWinters.c
making PPsum.d from PPsum.c
making arima.d from arima.c
making burg.d from burg.c
making filter.d from filter.c
making mAR.d from mAR.c
making pacf.d from pacf.c
making starma.d from starma.c
making port.d from port.c
making family.d from family.c
making sbart.d from sbart.c
making approx.d from approx.c
making loglin.d from loglin.c
making lowess.d from lowess.c
making massdist.d from massdist.c
making splines.d from splines.c
making lm.d from lm.c
making complete_cases.d from complete_cases.c
making cov.d from cov.c
making deriv.d from deriv.c
making fft.d from fft.c
making fourier.d from fourier.c
making model.d from model.c
making optim.d from optim.c
making optimize.d from optimize.c
making integrate.d from integrate.c
making random.d from random.c
making distn.d from distn.c
making zeroin.d from zeroin.c
making rcont.d from rcont.c
making influence.d from influence.c
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -DHAVE_CONFIG_H -I../../../../src/include    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c init.c -o init.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -DHAVE_CONFIG_H -I../../../../src/include    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c kmeans.c -o kmeans.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -DHAVE_CONFIG_H -I../../../../src/include    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ansari.c -o ansari.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -DHAVE_CONFIG_H -I../../../../src/include    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c bandwidths.c -o bandwidths.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -DHAVE_CONFIG_H -I../../../../src/include    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c chisqsim.c -o chisqsim.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -DHAVE_CONFIG_H -I../../../../src/include    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c d2x2xk.c -o d2x2xk.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -DHAVE_CONFIG_H -I../../../../src/include    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c fexact.c -o fexact.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -DHAVE_CONFIG_H -I../../../../src/include    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c kendall.c -o kendall.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -DHAVE_CONFIG_H -I../../../../src/include    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ks.c -o ks.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -DHAVE_CONFIG_H -I../../../../src/include    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c line.c -o line.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -DHAVE_CONFIG_H -I../../../../src/include    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c smooth.c -o smooth.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -DHAVE_CONFIG_H -I../../../../src/include    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c prho.c -o prho.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -DHAVE_CONFIG_H -I../../../../src/include    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c swilk.c -o swilk.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -DHAVE_CONFIG_H -I../../../../src/include    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ksmooth.c -o ksmooth.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -DHAVE_CONFIG_H -I../../../../src/include    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c loessc.c -o loessc.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -DHAVE_CONFIG_H -I../../../../src/include    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c monoSpl.c -o monoSpl.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -DHAVE_CONFIG_H -I../../../../src/include    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c isoreg.c -o isoreg.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -DHAVE_CONFIG_H -I../../../../src/include    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c Srunmed.c -o Srunmed.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -DHAVE_CONFIG_H -I../../../../src/include    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c dblcen.c -o dblcen.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -DHAVE_CONFIG_H -I../../../../src/include    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c distance.c -o distance.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -DHAVE_CONFIG_H -I../../../../src/include    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c hclust-utils.c -o hclust-utils.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -DHAVE_CONFIG_H -I../../../../src/include    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c nls.c -o nls.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -DHAVE_CONFIG_H -I../../../../src/include    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c rWishart.c -o rWishart.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -DHAVE_CONFIG_H -I../../../../src/include    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c HoltWinters.c -o HoltWinters.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -DHAVE_CONFIG_H -I../../../../src/include    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c PPsum.c -o PPsum.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -DHAVE_CONFIG_H -I../../../../src/include    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c arima.c -o arima.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -DHAVE_CONFIG_H -I../../../../src/include    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c burg.c -o burg.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -DHAVE_CONFIG_H -I../../../../src/include    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c filter.c -o filter.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -DHAVE_CONFIG_H -I../../../../src/include    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c mAR.c -o mAR.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -DHAVE_CONFIG_H -I../../../../src/include    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c pacf.c -o pacf.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -DHAVE_CONFIG_H -I../../../../src/include    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c starma.c -o starma.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -DHAVE_CONFIG_H -I../../../../src/include    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c port.c -o port.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -DHAVE_CONFIG_H -I../../../../src/include    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c family.c -o family.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -DHAVE_CONFIG_H -I../../../../src/include    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c sbart.c -o sbart.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -DHAVE_CONFIG_H -I../../../../src/include    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c approx.c -o approx.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -DHAVE_CONFIG_H -I../../../../src/include    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c loglin.c -o loglin.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -DHAVE_CONFIG_H -I../../../../src/include    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c lowess.c -o lowess.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -DHAVE_CONFIG_H -I../../../../src/include    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c massdist.c -o massdist.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -DHAVE_CONFIG_H -I../../../../src/include    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c splines.c -o splines.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -DHAVE_CONFIG_H -I../../../../src/include    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c lm.c -o lm.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -DHAVE_CONFIG_H -I../../../../src/include    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c complete_cases.c -o complete_cases.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -DHAVE_CONFIG_H -I../../../../src/include    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c cov.c -o cov.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -DHAVE_CONFIG_H -I../../../../src/include    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c deriv.c -o deriv.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -DHAVE_CONFIG_H -I../../../../src/include    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c fft.c -o fft.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -DHAVE_CONFIG_H -I../../../../src/include    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c fourier.c -o fourier.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -DHAVE_CONFIG_H -I../../../../src/include    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c model.c -o model.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -DHAVE_CONFIG_H -I../../../../src/include    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c optim.c -o optim.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -DHAVE_CONFIG_H -I../../../../src/include    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c optimize.c -o optimize.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -DHAVE_CONFIG_H -I../../../../src/include    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c integrate.c -o integrate.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -DHAVE_CONFIG_H -I../../../../src/include    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c random.c -o random.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -DHAVE_CONFIG_H -I../../../../src/include    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c distn.c -o distn.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -DHAVE_CONFIG_H -I../../../../src/include    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c zeroin.c -o zeroin.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -DHAVE_CONFIG_H -I../../../../src/include    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c rcont.c -o rcont.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -DHAVE_CONFIG_H -I../../../../src/include    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c influence.c -o influence.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c bsplvd.f -o bsplvd.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c bvalue.f -o bvalue.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c bvalus.f -o bvalus.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c loessf.f -o loessf.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c ppr.f -o ppr.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c qsbart.f -o qsbart.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c sgram.f -o sgram.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c sinerp.f -o sinerp.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c sslvrg.f -o sslvrg.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c stxwx.f -o stxwx.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c hclust.f -o hclust.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c kmns.f -o kmns.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c eureka.f -o eureka.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c stl.f -o stl.o
C:/Rtools/mingw_64/bin/gfortran  -O2 -msse2 -mfpmath=sse -c portsrc.f -o portsrc.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c lminfl.f -o lminfl.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o stats.dll stats-win.def init.o kmeans.o ansari.o bandwidths.o chisqsim.o d2x2xk.o fexact.o kendall.o ks.o line.o smooth.o prho.o swilk.o ksmooth.o loessc.o monoSpl.o isoreg.o Srunmed.o dblcen.o distance.o hclust-utils.o nls.o rWishart.o HoltWinters.o PPsum.o arima.o burg.o filter.o mAR.o pacf.o starma.o port.o family.o sbart.o approx.o loglin.o lowess.o massdist.o splines.o lm.o complete_cases.o cov.o deriv.o fft.o fourier.o model.o optim.o optimize.o integrate.o random.o distn.o zeroin.o rcont.o influence.o bsplvd.o bvalue.o bvalus.o loessf.o ppr.o qsbart.o sgram.o sinerp.o sslvrg.o stxwx.o hclust.o kmns.o eureka.o stl.o portsrc.o lminfl.o ../../../gnuwin32/dllversion.o -L../../../../bin/x64 -lRlapack -L../../../../bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/projects/BUILD/R-source-win64/extsoft/lib/x64 -LC:/projects/BUILD/R-source-win64/extsoft/lib -L../../../../bin/x64 -lR
byte-compiling package 'stats'
building package 'datasets'
building package 'methods'
making do_substitute_direct.d from do_substitute_direct.c
making init.d from init.c
making methods_list_dispatch.d from methods_list_dispatch.c
making slot.d from slot.c
making class_support.d from class_support.c
making tests.d from tests.c
making utils.d from utils.c
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -I../../../../src/include -DHAVE_CONFIG_H    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c do_substitute_direct.c -o do_substitute_direct.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -I../../../../src/include -DHAVE_CONFIG_H    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c init.c -o init.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -I../../../../src/include -DHAVE_CONFIG_H    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c methods_list_dispatch.c -o methods_list_dispatch.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -I../../../../src/include -DHAVE_CONFIG_H    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c slot.c -o slot.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -I../../../../src/include -DHAVE_CONFIG_H    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c class_support.c -o class_support.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -I../../../../src/include -DHAVE_CONFIG_H    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c tests.c -o tests.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -I../../../../src/include -DHAVE_CONFIG_H    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c utils.c -o utils.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o methods.dll tmp.def do_substitute_direct.o init.o methods_list_dispatch.o slot.o class_support.o tests.o utils.o ../../../gnuwin32/dllversion.o -LC:/projects/BUILD/R-source-win64/extsoft/lib/x64 -LC:/projects/BUILD/R-source-win64/extsoft/lib -L../../../../bin/x64 -lR
byte-compiling 'methods'
initializing class and method definitions ... done
building package 'grid'
making gpar.d from gpar.c
making grid.d from grid.c
making just.d from just.c
making layout.d from layout.c
making matrix.d from matrix.c
making register.d from register.c
making state.d from state.c
making unit.d from unit.c
making util.d from util.c
making viewport.d from viewport.c
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c gpar.c -o gpar.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c grid.c -o grid.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c just.c -o just.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c layout.c -o layout.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c matrix.c -o matrix.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c register.c -o register.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c state.c -o state.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c unit.c -o unit.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c util.c -o util.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c viewport.c -o viewport.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o grid.dll grid-win.def gpar.o grid.o just.o layout.o matrix.o register.o state.o unit.o util.o viewport.o ../../../gnuwin32/dllversion.o -LC:/projects/BUILD/R-source-win64/extsoft/lib/x64 -LC:/projects/BUILD/R-source-win64/extsoft/lib -L../../../../bin/x64 -lR
byte-compiling package 'grid'
building package 'splines'
making splines.d from splines.c
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c splines.c -o splines.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o splines.dll tmp.def splines.o ../../../gnuwin32/dllversion.o -LC:/projects/BUILD/R-source-win64/extsoft/lib/x64 -LC:/projects/BUILD/R-source-win64/extsoft/lib -L../../../../bin/x64 -lR
byte-compiling package 'splines'
building package 'stats4'
byte-compiling package 'stats4'
building package 'tcltk'
making init.d from init.c
making tcltk.d from tcltk.c
making tcltk_win.d from tcltk_win.c
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -I "../../../../Tcl"/include -DWin32 -I../../../../src/include -DHAVE_CONFIG_H    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c init.c -o init.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -I "../../../../Tcl"/include -DWin32 -I../../../../src/include -DHAVE_CONFIG_H    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c tcltk.c -o tcltk.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG -I "../../../../Tcl"/include -DWin32 -I../../../../src/include -DHAVE_CONFIG_H    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c tcltk_win.c -o tcltk_win.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o tcltk.dll tmp.def init.o tcltk.o tcltk_win.o ../../../gnuwin32/dllversion.o -L../../../../Tcl/bin64 -ltcl86 -ltk86 -LC:/projects/BUILD/R-source-win64/extsoft/lib/x64 -LC:/projects/BUILD/R-source-win64/extsoft/lib -L../../../../bin/x64 -lR
byte-compiling package 'tcltk'
building package 'parallel'
making init.d from init.c
making rngstream.d from rngstream.c
making ncpus.d from ncpus.c
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c init.c -o init.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c rngstream.c -o rngstream.o
C:/Rtools/mingw_64/bin/gcc  -I"../../../../include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ncpus.c -o ncpus.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o parallel.dll tmp.def init.o rngstream.o ncpus.o ../../../gnuwin32/dllversion.o -LC:/projects/BUILD/R-source-win64/extsoft/lib/x64 -LC:/projects/BUILD/R-source-win64/extsoft/lib -L../../../../bin/x64 -lR
byte-compiling package 'parallel'
building package 'translations'
installing parsed NAMESPACE files
installing parsed Rd: base stats utils methods graphics grDevices datasets grid tools tcltk splines stats4 compiler parallel
building/updating package metadata ...
writing indices for package: base tools utils grDevices graphics stats datasets methods grid splines stats4 tcltk compiler parallel
building all R object docs
  converting help for package 'base'
    abbreviate                              html  
    agrep                                   html  
    all.equal                               html  
    all                                     html  
    allnames                                html  
    any                                     html  
    aperm                                   html  
    append                                  html  
    apply                                   html  
    args                                    html  
    Arithmetic                              html  
Rd warning: C:/projects/BUILD/R-source-win64/src/library/base/man/Arithmetic.Rd:158: file link 'Ops' in package 'base' does not exist and so has been treated as a topic
    array                                   html  
    as.data.frame                           html  
    as.Date                                 html  
    as.environment                          html  
    as.function                             html  
    as.POSIXlt                              html  
Rd warning: C:/projects/BUILD/R-source-win64/src/library/base/man/as.POSIXlt.Rd:141: file link 'format.POSIXlt' in package 'base' does not exist and so has been treated as a topic
    AsIs                                    html  
    asplit                                  html  
    assign                                  html  
    assignOps                               html  
    attach                                  html  
    attr                                    html  
    attributes                              html  
    autoload                                html  
    backsolve                               html  
    base-defunct                            html  
    base-deprecated                         html  
    base-internal                           html  
    base-package                            html  
    basename                                html  
    Bessel                                  html  
    bincode                                 html  
    bindenv                                 html  
    bitwise                                 html  
    body                                    html  
    bquote                                  html  
    browser                                 html  
    browserText                             html  
    builtins                                html  
    by                                      html  
    c                                       html  
    call                                    html  
    callCC                                  html  
    CallExternal                            html  
    capabilities                            html  
    cat                                     html  
    cbind                                   html  
    char.expand                             html  
    character                               html  
    charmatch                               html  
    chartr                                  html  
    chkDots                                 html  
    chol                                    html  
    chol2inv                                html  
    class                                   html  
    col                                     html  
    colnames                                html  
    Colon                                   html  
    colSums                                 html  
    commandArgs                             html  
    comment                                 html  
    Comparison                              html  
Rd warning: C:/projects/BUILD/R-source-win64/src/library/base/man/Comparison.Rd:101: file link 'Ops' in package 'base' does not exist and so has been treated as a topic
    complex                                 html  
    conditions                              html  
    conflicts                               html  
    connections                             html  
    Constants                               html  
    contributors                            html  
    Control                                 html  
    copyright                               html  
    crossprod                               html  
    Cstack_info                             html  
    cumsum                                  html  
    curlGetHeaders                          html  
    cut.POSIXt                              html  
    cut                                     html  
    data.class                              html  
    data.frame                              html  
    data.matrix                             html  
    dataframeHelpers                        html  
    date                                    html  
    Dates                                   html  
    DateTimeClasses                         html  
    dcf                                     html  
    debug                                   html  
Rd warning: C:/projects/BUILD/R-source-win64/src/library/base/man/debug.Rd:73: file link 'isRematched' in package 'methods' does not exist and so has been treated as a topic
    Defunct                                 html  
    delayedAssign                           html  
    deparse                                 html  
    deparseOpts                             html  
    Deprecated                              html  
    det                                     html  
    detach                                  html  
    dev                                     html  
    diag                                    html  
    diff                                    html  
    difftime                                html  
    dim                                     html  
    dimnames                                html  
    do.call                                 html  
    dontCheck                               html  
    dots                                    html  
    double                                  html  
    dput                                    html  
    drop                                    html  
    droplevels                              html  
    dump                                    html  
    duplicated                              html  
    dynload                                 html  
    eapply                                  html  
    eigen                                   html  
    encodeString                            html  
    Encoding                                html  
    environment                             html  
    EnvVar                                  html  
    eval                                    html  
    exists                                  html  
    expand.grid                             html  
    expression                              html  
    Extract.data.frame                      html  
    Extract.factor                          html  
    Extract                                 html  
    Extremes                                html  
    extSoftVersion                          html  
    factor                                  html  
    file.access                             html  
    file.choose                             html  
    file.info                               html  
    file.path                               html  
    file.show                               html  
    files                                   html  
    files2                                  html  
    find.package                            html  
    findInterval                            html  
    force                                   html  
    forceAndCall                            html  
    Foreign-internal                        html  
    Foreign                                 html  
    formals                                 html  
    format.info                             html  
    format.pval                             html  
    format                                  html  
    formatc                                 html  
    formatDL                                html  
    function                                html  
    funprog                                 html  
    gc                                      html  
    gc.time                                 html  
    gctorture                               html  
    get                                     html  
    getCallingDLL                           html  
    getDLLRegisteredRoutines                html  
    getLoadedDLLs                           html  
    getNativeSymbolInfo                     html  
    gettext                                 html  
    getwd                                   html  
    gl                                      html  
    grep                                    html  
    grepRaw                                 html  
    groupGeneric                            html  
    grouping                                html  
    gzcon                                   html  
    hexmode                                 html  
    Hyperbolic                              html  
    iconv                                   html  
    icuSetCollate                           html  
    identical                               html  
    identity                                html  
    ifelse                                  html  
    integer                                 html  
    interaction                             html  
    interactive                             html  
    Internal                                html  
    InternalMethods                         html  
    invisible                               html  
    is.finite                               html  
    is.function                             html  
    is.language                             html  
    is.object                               html  
    is.recursive                            html  
    is.single                               html  
    is.unsorted                             html  
    ISOdatetime                             html  
    isR                                     html  
    isS4                                    html  
    isSymmetric                             html  
    jitter                                  html  
    kappa                                   html  
    kronecker                               html  
    l10n_info                               html  
    La_library                              html  
    La_version                              html  
    labels                                  html  
    lapply                                  html  
    Last.value                              html  
    lazyload                                html  
    length                                  html  
    lengths                                 html  
    levels                                  html  
    libcurlVersion                          html  
    libPaths                                html  
    library.dynam                           html  
    library                                 html  
    license                                 html  
    list.files                              html  
    list                                    html  
    list2env                                html  
    load                                    html  
    locales                                 html  
    Log                                     html  
    Logic                                   html  
Rd warning: C:/projects/BUILD/R-source-win64/src/library/base/man/Logic.Rd:110: file link 'Ops' in package 'base' does not exist and so has been treated as a topic
    logical                                 html  
    LongVectors                             html  
    lower.tri                               html  
    ls                                      html  
    make.names                              html  
    make.unique                             html  
    mapply                                  html  
    margin.table                            html  
    mat.or.vec                              html  
    match.arg                               html  
    match.call                              html  
    match.fun                               html  
    match                                   html  
    MathFun                                 html  
    matmult                                 html  
    matrix                                  html  
    maxCol                                  html  
    mean                                    html  
    memCompress                             html  
    memlimits                               html  
    Memory-limits                           html  
    memory.profile                          html  
    Memory                                  html  
    merge                                   html  
    message                                 html  
    missing                                 html  
    mode                                    html  
    NA                                      html  
    name                                    html  
    names                                   html  
    nargs                                   html  
    nchar                                   html  
    nlevels                                 html  
    noquote                                 html  
    norm                                    html  
    normalizePath                           html  
    notyet                                  html  
    nrow                                    html  
    ns-dblcolon                             html  
    ns-hooks                                html  
    ns-internal                             html  
    ns-load                                 html  
    ns-reflect                              html  
    ns-topenv                               html  
    NULL                                    html  
    numeric                                 html  
    numeric_version                         html  
    NumericConstants                        html  
    octmode                                 html  
    on.exit                                 html  
    Ops.Date                                html  
    options                                 html  
    order                                   html  
    outer                                   html  
    Paren                                   html  
    parse                                   html  
    paste                                   html  
    path.expand                             html  
    pcre_config                             html  
    Platform                                html  
    pmatch                                  html  
    polyroot                                html  
    pos.to.env                              html  
    pretty                                  html  
    Primitive                               html  
    print.dataframe                         html  
    print.default                           html  
    print                                   html  
Rd warning: C:/projects/BUILD/R-source-win64/src/library/base/man/print.Rd:86: file link '.print.via.format' in package 'tools' does not exist and so has been treated as a topic
    prmatrix                                html  
    proc.time                               html  
    prod                                    html  
    prop.table                              html  
    pushBack                                html  
    qr                                      html  
    qraux                                   html  
    quit                                    html  
    Quotes                                  html  
    Random-user                             html  
    Random                                  html  
    range                                   html  
    rank                                    html  
    rapply                                  html  
    raw                                     html  
    rawConnection                           html  
    rawConversion                           html  
    RdUtils                                 html  
    readBin                                 html  
    readChar                                html  
    readline                                html  
    readLines                               html  
    readRDS                                 html  
    readRenviron                            html  
    Recall                                  html  
    reg.finalizer                           html  
    regex                                   html  
    regmatches                              html  
    rep                                     html  
    replace                                 html  
    Reserved                                html  
    rev                                     html  
    Rhome                                   html  
    rle                                     html  
    rm                                      html  
    round.POSIXt                            html  
    Round                                   html  
    row.names                               html  
    row                                     html  
    rowsum                                  html  
    sample                                  html  
    save                                    html  
    scale                                   html  
    scan                                    html  
    search                                  html  
    seek                                    html  
    seq.Date                                html  
    seq.POSIXt                              html  
    seq                                     html  
    sequence                                html  
    serialize                               html  
    sets                                    html  
    setTimeLimit                            html  
    showConnections                         html  
    shQuote                                 html  
    sign                                    html  
    sink                                    html  
    slice.index                             html  
    slotOp                                  html  
    socketSelect                            html  
    solve                                   html  
    sort                                    html  
    source                                  html  
    Special                                 html  
    split                                   html  
    sprintf                                 html  
    sQuote                                  html  
    srcfile                                 html  
    standardGeneric                         html  
    startsWith                              html  
    Startup                                 html  
    stop                                    html  
    stopifnot                               html  
    strptime                                html  
    strrep                                  html  
    strsplit                                html  
    strtoi                                  html  
    strtrim                                 html  
    structure                               html  
    strwrap                                 html  
    subset                                  html  
    substitute                              html  
    substr                                  html  
    sum                                     html  
    summary                                 html  
    svd                                     html  
    sweep                                   html  
    switch                                  html  
    Syntax                                  html  
    Sys.getenv                              html  
    Sys.getpid                              html  
    Sys.glob                                html  
    Sys.info                                html  
    Sys.localeconv                          html  
    sys.parent                              html  
    Sys.readlink                            html  
    Sys.setenv                              html  
    Sys.setFileTime                         html  
    Sys.sleep                               html  
    sys.source                              html  
    Sys.time                                html  
    Sys.which                               html  
    system.file                             html  
    system                                  html  
    system.time                             html  
    system2                                 html  
    t                                       html  
    table                                   html  
    tabulate                                html  
    tapply                                  html  
    taskCallback                            html  
    taskCallbackManager                     html  
    taskCallbackNames                       html  
    tempfile                                html  
    textconnections                         html  
    tilde                                   html  
    timezones                               html  
    toString                                html  
    trace                                   html  
    traceback                               html  
    tracemem                                html  
    transform                               html  
    Trig                                    html  
    trimws                                  html  
    try                                     html  
    typeof                                  html  
    unique                                  html  
    unlink                                  html  
    unlist                                  html  
    unname                                  html  
    UseMethod                               html  
    userhooks                               html  
    utf8Conversion                          html  
    validUTF8                               html  
    vector                                  html  
    Vectorize                               html  
    Version                                 html  
    warning                                 html  
    warnings                                html  
    weekday.POSIXt                          html  
    which.min                               html  
    which                                   html  
    with                                    html  
    withVisible                             html  
    write                                   html  
    writeLines                              html  
    xtfrm                                   html  
    zapsmall                                html  
    zMachine                                html  
    zpackages                               html  
    zScript                                 html  
    zutils                                  html  
    shell.exec                              html  
    shell                                   html  
  converting help for package 'tools'
    add_datalist                            html  
    assertCondition                         html  
    bibstyle                                html  
    buildVignette                           html  
    buildVignettes                          html  
    charsets                                html  
    check_packages_in_dir                   html  
Rd warning: C:/projects/BUILD/R-source-win64/src/library/tools/man/check_packages_in_dir.Rd:122: file link 'mclapply' in package 'parallel' does not exist and so has been treated as a topic
Rd warning: C:/projects/BUILD/R-source-win64/src/library/tools/man/check_packages_in_dir.Rd:123: file link 'parLapply' in package 'parallel' does not exist and so has been treated as a topic
    checkFF                                 html  
    checkMD5sums                            html  
    checkPoFiles                            html  
    checkRd                                 html  
    checkRdaFiles                           html  
    checkTnF                                html  
    checkVignettes                          html  
    codoc                                   html  
    compactPDF                              html  
    CRANtools                               html  
    delimMatch                              html  
    dependsOnPkgs                           html  
    encoded                                 html  
    fileutils                               html  
    find_gs_cmd                             html  
    getVignetteInfo                         html  
    HTMLheader                              html  
    HTMLlinks                               html  
    loadRdMacros                            html  
    make_translations_pkg                   html  
    makeLazyLoading                         html  
    makevars                                html  
    md5sum                                  html  
    package_dependencies                    html  
    package_native_routine_registration_skeleton
                                            html  
    parse_Rd                                html  
    parseLatex                              html  
    print.via.format                        html  
    pskill                                  html  
    psnice                                  html  
    QC                                      html  
    Rcmd                                    html  
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    Rdutils                                 html  
    read.00Index                            html  
    showNonASCII                            html  
    startDynamicHelp                        html  
    SweaveTeXFilter                         html  
    testInstalledPackage                    html  
    texi2dvi                                html  
    toHTML                                  html  
    tools-defunct                           html  
    tools-deprecated                        html  
    tools-package                           html  
    toRd                                    html  
    toTitleCase                             html  
    undoc                                   html  
    update_pkg_po                           html  
    updatePACKAGES                          html  
    vignetteEngine                          html  
    vignetteInfo                            html  
    writePACKAGES                           html  
    xgettext                                html  
  converting help for package 'utils'
    adist                                   html  
    alarm                                   html  
    apropos                                 html  
    aregexec                                html  
    arrangeWindows                          html  
    askYesNo                                html  
    aspell-utils                            html  
    aspell                                  html  
    available.packages                      html  
    BATCH                                   html  
    bibentry                                html  
    browseEnv                               html  
    browseURL                               html  
    browseVignettes                         html  
    bug.report                              html  
    capture.output                          html  
    changedFiles                            html  
    choose.dir                              html  
    choose.files                            html  
    chooseBioCmirror                        html  
    chooseCRANmirror                        html  
    citation                                html  
    cite                                    html  
    citEntry                                html  
    clipboard                               html  
    close.socket                            html  
    combn                                   html  
    compareVersion                          html  
    COMPILE                                 html  
    contrib.url                             html  
    count.fields                            html  
    create.post                             html  
    data                                    html  
    dataentry                               html  
    debugcall                               html  
    debugger                                html  
    demo                                    html  
    DLL.version                             html  
    download.file                           html  
    download.packages                       html  
    edit.data.frame                         html  
    edit                                    html  
    example                                 html  
    file.edit                               html  
    filetest                                html  
    findLineNum                             html  
    fix                                     html  
    flush.console                           html  
    format                                  html  
    getAnywhere                             html  
    getFromNamespace                        html  
    getParseData                            html  
    getS3method                             html  
    getWindowsHandle                        html  
    getWindowsHandles                       html  
    glob2rx                                 html  
    globalVariables                         html  
    hasName                                 html  
    head                                    html  
    help                                    html  
    help.request                            html  
    help.search                             html  
    help.start                              html  
    hsearch-utils                           html  
    install.packages                        html  
    INSTALL                                 html  
    installed.packages                      html  
    isS3method                              html  
    isS3stdGen                              html  
    LINK                                    html  
    localeToCharset                         html  
    ls_str                                  html  
    maintainer                              html  
    make.packages.html                      html  
    make.socket                             html  
    memory.size                             html  
    menu                                    html  
    methods                                 html  
    mirrorAdmin                             html  
    modifyList                              html  
    news                                    html  
    nsl                                     html  
    object.size                             html  
    package.skeleton                        html  
    packageDescription                      html  
    packageName                             html  
    packageStatus                           html  
    page                                    html  
    person                                  html  
    PkgUtils                                html  
    process.events                          html  
    prompt                                  html  
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    Question                                html  
    rcompgen                                html  
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    read.table                              html  
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    recover                                 html  
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    remove.packages                         html  
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    Rprof                                   html  
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    Rtangle                                 html  
    RweaveLatex                             html  
    savehistory                             html  
    select.list                             html  
    sessionInfo                             html  
    setRepositories                         html  
    setWindowTitle                          html  
    SHLIB                                   html  
    shortPathName                           html  
    sourceutils                             html  
    stack                                   html  
    str                                     html  
    strcapture                              html  
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    toLatex                                 html  
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    type.convert                            html  
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    unzip                                   html  
    update.packages                         html  
    url.show                                html  
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    utils-defunct                           html  
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    utils-package                           html  
    View                                    html  
    vignette                                html  
    warnErrList                             html  
    winDialog                               html  
    winextras                               html  
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    zip                                     html  
  converting help for package 'grDevices'
    adjustcolor                             html  
    as.graphicsAnnot                        html  
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    boxplot.stats                           html  
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    cairo                                   html  
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    cm                                      html  
    col2rgb                                 html  
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    contourLines                            html  
    convertColor                            html  
    densCols                                html  
    dev.capabilities                        html  
    dev.capture                             html  
    dev.flush                               html  
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    devAskNewPage                           html  
    Devices                                 html  
    embedFonts                              html  
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    getGraphicsEvent                        html  
    gray.colors                             html  
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    grDevices-package                       html  
    grSoftVersion                           html  
    hcl                                     html  
    Hershey                                 html  
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    make.rgb                                html  
    msgWindow                               html  
    n2mfrow                                 html  
    nclass                                  html  
    palette                                 html  
    palettes                                html  
    pdf.options                             html  
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    pictex                                  html  
    plotmath                                html  
    postscript                              html  
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    pretty.Date                             html  
    ps.options                              html  
    quartz                                  html  
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    Type1Font                               html  
    windows.options                         html  
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    x11Fonts                                html  
    xfig                                    html  
    xy.coords                               html  
    xyTable                                 html  
    xyz.coords                              html  
    png                                     html  
    savePlot                                html  
  converting help for package 'graphics'
    abline                                  html  
    arrows                                  html  
    assocplot                               html  
    axis.POSIXct                            html  
    axis                                    html  
    axTicks                                 html  
    barplot                                 html  
    box                                     html  
    boxplot.matrix                          html  
    boxplot                                 html  
    bxp                                     html  
    cdplot                                  html  
    clip                                    html  
    contour                                 html  
    convertXY                               html  
    coplot                                  html  
    curve                                   html  
    dotchart                                html  
    filled.contour                          html  
    fourfoldplot                            html  
    frame                                   html  
    graphics-defunct                        html  
    graphics-package                        html  
    grid                                    html  
    hist.POSIXt                             html  
    hist                                    html  
    identify                                html  
    image                                   html  
    layout                                  html  
    legend                                  html  
    lines                                   html  
    locator                                 html  
    matplot                                 html  
    mosaicplot                              html  
    mtext                                   html  
    pairs                                   html  
    panel.smooth                            html  
    par                                     html  
    persp                                   html  
    pie                                     html  
    plot.dataframe                          html  
    plot.default                            html  
    plot.design                             html  
    plot.factor                             html  
    plot.formula                            html  
    plot.raster                             html  
    plot                                    html  
    plot.table                              html  
    plot.window                             html  
    plot.xy                                 html  
    plothistogram                           html  
    points                                  html  
    polygon                                 html  
    polypath                                html  
    rasterImage                             html  
    rect                                    html  
    rug                                     html  
    screen                                  html  
    segments                                html  
    smoothScatter                           html  
    spineplot                               html  
    stars                                   html  
    stem                                    html  
    stripchart                              html  
    strwidth                                html  
    sunflowerplot                           html  
    symbols                                 html  
    text                                    html  
    title                                   html  
    units                                   html  
    xspline                                 html  
    zAxis                                   html  
  converting help for package 'stats'
    acf                                     html  
    acf2AR                                  html  
    add1                                    html  
    addmargins                              html  
    aggregate                               html  
    AIC                                     html  
    alias                                   html  
    anova.glm                               html  
    anova.lm                                html  
    anova.mlm                               html  
    anova                                   html  
    ansari.test                             html  
    aov                                     html  
    approxfun                               html  
    ar.ols                                  html  
    ar                                      html  
    arima                                   html  
    arima.sim                               html  
    arima0                                  html  
    ARMAacf                                 html  
    ARMAtoMA                                html  
    as.hclust                               html  
    asOneSidedFormula                       html  
    ave                                     html  
    bandwidth                               html  
    bartlett.test                           html  
    Beta                                    html  
    binom.test                              html  
    Binomial                                html  
    biplot.princomp                         html  
    biplot                                  html  
    birthday                                html  
    box.test                                html  
    cancor                                  html  
    case.names                              html  
    Cauchy                                  html  
    checkMFClasses                          html  
    chisq.test                              html  
    Chisquare                               html  
    cmdscale                                html  
    coef                                    html  
    complete.cases                          html  
    confint                                 html  
    constrOptim                             html  
    contrast                                html  
    contrasts                               html  
    convolve                                html  
    cophenetic                              html  
    cor                                     html  
    cor.test                                html  
    cov.wt                                  html  
    cpgram                                  html  
    cutree                                  html  
    decompose                               html  
    delete.response                         html  
    dendrapply                              html  
    dendrogram                              html  
    density                                 html  
    deriv                                   html  
    deviance                                html  
    df.residual                             html  
    diffinv                                 html  
    dist                                    html  
    Distributions                           html  
    dummy.coef                              html  
    ecdf                                    html  
    eff.aovlist                             html  
    effects                                 html  
    embed                                   html  
    expand.model.frame                      html  
    Exponential                             html  
    extractAIC                              html  
    factanal                                html  
    factor.scope                            html  
    family                                  html  
    Fdist                                   html  
    fft                                     html  
    filter                                  html  
    fisher.test                             html  
    fitted.values                           html  
    fivenum                                 html  
    fligner.test                            html  
    formula.nls                             html  
    formula                                 html  
    friedman.test                           html  
    ftable.formula                          html  
    ftable                                  html  
    GammaDist                               html  
    Geometric                               html  
    getInitial                              html  
    glm.control                             html  
    glm                                     html  
    glm.summaries                           html  
    hclust                                  html  
    heatmap                                 html  
    HoltWinters                             html  
    Hypergeometric                          html  
    identify.hclust                         html  
    influence.measures                      html  
    integrate                               html  
    interaction.plot                        html  
    IQR                                     html  
    is.empty                                html  
    isoreg                                  html  
    KalmanLike                              html  
    kernapply                               html  
    kernel                                  html  
    kmeans                                  html  
    kruskal.test                            html  
    ks.test                                 html  
    ksmooth                                 html  
    lag.plot                                html  
    lag                                     html  
    line                                    html  
    listof                                  html  
    lm.influence                            html  
    lm                                      html  
    lm.summaries                            html  
    lmfit                                   html  
    loadings                                html  
    loess.control                           html  
    loess                                   html  
    Logistic                                html  
    logLik                                  html  
    loglin                                  html  
    Lognormal                               html  
    lowess                                  html  
    ls.diag                                 html  
    ls.print                                html  
    lsfit                                   html  
    mad                                     html  
    mahalanobis                             html  
    make.link                               html  
    makepredictcall                         html  
    manova                                  html  
    mantelhaen.test                         html  
    mauchly.test                            html  
    mcnemar.test                            html  
    median                                  html  
    medpolish                               html  
    model.extract                           html  
    model.frame                             html  
    model.matrix                            html  
    model.tables                            html  
    monthplot                               html  
    mood.test                               html  
    Multinom                                html  
    na.action                               html  
    na.contiguous                           html  
    na.fail                                 html  
    nafns                                   html  
    naprint                                 html  
    NegBinomial                             html  
    nextn                                   html  
    nlm                                     html  
    nlminb                                  html  
    nls.control                             html  
    nls                                     html  
    NLSstAsymptotic                         html  
    NLSstClosestX                           html  
    NLSstLfAsymptote                        html  
    NLSstRtAsymptote                        html  
    nobs                                    html  
    Normal                                  html  
    numericDeriv                            html  
    offset                                  html  
    oneway.test                             html  
    optim                                   html  
    optimize                                html  
    order.dendrogram                        html  
    p.adjust                                html  
    pairwise.prop.test                      html  
    pairwise.t.test                         html  
    pairwise.table                          html  
    pairwise.wilcox.test                    html  
    plot.acf                                html  
    plot.density                            html  
    plot.HoltWinters                        html  
    plot.isoreg                             html  
    plot.lm                                 html  
    plot.ppr                                html  
    plot.profile.nls                        html  
    plot.spec                               html  
    plot.stepfun                            html  
    plot.ts                                 html  
    Poisson                                 html  
    poisson.test                            html  
    poly                                    html  
    power.anova.test                        html  
    power.prop.test                         html  
    power                                   html  
    power.t.test                            html  
    pp.test                                 html  
    ppoints                                 html  
    ppr                                     html  
    prcomp                                  html  
    predict.arima                           html  
    predict.glm                             html  
    predict.HoltWinters                     html  
    predict.lm                              html  
    predict.loess                           html  
    predict.nls                             html  
    predict                                 html  
    predict.smooth.spline                   html  
    preplot                                 html  
    princomp                                html  
    print.power.htest                       html  
    print.ts                                html  
    printCoefmat                            html  
    profile.nls                             html  
    profile                                 html  
    proj                                    html  
    prop.test                               html  
    prop.trend.test                         html  
    qqnorm                                  html  
    quade.test                              html  
    quantile                                html  
    r2dtable                                html  
    read.ftable                             html  
    rect.hclust                             html  
    relevel                                 html  
    reorder.dendrogram                      html  
    reorder.factor                          html  
    replications                            html  
    reshape                                 html  
    residuals                               html  
    runmed                                  html  
    rWishart                                html  
    scatter.smooth                          html  
    screeplot                               html  
    sd                                      html  
    se.contrast                             html  
    selfStart                               html  
    setNames                                html  
    shapiro.test                            html  
    sigma                                   html  
    SignRank                                html  
    simulate                                html  
    smooth                                  html  
    smooth.spline                           html  
    smoothEnds                              html  
    sortedXyData                            html  
    spec.ar                                 html  
    spec.pgram                              html  
    spec.taper                              html  
    spectrum                                html  
    splinefun                               html  
    SSasymp                                 html  
    SSasympOff                              html  
    SSasympOrig                             html  
    SSbiexp                                 html  
    SSD                                     html  
    SSfol                                   html  
    SSfpl                                   html  
    SSgompertz                              html  
    SSlogis                                 html  
    SSmicmen                                html  
    SSweibull                               html  
    start                                   html  
    stat.anova                              html  
    stats-defunct                           html  
    stats-deprecated                        html  
    stats-package                           html  
    step                                    html  
    stepfun                                 html  
    stl                                     html  
    stlmethods                              html  
    StructTS                                html  
    summary.aov                             html  
    summary.glm                             html  
    summary.lm                              html  
    summary.manova                          html  
    summary.nls                             html  
    summary.princomp                        html  
    supsmu                                  html  
    symnum                                  html  
    t.test                                  html  
    TDist                                   html  
    termplot                                html  
    terms.formula                           html  
    terms.object                            html  
    terms                                   html  
    time                                    html  
    toeplitz                                html  
    ts-methods                              html  
    ts.plot                                 html  
    ts                                      html  
    ts.union                                html  
    tsdiag                                  html  
    tsp                                     html  
    tsSmooth                                html  
    Tukey                                   html  
    TukeyHSD                                html  
    Uniform                                 html  
    uniroot                                 html  
    update.formula                          html  
    update                                  html  
    var.test                                html  
    varimax                                 html  
    vcov                                    html  
    Weibull                                 html  
    weighted.mean                           html  
    weighted.residuals                      html  
    weights                                 html  
    wilcox.test                             html  
    Wilcoxon                                html  
    window                                  html  
    xtabs                                   html  
    zC                                      html  
  converting help for package 'datasets'
    ability.cov                             html  
    airmiles                                html  
    AirPassengers                           html  
    airquality                              html  
    anscombe                                html  
    attenu                                  html  
    attitude                                html  
    austres                                 html  
    beavers                                 html  
    BJsales                                 html  
    BOD                                     html  
    cars                                    html  
    ChickWeight                             html  
    chickwts                                html  
    co2                                     html  
    crimtab                                 html  
    datasets-package                        html  
    discoveries                             html  
    DNase                                   html  
    esoph                                   html  
    euro                                    html  
    eurodist                                html  
    EuStockMarkets                          html  
    faithful                                html  
    Formaldehyde                            html  
    freeny                                  html  
    HairEyeColor                            html  
    Harman23.cor                            html  
    Harman74.cor                            html  
    Indometh                                html  
    infert                                  html  
    InsectSprays                            html  
    iris                                    html  
    islands                                 html  
    JohnsonJohnson                          html  
    LakeHuron                               html  
    lh                                      html  
    LifeCycleSavings                        html  
    Loblolly                                html  
    longley                                 html  
    lynx                                    html  
    morley                                  html  
    mtcars                                  html  
    nhtemp                                  html  
    Nile                                    html  
    nottem                                  html  
    npk                                     html  
    occupationalStatus                      html  
    Orange                                  html  
    OrchardSprays                           html  
    PlantGrowth                             html  
    precip                                  html  
    presidents                              html  
    pressure                                html  
    Puromycin                               html  
    quakes                                  html  
    randu                                   html  
    rivers                                  html  
    rock                                    html  
    sleep                                   html  
    stackloss                               html  
    state                                   html  
    sunspot.month                           html  
    sunspot.year                            html  
    sunspots                                html  
    swiss                                   html  
    Theoph                                  html  
    Titanic                                 html  
    ToothGrowth                             html  
    treering                                html  
    trees                                   html  
    UCBAdmissions                           html  
    UKDriverDeaths                          html  
    UKgas                                   html  
    UKLungDeaths                            html  
    USAccDeaths                             html  
    USArrests                               html  
    USJudgeRatings                          html  
    USPersonalExpenditure                   html  
    uspop                                   html  
    VADeaths                                html  
    volcano                                 html  
    warpbreaks                              html  
    women                                   html  
    WorldPhones                             html  
    WWWusage                                html  
    zCO2                                    html  
  converting help for package 'methods'
    as                                      html  
    BasicClasses                            html  
    callGeneric                             html  
    canCoerce                               html  
    cbind2                                  html  
    Classes                                 html  
    Classes_Details                         html  
    classesToAM                             html  
    className                               html  
    classRepresentation-class               html  
    Documentation                           html  
    dotsMethods                             html  
    EmptyMethodsList-class                  html  
    EnvironmentClass                        html  
    evalSource                              html  
    findClass                               html  
    findMethods                             html  
    fixPrevious                             html  
    genericFunction-class                   html  
    GenericFunctions                        html  
    getClass                                html  
    getMethod                               html  
    getPackageName                          html  
    hasArg                                  html  
    implicitGeneric                         html  
    inheritedSlotNames                      html  
    initialize-methods                      html  
    Introduction                            html  
    is                                      html  
    isSealedMethod                          html  
    LanguageClasses                         html  
    languageEl                              html  
    LinearMethodsList-class                 html  
    localRefClass                           html  
    method.skeleton                         html  
    MethodDefinition-class                  html  
    methods-defunct                         html  
    methods-deprecated                      html  
    methods-package                         html  
    Methods                                 html  
    Methods_Details                         html  
    Methods_for_Nongenerics                 html  
    Methods_for_S3                          html  
    MethodsList-class                       html  
    MethodsList                             html  
    MethodSupport                           html  
    methodUtilities                         html  
    MethodWithNext-class                    html  
    new                                     html  
    NextMethod                              html  
    nonStructure-class                      html  
    ObjectsWithPackage-class                html  
    promptClass                             html  
    promptMethods                           html  
    RClassUtils                             html  
    refClass                                html  
    removeMethod                            html  
    representation                          html  
    RMethodUtils                            html  
    S3Part                                  html  
    S4groupGeneric                          html  
    SClassExtension-class                   html  
    selectSuperClasses                      html  
    setAs                                   html  
    setClass                                html  
    setClassUnion                           html  
    setGeneric                              html  
    setGroupGeneric                         html  
    setIs                                   html  
    setLoadActions                          html  
    setMethod                               html  
    setOldClass                             html  
    setSClass                               html  
    show                                    html  
    showMethods                             html  
    signature-class                         html  
    slot                                    html  
    stdRefClass                             html  
    StructureClasses                        html  
    substituteDirect                        html  
    testInheritedMethods                    html  
    TraceClasses                            html  
    validObject                             html  
    zBasicFunsList                          html  
  converting help for package 'grid'
    absolute.size                           html  
    arrow                                   html  
    calcStringMetric                        html  
    current.viewport                        html  
    dataViewport                            html  
    depth                                   html  
    deviceLoc                               html  
    drawDetails                             html  
    editDetails                             html  
    explode                                 html  
    gEdit                                   html  
    getNames                                html  
    gpar                                    html  
    gPath                                   html  
    grid-defunct                            html  
    grid-internal                           html  
    grid-package                            html  
    grid.add                                html  
    grid.bezier                             html  
    grid.cap                                html  
    grid.circle                             html  
    grid.clip                               html  
    grid.convert                            html  
    grid.copy                               html  
    grid.curve                              html  
    grid.delay                              html  
    grid.display.list                       html  
    grid.DLapply                            html  
    grid.draw                               html  
    grid.edit                               html  
    grid.force                              html  
    grid.frame                              html  
    grid.function                           html  
    grid.get                                html  
    grid.grab                               html  
    grid.grep                               html  
    grid.grill                              html  
    grid.grob                               html  
    grid.layout                             html  
    grid.lines                              html  
    grid.locator                            html  
    grid.ls                                 html  
    grid.move.to                            html  
    grid.newpage                            html  
    grid.null                               html  
    grid.pack                               html  
    grid.path                               html  
    grid.place                              html  
    grid.plot.and.legend                    html  
    grid.points                             html  
    grid.polygon                            html  
    grid.pretty                             html  
    grid.raster                             html  
    Grid                                    html  
    grid.record                             html  
    grid.rect                               html  
    grid.refresh                            html  
    grid.remove                             html  
    grid.reorder                            html  
    grid.roundrect                          html  
    grid.segments                           html  
    grid.set                                html  
    grid.show.layout                        html  
    grid.show.viewport                      html  
    grid.text                               html  
    grid.xaxis                              html  
    grid.xspline                            html  
    grid.yaxis                              html  
    grobCoords                              html  
    grobName                                html  
    grobWidth                               html  
    grobX                                   html  
    legendGrob                              html  
    makeContent                             html  
    plotViewport                            html  
    resolveRasterSize                       html  
    showGrob                                html  
    showViewport                            html  
    stringWidth                             html  
    unit.c                                  html  
    unit.length                             html  
    unit.pmin                               html  
    unit                                    html  
    unit.rep                                html  
    valid.just                              html  
    validDetails                            html  
    viewport                                html  
    viewports                               html  
    vpPath                                  html  
    widthDetails                            html  
    xDetails                                html  
    xsplinePoints                           html  
  converting help for package 'splines'
    asVector                                html  
    backSpline                              html  
    bs                                      html  
    interpSpline                            html  
    ns                                      html  
    periodicSpline                          html  
    polySpline                              html  
    predict.bs                              html  
    predict.bSpline                         html  
    splineDesign                            html  
    splineKnots                             html  
    splineOrder                             html  
    splines-package                         html  
    xyVector                                html  
  converting help for package 'stats4'
    coef-methods                            html  
    confint-methods                         html  
    logLik-methods                          html  
    mle-class                               html  
    mle                                     html  
    plot-methods                            html  
    profile-methods                         html  
    profile.mle-class                       html  
    show-methods                            html  
    stats4-package                          html  
    summary-methods                         html  
    summary.mle-class                       html  
    update-methods                          html  
    vcov-methods                            html  
  converting help for package 'tcltk'
    TclInterface                            html  
    tclServiceMode                          html  
    tcltk-defunct                           html  
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    tk_choose.dir                           html  
    tk_choose.files                         html  
    tk_messageBox                           html  
    tk_select.list                          html  
    TkCommands                              html  
    tkpager                                 html  
    tkProgressBar                           html  
    tkStartGUI                              html  
    TkWidgetcmds                            html  
    TkWidgets                               html  
  converting help for package 'compiler'
    compile                                 html  
  converting help for package 'parallel'
    clusterApply                            html  
    detectCores                             html  
    makeCluster                             html  
    parallel-package                        html  
    RngStream                               html  
    splitIndices                            html  
    mcdummies                               html  
creating doc/NEWS
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------ Making HTML documentation ------
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creating doc/manual/R-intro.html
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creating doc/manual/R-ints.html
Unescaped left brace in regex is deprecated here (and will be fatal in Perl 5.32), passed through in regex; marked by <-- HERE in m/^\s+@([[:alnum:]][[:alnum:]\-]*)({ <-- HERE })?\s*/ at C:/Rtools/texinfo5/Texinfo/Parser.pm line 5441.
Unescaped left brace in regex is deprecated here (and will be fatal in Perl 5.32), passed through in regex; marked by <-- HERE in m/^\s+@([[:alnum:]][[:alnum:]\-]*)({ <-- HERE })?\s*(\@(c|comment)((\@|\s+).*)?)?/ at C:/Rtools/texinfo5/Texinfo/Parser.pm line 5446.
creating doc/manual/R-lang.html
Unescaped left brace in regex is deprecated here (and will be fatal in Perl 5.32), passed through in regex; marked by <-- HERE in m/^\s+@([[:alnum:]][[:alnum:]\-]*)({ <-- HERE })?\s*/ at C:/Rtools/texinfo5/Texinfo/Parser.pm line 5441.
Unescaped left brace in regex is deprecated here (and will be fatal in Perl 5.32), passed through in regex; marked by <-- HERE in m/^\s+@([[:alnum:]][[:alnum:]\-]*)({ <-- HERE })?\s*(\@(c|comment)((\@|\s+).*)?)?/ at C:/Rtools/texinfo5/Texinfo/Parser.pm line 5446.
making rw-FAQ
Unescaped left brace in regex is deprecated here (and will be fatal in Perl 5.32), passed through in regex; marked by <-- HERE in m/^\s+@([[:alnum:]][[:alnum:]\-]*)({ <-- HERE })?\s*/ at C:/Rtools/texinfo5/Texinfo/Parser.pm line 5441.
Unescaped left brace in regex is deprecated here (and will be fatal in Perl 5.32), passed through in regex; marked by <-- HERE in m/^\s+@([[:alnum:]][[:alnum:]\-]*)({ <-- HERE })?\s*(\@(c|comment)((\@|\s+).*)?)?/ at C:/Rtools/texinfo5/Texinfo/Parser.pm line 5446.
Negative repeat count does nothing at C:/Rtools/texinfo5/Texinfo/Convert/Plaintext.pm line 1065.
Negative repeat count does nothing at C:/Rtools/texinfo5/Texinfo/Convert/Plaintext.pm line 1065.
Negative repeat count does nothing at C:/Rtools/texinfo5/Texinfo/Convert/Plaintext.pm line 1065.
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Negative repeat count does nothing at C:/Rtools/texinfo5/Texinfo/Convert/Plaintext.pm line 1065.
Negative repeat count does nothing at C:/Rtools/texinfo5/Texinfo/Convert/Plaintext.pm line 1065.
Negative repeat count does nothing at C:/Rtools/texinfo5/Texinfo/Convert/Plaintext.pm line 1065.
making rw-FAQ.html
Unescaped left brace in regex is deprecated here (and will be fatal in Perl 5.32), passed through in regex; marked by <-- HERE in m/^\s+@([[:alnum:]][[:alnum:]\-]*)({ <-- HERE })?\s*/ at C:/Rtools/texinfo5/Texinfo/Parser.pm line 5441.
Unescaped left brace in regex is deprecated here (and will be fatal in Perl 5.32), passed through in regex; marked by <-- HERE in m/^\s+@([[:alnum:]][[:alnum:]\-]*)({ <-- HERE })?\s*(\@(c|comment)((\@|\s+).*)?)?/ at C:/Rtools/texinfo5/Texinfo/Parser.pm line 5446.
make[2]: Nothing to be done for 'all'.
making cairoBM.d from cairoBM.c
C:/Rtools/mingw_64/bin/gcc  -I"../../../../../include" -DNDEBUG -I../../../../../src/include -I. -I.. -DHAVE_CONFIG_H -DR_ARCH='"x64"' -I"C:/projects/BUILD/R-source-win64/cairo/win64"    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c cairoBM.c -o cairoBM.o
C:/Rtools/mingw_64/bin/gcc  -shared -s -static-libgcc -o winCairo.dll winCairo.def cairoBM.o -L"C:/projects/BUILD/R-source-win64/cairo/win64" -lcairo -lfreetype -lpng -lpixman-1 -lharfbuzz -lbz2 -lz -lgdi32 -lmsimg32 -L.. -lgrDevices -L"C:/projects/BUILD/R-source-win64/extsoft/lib/x64" -L"C:/projects/BUILD/R-source-win64/extsoft/lib"  -L"../../../../../bin/x64" -lR 
--- Making recommended packages

----- installing recommended package MASS
* installing *source* package 'MASS' ...
** package 'MASS' successfully unpacked and MD5 sums checked
** using non-staged installation
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c MASS.c -o MASS.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c lqs.c -o lqs.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o MASS.dll tmp.def MASS.o lqs.o -LC:/projects/BUILD/R-source-win64/extsoft/lib/x64 -LC:/projects/BUILD/R-source-win64/extsoft/lib -LC:/projects/BUILD/R-source-win64/bin/x64 -lR
installing to C:/projects/BUILD/R-source-win64/library/MASS/libs/x64
** R
** data
*** moving datasets to lazyload DB
** inst
** tests
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'MASS'
    finding HTML links ... done
    Aids2                                   html  
    Animals                                 html  
    Boston                                  html  
    Cars93                                  html  
    Cushings                                html  
    DDT                                     html  
    GAGurine                                html  
    Insurance                               html  
    MASS-internal                           html  
    Melanoma                                html  
    Null                                    html  
    OME                                     html  
    Pima.tr                                 html  
    Rabbit                                  html  
    Rubber                                  html  
    SP500                                   html  
    Sitka                                   html  
    Sitka89                                 html  
    Skye                                    html  
    Traffic                                 html  
    UScereal                                html  
    UScrime                                 html  
    VA                                      html  
    abbey                                   html  
    accdeaths                               html  
    addterm                                 html  
    anorexia                                html  
    anova.negbin                            html  
    area                                    html  
    bacteria                                html  
    bandwidth.nrd                           html  
    bcv                                     html  
    beav1                                   html  
    beav2                                   html  
    biopsy                                  html  
    birthwt                                 html  
    boxcox                                  html  
    cabbages                                html  
    caith                                   html  
    cats                                    html  
    cement                                  html  
    chem                                    html  
    con2tr                                  html  
    confint                                 html  
    contr.sdif                              html  
    coop                                    html  
    corresp                                 html  
    cov.rob                                 html  
    cov.trob                                html  
    cpus                                    html  
    crabs                                   html  
    deaths                                  html  
    denumerate                              html  
    dose.p                                  html  
    drivers                                 html  
    dropterm                                html  
    eagles                                  html  
    epil                                    html  
    eqscplot                                html  
    farms                                   html  
    fgl                                     html  
    fitdistr                                html  
    forbes                                  html  
    fractions                               html  
    galaxies                                html  
    gamma.dispersion                        html  
    gamma.shape.glm                         html  
    gehan                                   html  
    genotype                                html  
    geyser                                  html  
    gilgais                                 html  
    ginv                                    html  
    glm.convert                             html  
    glm.nb                                  html  
    glmmPQL                                 html  
    hills                                   html  
    hist.scott                              html  
    housing                                 html  
    huber                                   html  
    hubers                                  html  
    immer                                   html  
    isoMDS                                  html  
    kde2d                                   html  
    lda                                     html  
    ldahist                                 html  
    leuk                                    html  
    lm.gls                                  html  
    lm.ridge                                html  
    loglm                                   html  
    loglm1                                  html  
    logtrans                                html  
    lqs                                     html  
    mammals                                 html  
    mca                                     html  
    mcycle                                  html  
    menarche                                html  
    michelson                               html  
    minn38                                  html  
    motors                                  html  
    muscle                                  html  
    mvrnorm                                 html  
    negative.binomial                       html  
    newcomb                                 html  
    nlschools                               html  
    npk                                     html  
    npr1                                    html  
    oats                                    html  
    painters                                html  
    pairs.lda                               html  
    parcoord                                html  
    petrol                                  html  
    phones                                  html  
    plot.lda                                html  
    plot.mca                                html  
    plot.profile                            html  
    polr                                    html  
    predict.glmmPQL                         html  
    predict.lda                             html  
    predict.lqs                             html  
    predict.mca                             html  
    predict.qda                             html  
    profile.glm                             html  
    qda                                     html  
    quine                                   html  
    rational                                html  
    renumerate                              html  
    rlm                                     html  
    rms.curv                                html  
    rnegbin                                 html  
    road                                    html  
    rotifer                                 html  
    sammon                                  html  
    ships                                   html  
    shoes                                   html  
    shrimp                                  html  
    shuttle                                 html  
    snails                                  html  
    stdres                                  html  
    steam                                   html  
    stepAIC                                 html  
    stormer                                 html  
    studres                                 html  
    summary.loglm                           html  
    summary.negbin                          html  
    summary.rlm                             html  
    survey                                  html  
    synth.tr                                html  
    theta.md                                html  
    topo                                    html  
    truehist                                html  
    ucv                                     html  
    waders                                  html  
    whiteside                               html  
    width.SJ                                html  
    write.matrix                            html  
    wtloss                                  html  
** building package indices
** testing if installed package can be loaded
* DONE (MASS)
Making 'packages.html' ... done

----- installing recommended package lattice
* installing *source* package 'lattice' ...
** package 'lattice' successfully unpacked and MD5 sums checked
** using non-staged installation
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c init.c -o init.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c threeDplot.c -o threeDplot.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o lattice.dll tmp.def init.o threeDplot.o -LC:/projects/BUILD/R-source-win64/extsoft/lib/x64 -LC:/projects/BUILD/R-source-win64/extsoft/lib -LC:/projects/BUILD/R-source-win64/bin/x64 -lR
installing to C:/projects/BUILD/R-source-win64/library/lattice/libs/x64
** R
** data
*** moving datasets to lazyload DB
** demo
** inst
** tests
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'lattice'
    finding HTML links ... done
    Lattice                                 html  
    Rows                                    html  
    USMortality                             html  
    axis.default                            html  
    banking                                 html  
    barchart.table                          html  
    barley                                  html  
    cloud                                   html  
    draw.colorkey                           html  
    draw.key                                html  
    environmental                           html  
    ethanol                                 html  
    histogram                               html  
    interaction                             html  
    lattice.options                         html  
    latticeParseFormula                     html  
    level.colors                            html  
    levelplot                               html  
    llines                                  html  
    lset                                    html  
    make.groups                             html  
    melanoma                                html  
    oneway                                  html  
    packet.panel.default                    html  
    panel.axis                              html  
    panel.barchart                          html  
    panel.bwplot                            html  
    panel.cloud                             html  
    panel.densityplot                       html  
    panel.dotplot                           html  
    panel.functions                         html  
    panel.histogram                         html  
    panel.levelplot                         html  
    panel.loess                             html  
    panel.number                            html  
    panel.pairs                             html  
    panel.parallel                          html  
    panel.qqmath                            html  
    panel.qqmathline                        html  
    panel.smoothScatter                     html  
    panel.spline                            html  
    panel.stripplot                         html  
    panel.superpose                         html  
    panel.violin                            html  
    panel.xyplot                            html  
    prepanel.default                        html  
    prepanel.functions                      html  
    print.trellis                           html  
    qq                                      html  
    qqmath                                  html  
    rfs                                     html  
    shingles                                html  
    simpleKey                               html  
    simpleTheme                             html  
    singer                                  html  
    splom                                   html  
    strip.default                           html  
    tmd                                     html  
    trellis.device                          html  
    trellis.object                          html  
    trellis.par.get                         html  
    update.trellis                          html  
    utilities.3d                            html  
    xyplot                                  html  
    xyplot.ts                               html  
** building package indices
** testing if installed package can be loaded
* DONE (lattice)
Making 'packages.html' ... done

----- installing recommended package Matrix
* installing *source* package 'Matrix' ...
** package 'Matrix' successfully unpacked and MD5 sums checked
** using non-staged installation
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c CHMfactor.c -o CHMfactor.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c Csparse.c -o Csparse.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c TMatrix_as.c -o TMatrix_as.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c Tsparse.c -o Tsparse.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c init.c -o init.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c Mutils.c -o Mutils.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c chm_common.c -o chm_common.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c cs.c -o cs.o
cs.c: In function 'cs_qr':
cs.c:1408:18: warning: variable 'm' set but not used [-Wunused-but-set-variable]
     csi i, k, p, m, n, vnz, p1, top, m2, len, col, rnz, *s, *leftmost, *Ap, *Ai,
                  ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c cs_utils.c -o cs_utils.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c dense.c -o dense.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c dgCMatrix.c -o dgCMatrix.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c dgTMatrix.c -o dgTMatrix.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c dgeMatrix.c -o dgeMatrix.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c dpoMatrix.c -o dpoMatrix.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c dppMatrix.c -o dppMatrix.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c dsCMatrix.c -o dsCMatrix.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c dsyMatrix.c -o dsyMatrix.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c dspMatrix.c -o dspMatrix.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c dtCMatrix.c -o dtCMatrix.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c dtTMatrix.c -o dtTMatrix.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c dtrMatrix.c -o dtrMatrix.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c dtpMatrix.c -o dtpMatrix.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c factorizations.c -o factorizations.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ldense.c -o ldense.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c lgCMatrix.c -o lgCMatrix.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c sparseQR.c -o sparseQR.o
In file included from C:/projects/BUILD/R-source-win64/include/R.h:91:0,
                 from Mutils.h:12,
                 from sparseQR.h:4,
                 from sparseQR.c:1:
sparseQR.c: In function 'sparseQR_coef':
C:/projects/BUILD/R-source-win64/include/R_ext/RS.h:80:24: warning: 'x' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define Memcpy(p,q,n)  memcpy( p, q, (R_SIZE_T)(n) * sizeof(*p) )
                        ^
sparseQR.c:172:53: note: 'x' was declared here
     double *ax = REAL(GET_SLOT(ans, Matrix_xSym)), *x;
                                                     ^
sparseQR.c: In function 'sparseQR_resid_fitted':
sparseQR.c:125:9: warning: 'd_a' may be used uninitialized in this function [-Wmaybe-uninitialized]
  d_a[0] = m;/* -> @Dim is ok;  @Dimnames (i.e. colnames) still are */ \
         ^
sparseQR.c:99:41: note: 'd_a' was declared here
  m = ydims[0], n = ydims[1], M = V->m, *d_a;   \
                                         ^
sparseQR.c:202:5: note: in expansion of macro 'INIT_sparseQR_'
     INIT_sparseQR_(FALSE);
     ^
In file included from Mutils.h:14:0,
                 from sparseQR.h:4,
                 from sparseQR.c:1:
C:/projects/BUILD/R-source-win64/include/Rdefines.h:161:35: warning: 'aa' may be used uninitialized in this function [-Wmaybe-uninitialized]
 #define SET_SLOT(x, what, value)  R_do_slot_assign(x, what, value)
                                   ^
sparseQR.c:94:15: note: 'aa' was declared here
     SEXP ans, aa, dmns = R_NilValue;     \
               ^
sparseQR.c:202:5: note: in expansion of macro 'INIT_sparseQR_'
     INIT_sparseQR_(FALSE);
     ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c abIndex.c -o abIndex.o
( cd Lib ; /rtools/bin/make clean )
( cd Source ; /rtools/bin/make clean )
( cd Source ; /rtools/bin/make clean )
( cd Lib ; /rtools/bin/make -f "C:/projects/BUILD/R-source-win64/etc/x64/Makeconf" -f Makefile )
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ../Core/cholmod_aat.c -o cholmod_aat.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ../Core/cholmod_add.c -o cholmod_add.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ../Core/cholmod_band.c -o cholmod_band.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ../Core/cholmod_change_factor.c -o cholmod_change_factor.o
In file included from ../Core/cholmod_change_factor.c:116:0:
../Core/t_cholmod_change_factor.c: In function 'r_change_simplicial_numeric':
../Core/t_cholmod_change_factor.c:40:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
     double *Lx, *Lz ;
                  ^
In file included from ../Core/cholmod_change_factor.c:118:0:
../Core/t_cholmod_change_factor.c: In function 'c_change_simplicial_numeric':
../Core/t_cholmod_change_factor.c:40:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
     double *Lx, *Lz ;
                  ^
../Core/cholmod_change_factor.c: In function 'simplicial_symbolic_to_super_symbolic':
../Core/cholmod_change_factor.c:265:17: warning: variable 'xsize' set but not used [-Wunused-but-set-variable]
     Int nsuper, xsize, ssize ;
                 ^
../Core/cholmod_change_factor.c: In function 'change_simplicial_numeric':
../Core/cholmod_change_factor.c:680:15: warning: variable 'Li' set but not used [-Wunused-but-set-variable]
     Int *Lp, *Li, *Lnz ;
               ^
../Core/cholmod_change_factor.c:680:10: warning: variable 'Lp' set but not used [-Wunused-but-set-variable]
     Int *Lp, *Li, *Lnz ;
          ^
../Core/cholmod_change_factor.c:679:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
     double *Lx, *Lz ;
                  ^
../Core/cholmod_change_factor.c:679:13: warning: variable 'Lx' set but not used [-Wunused-but-set-variable]
     double *Lx, *Lz ;
             ^
../Core/cholmod_change_factor.c: In function 'll_super_to_simplicial_numeric':
../Core/cholmod_change_factor.c:827:9: warning: variable 'n' set but not used [-Wunused-but-set-variable]
     Int n, lnz, s, nsuper, psi, psend, nsrow, nscol, k1, k2, erows ;
         ^
../Core/cholmod_change_factor.c:826:21: warning: variable 'Lpx' set but not used [-Wunused-but-set-variable]
     Int *Ls, *Lpi, *Lpx, *Super, *Li ;
                     ^
../Core/cholmod_change_factor.c:826:10: warning: variable 'Ls' set but not used [-Wunused-but-set-variable]
     Int *Ls, *Lpi, *Lpx, *Super, *Li ;
          ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ../Core/cholmod_common.c -o cholmod_common.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ../Core/cholmod_complex.c -o cholmod_complex.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ../Core/cholmod_copy.c -o cholmod_copy.o
../Core/cholmod_copy.c: In function 'cholmod_copy':
../Core/cholmod_copy.c:278:25: warning: variable 'lo' set but not used [-Wunused-but-set-variable]
     Int nrow, ncol, up, lo, values, diag, astype ;
                         ^
../Core/cholmod_copy.c:278:21: warning: variable 'up' set but not used [-Wunused-but-set-variable]
     Int nrow, ncol, up, lo, values, diag, astype ;
                     ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ../Core/cholmod_dense.c -o cholmod_dense.o
In file included from ../Core/cholmod_dense.c:48:0:
../Core/t_cholmod_dense.c: In function 'p_cholmod_sparse_to_dense':
../Core/t_cholmod_dense.c:30:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Xx, *Az, *Xz ;
                            ^
../Core/t_cholmod_dense.c:30:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Xx, *Az, *Xz ;
                       ^
../Core/t_cholmod_dense.c:30:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable]
     double *Ax, *Xx, *Az, *Xz ;
             ^
In file included from ../Core/cholmod_dense.c:50:0:
../Core/t_cholmod_dense.c: In function 'r_cholmod_sparse_to_dense':
../Core/t_cholmod_dense.c:30:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Xx, *Az, *Xz ;
                            ^
../Core/t_cholmod_dense.c:30:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Xx, *Az, *Xz ;
                       ^
../Core/t_cholmod_dense.c: In function 'r_cholmod_dense_to_sparse':
../Core/t_cholmod_dense.c:136:28: warning: variable 'Cz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Cx, *Xz, *Cz ;
                            ^
../Core/t_cholmod_dense.c:136:23: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Cx, *Xz, *Cz ;
                       ^
../Core/t_cholmod_dense.c: In function 'r_cholmod_copy_dense2':
../Core/t_cholmod_dense.c:229:28: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Xz, *Yx, *Yz ;
                            ^
../Core/t_cholmod_dense.c:229:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Xz, *Yx, *Yz ;
                  ^
In file included from ../Core/cholmod_dense.c:52:0:
../Core/t_cholmod_dense.c: In function 'c_cholmod_sparse_to_dense':
../Core/t_cholmod_dense.c:30:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Xx, *Az, *Xz ;
                            ^
../Core/t_cholmod_dense.c:30:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Xx, *Az, *Xz ;
                       ^
../Core/t_cholmod_dense.c: In function 'c_cholmod_dense_to_sparse':
../Core/t_cholmod_dense.c:136:28: warning: variable 'Cz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Cx, *Xz, *Cz ;
                            ^
../Core/t_cholmod_dense.c:136:23: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Cx, *Xz, *Cz ;
                       ^
../Core/t_cholmod_dense.c: In function 'c_cholmod_copy_dense2':
../Core/t_cholmod_dense.c:229:28: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Xz, *Yx, *Yz ;
                            ^
../Core/t_cholmod_dense.c:229:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Xz, *Yx, *Yz ;
                  ^
../Core/cholmod_dense.c: In function 'cholmod_eye':
../Core/cholmod_dense.c:303:15: warning: variable 'nz' set but not used [-Wunused-but-set-variable]
     Int i, n, nz ;
               ^
../Core/cholmod_dense.c:302:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Xz ;
                  ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ../Core/cholmod_error.c -o cholmod_error.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ../Core/cholmod_factor.c -o cholmod_factor.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ../Core/cholmod_memory.c -o cholmod_memory.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ../Core/cholmod_sparse.c -o cholmod_sparse.o
../Core/cholmod_sparse.c: In function 'cholmod_copy_sparse':
../Core/cholmod_sparse.c:488:35: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
     Int p, pend, j, ncol, packed, nzmax, nz, xtype ;
                                   ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ../Core/cholmod_transpose.c -o cholmod_transpose.o
In file included from ../Core/cholmod_transpose.c:124:0:
../Core/t_cholmod_transpose.c: In function 'p_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                                     ^
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                        ^
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                     ^
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                               ^
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^
../Core/t_cholmod_transpose.c:45:23: warning: variable 'Fx' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                       ^
../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^
../Core/t_cholmod_transpose.c:45:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
             ^
../Core/t_cholmod_transpose.c: In function 'p_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^
../Core/t_cholmod_transpose.c:142:23: warning: variable 'Fx' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                       ^
../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^
../Core/t_cholmod_transpose.c:142:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
             ^
In file included from ../Core/cholmod_transpose.c:126:0:
../Core/t_cholmod_transpose.c: In function 'r_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                                     ^
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                        ^
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                     ^
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                               ^
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^
../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^
../Core/t_cholmod_transpose.c: In function 'r_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^
../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^
In file included from ../Core/cholmod_transpose.c:128:0:
../Core/t_cholmod_transpose.c: In function 'c_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                                     ^
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                        ^
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                     ^
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                               ^
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^
../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^
../Core/t_cholmod_transpose.c: In function 'c_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^
../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^
In file included from ../Core/cholmod_transpose.c:131:0:
../Core/t_cholmod_transpose.c: In function 'ct_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                                     ^
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                        ^
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                     ^
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                               ^
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^
../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^
../Core/t_cholmod_transpose.c: In function 'ct_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^
../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^
In file included from ../Core/cholmod_transpose.c:133:0:
../Core/t_cholmod_transpose.c: In function 'z_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                                     ^
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                        ^
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                     ^
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                               ^
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c: In function 'z_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
                          ^
In file included from ../Core/cholmod_transpose.c:136:0:
../Core/t_cholmod_transpose.c: In function 'zt_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                                     ^
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                        ^
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                     ^
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                               ^
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c: In function 'zt_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
                          ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ../Core/cholmod_triplet.c -o cholmod_triplet.o
In file included from ../Core/cholmod_triplet.c:108:0:
../Core/t_cholmod_triplet.c: In function 'p_cholmod_triplet_to_sparse':
../Core/t_cholmod_triplet.c:31:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
                            ^
../Core/t_cholmod_triplet.c:31:23: warning: variable 'Tx' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
                       ^
../Core/t_cholmod_triplet.c:31:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
                  ^
../Core/t_cholmod_triplet.c:31:13: warning: variable 'Rx' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
             ^
In file included from ../Core/cholmod_triplet.c:110:0:
../Core/t_cholmod_triplet.c: In function 'r_cholmod_triplet_to_sparse':
../Core/t_cholmod_triplet.c:31:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
                            ^
../Core/t_cholmod_triplet.c:31:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
                  ^
In file included from ../Core/cholmod_triplet.c:112:0:
../Core/t_cholmod_triplet.c: In function 'c_cholmod_triplet_to_sparse':
../Core/t_cholmod_triplet.c:31:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
                            ^
../Core/t_cholmod_triplet.c:31:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
                  ^
../Core/cholmod_triplet.c: In function 'cholmod_triplet_to_sparse':
../Core/cholmod_triplet.c:345:44: warning: variable 'ok' set but not used [-Wunused-but-set-variable]
     Int i, j, p, k, stype, nrow, ncol, nz, ok ;
                                            ^
../Core/cholmod_triplet.c:344:20: warning: variable 'Ri' set but not used [-Wunused-but-set-variable]
     Int *Wj, *Rp, *Ri, *Rnz, *Ti, *Tj ;
                    ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ../Core/cholmod_version.c -o cholmod_version.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ../Check/cholmod_check.c -o cholmod_check.o
../Check/cholmod_check.c: In function 'check_common':
../Check/cholmod_check.c:207:61: warning: variable 'init_print' set but not used [-Wunused-but-set-variable]
     Int i, nrow, nmethods, ordering, xworksize, amd_backup, init_print ;
                                                             ^
../Check/cholmod_check.c: In function 'check_dense':
../Check/cholmod_check.c:961:37: warning: variable 'nz' set but not used [-Wunused-but-set-variable]
     Int i, j, d, nrow, ncol, nzmax, nz, init_print, count, xtype ;
                                     ^
../Check/cholmod_check.c: In function 'check_factor':
../Check/cholmod_check.c:1508:2: warning: variable 'ps2' set but not used [-Wunused-but-set-variable]
  ps2, psxend, ssize, xsize, maxcsize, maxesize, nsrow2, jj, ii, xtype ;
  ^
../Check/cholmod_check.c:1506:9: warning: variable 'precise' set but not used [-Wunused-but-set-variable]
  count, precise, init_print, ilast, lnz, head, tail, jprev, plast,
         ^
../Check/cholmod_check.c:1505:38: warning: variable 'ordering' set but not used [-Wunused-but-set-variable]
     Int n, nzmax, j, p, pend, i, nz, ordering, space, is_monotonic, minor,
                                      ^
../Check/cholmod_check.c: In function 'check_factor.constprop':
../Check/cholmod_check.c:86:2: warning: 'psxend' may be used uninitialized in this function [-Wmaybe-uninitialized]
  (Common->print_function) (format, arg) ; \
  ^
../Check/cholmod_check.c:1508:7: note: 'psxend' was declared here
  ps2, psxend, ssize, xsize, maxcsize, maxesize, nsrow2, jj, ii, xtype ;
       ^
../Check/cholmod_check.c:1507:55: warning: 'psx' may be used uninitialized in this function [-Wmaybe-uninitialized]
  jnext, examine_super, nsuper, s, k1, k2, psi, psend, psx, nsrow, nscol,
                                                       ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ../Check/cholmod_read.c -o cholmod_read.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ../Check/cholmod_write.c -o cholmod_write.o
../Check/cholmod_write.c: In function 'cholmod_write_sparse':
../Check/cholmod_write.c:365:33: warning: variable 'symmetry' set but not used [-Wunused-but-set-variable]
     Int nrow, ncol, is_complex, symmetry, i, j, q, iz, p, nz, is_binary, stype,
                                 ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ../Cholesky/cholmod_amd.c -o cholmod_amd.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ../Cholesky/cholmod_analyze.c -o cholmod_analyze.o
../Cholesky/cholmod_analyze.c: In function 'cholmod_analyze_p2':
../Cholesky/cholmod_analyze.c:422:69: warning: variable 'ncol' set but not used [-Wunused-but-set-variable]
     Int k, n, ordering, method, nmethods, status, default_strategy, ncol, uncol,
                                                                     ^
../Cholesky/cholmod_analyze.c:419:45: warning: variable 'CParent' set but not used [-Wunused-but-set-variable]
     Int *First, *Level, *Work4n, *Cmember, *CParent, *ColCount, *Lperm, *Parent,
                                             ^
../Cholesky/cholmod_analyze.c:419:35: warning: variable 'Cmember' set but not used [-Wunused-but-set-variable]
     Int *First, *Level, *Work4n, *Cmember, *CParent, *ColCount, *Lperm, *Parent,
                                   ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ../Cholesky/cholmod_colamd.c -o cholmod_colamd.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ../Cholesky/cholmod_etree.c -o cholmod_etree.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ../Cholesky/cholmod_factorize.c -o cholmod_factorize.o
../Cholesky/cholmod_factorize.c: In function 'cholmod_factorize_p':
../Cholesky/cholmod_factorize.c:114:37: warning: variable 'n' set but not used [-Wunused-but-set-variable]
     Int nrow, ncol, stype, convert, n, nsuper, grow2, status ;
                                     ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ../Cholesky/cholmod_postorder.c -o cholmod_postorder.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ../Cholesky/cholmod_rcond.c -o cholmod_rcond.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ../Cholesky/cholmod_resymbol.c -o cholmod_resymbol.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ../Cholesky/cholmod_rowcolcounts.c -o cholmod_rowcolcounts.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ../Cholesky/cholmod_rowfac.c -o cholmod_rowfac.o
In file included from ../Cholesky/cholmod_rowfac.c:164:0:
../Cholesky/t_cholmod_rowfac.c: In function 'r_cholmod_rowfac':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
  use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
                                              ^
../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                                ^
../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                      ^
../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                            ^
../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                  ^
In file included from ../Cholesky/cholmod_rowfac.c:166:0:
../Cholesky/t_cholmod_rowfac.c: In function 'c_cholmod_rowfac':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
  use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
                                              ^
../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                                ^
../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                      ^
../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                            ^
../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                  ^
In file included from ../Cholesky/cholmod_rowfac.c:168:0:
../Cholesky/t_cholmod_rowfac.c: In function 'z_cholmod_rowfac':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
  use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
                                              ^
In file included from ../Cholesky/cholmod_rowfac.c:172:0:
../Cholesky/t_cholmod_rowfac.c: In function 'r_cholmod_rowfac_mask':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
  use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
                                              ^
../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                                ^
../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                      ^
../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                            ^
../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                  ^
In file included from ../Cholesky/cholmod_rowfac.c:174:0:
../Cholesky/t_cholmod_rowfac.c: In function 'c_cholmod_rowfac_mask':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
  use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
                                              ^
../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                                ^
../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                      ^
../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                            ^
../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                  ^
In file included from ../Cholesky/cholmod_rowfac.c:176:0:
../Cholesky/t_cholmod_rowfac.c: In function 'z_cholmod_rowfac_mask':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
  use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
                                              ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ../Cholesky/cholmod_solve.c -o cholmod_solve.o
In file included from ../Cholesky/cholmod_solve.c:66:0:
../Cholesky/t_cholmod_solve.c: In function 'r_ldl_dsolve':
../Cholesky/t_cholmod_solve.c:64:23: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
     double *Lx, *Yx, *Yz ;
                       ^
In file included from ../Cholesky/cholmod_solve.c:69:0:
../Cholesky/t_cholmod_solve.c: In function 'c_ldl_dsolve':
../Cholesky/t_cholmod_solve.c:64:23: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
     double *Lx, *Yx, *Yz ;
                       ^
../Cholesky/cholmod_solve.c: In function 'iperm':
../Cholesky/cholmod_solve.c:337:13: warning: variable 'nk' set but not used [-Wunused-but-set-variable]
     Int k2, nk, p, k, j, nrow, ncol, d, dj, j2 ;
             ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ../Cholesky/cholmod_spsolve.c -o cholmod_spsolve.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ../MatrixOps/cholmod_drop.c -o cholmod_drop.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ../MatrixOps/cholmod_horzcat.c -o cholmod_horzcat.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ../MatrixOps/cholmod_norm.c -o cholmod_norm.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ../MatrixOps/cholmod_scale.c -o cholmod_scale.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ../MatrixOps/cholmod_sdmult.c -o cholmod_sdmult.o
In file included from ../MatrixOps/cholmod_sdmult.c:46:0:
../MatrixOps/t_cholmod_sdmult.c: In function 'r_cholmod_sdmult':
../MatrixOps/t_cholmod_sdmult.c:55:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int packed, nrow, ncol, j, k, p, pend, kcol, i ;
                 ^
../MatrixOps/t_cholmod_sdmult.c:52:47: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                                               ^
../MatrixOps/t_cholmod_sdmult.c:52:38: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                                      ^
../MatrixOps/t_cholmod_sdmult.c:52:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                            ^
../MatrixOps/t_cholmod_sdmult.c:52:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                  ^
In file included from ../MatrixOps/cholmod_sdmult.c:48:0:
../MatrixOps/t_cholmod_sdmult.c: In function 'c_cholmod_sdmult':
../MatrixOps/t_cholmod_sdmult.c:55:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int packed, nrow, ncol, j, k, p, pend, kcol, i ;
                 ^
../MatrixOps/t_cholmod_sdmult.c:52:47: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                                               ^
../MatrixOps/t_cholmod_sdmult.c:52:38: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                                      ^
../MatrixOps/t_cholmod_sdmult.c:52:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                            ^
../MatrixOps/t_cholmod_sdmult.c:52:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                  ^
In file included from ../MatrixOps/cholmod_sdmult.c:50:0:
../MatrixOps/t_cholmod_sdmult.c: In function 'z_cholmod_sdmult':
../MatrixOps/t_cholmod_sdmult.c:55:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int packed, nrow, ncol, j, k, p, pend, kcol, i ;
                 ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ../MatrixOps/cholmod_ssmult.c -o cholmod_ssmult.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ../MatrixOps/cholmod_submatrix.c -o cholmod_submatrix.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ../MatrixOps/cholmod_vertcat.c -o cholmod_vertcat.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ../MatrixOps/cholmod_symmetry.c -o cholmod_symmetry.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ../Modify/cholmod_rowadd.c -o cholmod_rowadd.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ../Modify/cholmod_rowdel.c -o cholmod_rowdel.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ../Modify/cholmod_updown.c -o cholmod_updown.o
../Modify/cholmod_updown.c: In function 'cholmod_updown_mask':
../Modify/cholmod_updown.c:410:33: warning: variable 'ps1' set but not used [-Wunused-but-set-variable]
  *Set_ps1 [32], *Set_ps2 [32], *ps1, *ps2 ;
                                 ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ../Supernodal/cholmod_super_numeric.c -o cholmod_super_numeric.o
In file included from ../Supernodal/cholmod_super_numeric.c:78:0:
../Supernodal/t_cholmod_super_numeric.c: In function 'r_cholmod_super_numeric':
../Supernodal/t_cholmod_super_numeric.c:111:33: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
                                 ^
../Supernodal/t_cholmod_super_numeric.c:111:28: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
                            ^
In file included from ../Supernodal/cholmod_super_numeric.c:80:0:
../Supernodal/t_cholmod_super_numeric.c: In function 'c_cholmod_super_numeric':
../Supernodal/t_cholmod_super_numeric.c:111:33: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
                                 ^
../Supernodal/t_cholmod_super_numeric.c:111:28: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
                            ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ../Supernodal/cholmod_super_solve.c -o cholmod_super_solve.o
In file included from ../Supernodal/cholmod_super_solve.c:28:0:
../Supernodal/t_cholmod_super_solve.c: In function 'r_cholmod_super_lsolve':
../Supernodal/t_cholmod_super_solve.c:33:10: warning: variable 'n' set but not used [-Wunused-but-set-variable]
  nsrow2, n, ps2, j, i, d, nrhs ;
          ^
../Supernodal/t_cholmod_super_solve.c: In function 'r_cholmod_super_ltsolve':
../Supernodal/t_cholmod_super_solve.c:241:10: warning: variable 'n' set but not used [-Wunused-but-set-variable]
  nsrow2, n, ps2, j, i, d, nrhs ;
          ^
In file included from ../Supernodal/cholmod_super_solve.c:30:0:
../Supernodal/t_cholmod_super_solve.c: In function 'c_cholmod_super_lsolve':
../Supernodal/t_cholmod_super_solve.c:33:10: warning: variable 'n' set but not used [-Wunused-but-set-variable]
  nsrow2, n, ps2, j, i, d, nrhs ;
          ^
../Supernodal/t_cholmod_super_solve.c: In function 'c_cholmod_super_ltsolve':
../Supernodal/t_cholmod_super_solve.c:241:10: warning: variable 'n' set but not used [-Wunused-but-set-variable]
  nsrow2, n, ps2, j, i, d, nrhs ;
          ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c ../Supernodal/cholmod_super_symbolic.c -o cholmod_super_symbolic.o
../Supernodal/cholmod_super_symbolic.c: In function 'cholmod_super_symbolic2':
../Supernodal/cholmod_super_symbolic.c:455:7: warning: variable 'totsize' set but not used [-Wunused-but-set-variable]
   Int totsize ;
       ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -DDLONG -c  ../Core/cholmod_aat.c -o cholmod_l_aat.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -DDLONG -c  ../Core/cholmod_add.c -o cholmod_l_add.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -DDLONG -c  ../Core/cholmod_band.c -o cholmod_l_band.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -DDLONG -c  ../Core/cholmod_change_factor.c -o cholmod_l_change_factor.o
In file included from ../Core/cholmod_change_factor.c:116:0:
../Core/t_cholmod_change_factor.c: In function 'r_change_simplicial_numeric':
../Core/t_cholmod_change_factor.c:40:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
     double *Lx, *Lz ;
                  ^
In file included from ../Core/cholmod_change_factor.c:118:0:
../Core/t_cholmod_change_factor.c: In function 'c_change_simplicial_numeric':
../Core/t_cholmod_change_factor.c:40:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
     double *Lx, *Lz ;
                  ^
../Core/cholmod_change_factor.c: In function 'simplicial_symbolic_to_super_symbolic':
../Core/cholmod_change_factor.c:265:17: warning: variable 'xsize' set but not used [-Wunused-but-set-variable]
     Int nsuper, xsize, ssize ;
                 ^
../Core/cholmod_change_factor.c: In function 'change_simplicial_numeric':
../Core/cholmod_change_factor.c:680:15: warning: variable 'Li' set but not used [-Wunused-but-set-variable]
     Int *Lp, *Li, *Lnz ;
               ^
../Core/cholmod_change_factor.c:680:10: warning: variable 'Lp' set but not used [-Wunused-but-set-variable]
     Int *Lp, *Li, *Lnz ;
          ^
../Core/cholmod_change_factor.c:679:18: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
     double *Lx, *Lz ;
                  ^
../Core/cholmod_change_factor.c:679:13: warning: variable 'Lx' set but not used [-Wunused-but-set-variable]
     double *Lx, *Lz ;
             ^
../Core/cholmod_change_factor.c: In function 'll_super_to_simplicial_numeric':
../Core/cholmod_change_factor.c:827:9: warning: variable 'n' set but not used [-Wunused-but-set-variable]
     Int n, lnz, s, nsuper, psi, psend, nsrow, nscol, k1, k2, erows ;
         ^
../Core/cholmod_change_factor.c:826:21: warning: variable 'Lpx' set but not used [-Wunused-but-set-variable]
     Int *Ls, *Lpi, *Lpx, *Super, *Li ;
                     ^
../Core/cholmod_change_factor.c:826:10: warning: variable 'Ls' set but not used [-Wunused-but-set-variable]
     Int *Ls, *Lpi, *Lpx, *Super, *Li ;
          ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -DDLONG -c  ../Core/cholmod_common.c -o cholmod_l_common.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -DDLONG -c  ../Core/cholmod_complex.c -o cholmod_l_complex.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -DDLONG -c  ../Core/cholmod_copy.c -o cholmod_l_copy.o
../Core/cholmod_copy.c: In function 'cholmod_l_copy':
../Core/cholmod_copy.c:278:25: warning: variable 'lo' set but not used [-Wunused-but-set-variable]
     Int nrow, ncol, up, lo, values, diag, astype ;
                         ^
../Core/cholmod_copy.c:278:21: warning: variable 'up' set but not used [-Wunused-but-set-variable]
     Int nrow, ncol, up, lo, values, diag, astype ;
                     ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -DDLONG -c  ../Core/cholmod_dense.c -o cholmod_l_dense.o
In file included from ../Core/cholmod_dense.c:48:0:
../Core/t_cholmod_dense.c: In function 'p_cholmod_sparse_to_dense':
../Core/t_cholmod_dense.c:30:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Xx, *Az, *Xz ;
                            ^
../Core/t_cholmod_dense.c:30:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Xx, *Az, *Xz ;
                       ^
../Core/t_cholmod_dense.c:30:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable]
     double *Ax, *Xx, *Az, *Xz ;
             ^
In file included from ../Core/cholmod_dense.c:50:0:
../Core/t_cholmod_dense.c: In function 'r_cholmod_sparse_to_dense':
../Core/t_cholmod_dense.c:30:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Xx, *Az, *Xz ;
                            ^
../Core/t_cholmod_dense.c:30:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Xx, *Az, *Xz ;
                       ^
../Core/t_cholmod_dense.c: In function 'r_cholmod_dense_to_sparse':
../Core/t_cholmod_dense.c:136:28: warning: variable 'Cz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Cx, *Xz, *Cz ;
                            ^
../Core/t_cholmod_dense.c:136:23: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Cx, *Xz, *Cz ;
                       ^
../Core/t_cholmod_dense.c: In function 'r_cholmod_copy_dense2':
../Core/t_cholmod_dense.c:229:28: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Xz, *Yx, *Yz ;
                            ^
../Core/t_cholmod_dense.c:229:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Xz, *Yx, *Yz ;
                  ^
In file included from ../Core/cholmod_dense.c:52:0:
../Core/t_cholmod_dense.c: In function 'c_cholmod_sparse_to_dense':
../Core/t_cholmod_dense.c:30:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Xx, *Az, *Xz ;
                            ^
../Core/t_cholmod_dense.c:30:23: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Xx, *Az, *Xz ;
                       ^
../Core/t_cholmod_dense.c: In function 'c_cholmod_dense_to_sparse':
../Core/t_cholmod_dense.c:136:28: warning: variable 'Cz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Cx, *Xz, *Cz ;
                            ^
../Core/t_cholmod_dense.c:136:23: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Cx, *Xz, *Cz ;
                       ^
../Core/t_cholmod_dense.c: In function 'c_cholmod_copy_dense2':
../Core/t_cholmod_dense.c:229:28: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Xz, *Yx, *Yz ;
                            ^
../Core/t_cholmod_dense.c:229:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Xz, *Yx, *Yz ;
                  ^
../Core/cholmod_dense.c: In function 'cholmod_l_eye':
../Core/cholmod_dense.c:303:15: warning: variable 'nz' set but not used [-Wunused-but-set-variable]
     Int i, n, nz ;
               ^
../Core/cholmod_dense.c:302:18: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Xx, *Xz ;
                  ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -DDLONG -c  ../Core/cholmod_error.c -o cholmod_l_error.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -DDLONG -c  ../Core/cholmod_factor.c -o cholmod_l_factor.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -DDLONG -c  ../Core/cholmod_memory.c -o cholmod_l_memory.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -DDLONG -c  ../Core/cholmod_sparse.c -o cholmod_l_sparse.o
../Core/cholmod_sparse.c: In function 'cholmod_l_copy_sparse':
../Core/cholmod_sparse.c:488:35: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
     Int p, pend, j, ncol, packed, nzmax, nz, xtype ;
                                   ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -DDLONG -c  ../Core/cholmod_transpose.c -o cholmod_l_transpose.o
In file included from ../Core/cholmod_transpose.c:124:0:
../Core/t_cholmod_transpose.c: In function 'p_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                                     ^
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                        ^
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                     ^
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                               ^
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^
../Core/t_cholmod_transpose.c:45:23: warning: variable 'Fx' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                       ^
../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^
../Core/t_cholmod_transpose.c:45:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
             ^
../Core/t_cholmod_transpose.c: In function 'p_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^
../Core/t_cholmod_transpose.c:142:23: warning: variable 'Fx' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                       ^
../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^
../Core/t_cholmod_transpose.c:142:13: warning: variable 'Ax' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
             ^
In file included from ../Core/cholmod_transpose.c:126:0:
../Core/t_cholmod_transpose.c: In function 'r_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                                     ^
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                        ^
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                     ^
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                               ^
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^
../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^
../Core/t_cholmod_transpose.c: In function 'r_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^
../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^
In file included from ../Core/cholmod_transpose.c:128:0:
../Core/t_cholmod_transpose.c: In function 'c_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                                     ^
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                        ^
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                     ^
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                               ^
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^
../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^
../Core/t_cholmod_transpose.c: In function 'c_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^
../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^
In file included from ../Core/cholmod_transpose.c:131:0:
../Core/t_cholmod_transpose.c: In function 'ct_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                                     ^
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                        ^
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                     ^
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                               ^
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c:45:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^
../Core/t_cholmod_transpose.c:45:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^
../Core/t_cholmod_transpose.c: In function 'ct_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c:142:28: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                            ^
../Core/t_cholmod_transpose.c:142:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Fx, *Fz ;
                  ^
In file included from ../Core/cholmod_transpose.c:133:0:
../Core/t_cholmod_transpose.c: In function 'z_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                                     ^
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                        ^
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                     ^
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                               ^
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c: In function 'z_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
                          ^
In file included from ../Core/cholmod_transpose.c:136:0:
../Core/t_cholmod_transpose.c: In function 'zt_cholmod_transpose_unsym':
../Core/t_cholmod_transpose.c:47:69: warning: variable 'permute' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                                     ^
../Core/t_cholmod_transpose.c:47:56: warning: variable 'Fpacked' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                                                        ^
../Core/t_cholmod_transpose.c:47:21: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int j, p, pend, nrow, ncol, Apacked, use_fset, fp, Fpacked, jj, permute ;
                     ^
../Core/t_cholmod_transpose.c:46:31: warning: variable 'Fnz' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                               ^
../Core/t_cholmod_transpose.c:46:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fnz, *Fj, *Wi, *Iwork ;
                          ^
../Core/t_cholmod_transpose.c: In function 'zt_cholmod_transpose_sym':
../Core/t_cholmod_transpose.c:143:26: warning: variable 'Fp' set but not used [-Wunused-but-set-variable]
     Int *Ap, *Anz, *Ai, *Fp, *Fj, *Wi, *Pinv, *Iwork ;
                          ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -DDLONG -c  ../Core/cholmod_triplet.c -o cholmod_l_triplet.o
In file included from ../Core/cholmod_triplet.c:108:0:
../Core/t_cholmod_triplet.c: In function 'p_cholmod_triplet_to_sparse':
../Core/t_cholmod_triplet.c:31:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
                            ^
../Core/t_cholmod_triplet.c:31:23: warning: variable 'Tx' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
                       ^
../Core/t_cholmod_triplet.c:31:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
                  ^
../Core/t_cholmod_triplet.c:31:13: warning: variable 'Rx' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
             ^
In file included from ../Core/cholmod_triplet.c:110:0:
../Core/t_cholmod_triplet.c: In function 'r_cholmod_triplet_to_sparse':
../Core/t_cholmod_triplet.c:31:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
                            ^
../Core/t_cholmod_triplet.c:31:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
                  ^
In file included from ../Core/cholmod_triplet.c:112:0:
../Core/t_cholmod_triplet.c: In function 'c_cholmod_triplet_to_sparse':
../Core/t_cholmod_triplet.c:31:28: warning: variable 'Tz' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
                            ^
../Core/t_cholmod_triplet.c:31:18: warning: variable 'Rz' set but not used [-Wunused-but-set-variable]
     double *Rx, *Rz, *Tx, *Tz ;
                  ^
../Core/cholmod_triplet.c: In function 'cholmod_l_triplet_to_sparse':
../Core/cholmod_triplet.c:345:44: warning: variable 'ok' set but not used [-Wunused-but-set-variable]
     Int i, j, p, k, stype, nrow, ncol, nz, ok ;
                                            ^
../Core/cholmod_triplet.c:344:20: warning: variable 'Ri' set but not used [-Wunused-but-set-variable]
     Int *Wj, *Rp, *Ri, *Rnz, *Ti, *Tj ;
                    ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -DDLONG -c  ../Core/cholmod_version.c -o cholmod_l_version.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -DDLONG -c  ../Check/cholmod_check.c -o cholmod_l_check.o
../Check/cholmod_check.c: In function 'check_common':
../Check/cholmod_check.c:207:61: warning: variable 'init_print' set but not used [-Wunused-but-set-variable]
     Int i, nrow, nmethods, ordering, xworksize, amd_backup, init_print ;
                                                             ^
../Check/cholmod_check.c: In function 'check_dense':
../Check/cholmod_check.c:961:37: warning: variable 'nz' set but not used [-Wunused-but-set-variable]
     Int i, j, d, nrow, ncol, nzmax, nz, init_print, count, xtype ;
                                     ^
../Check/cholmod_check.c: In function 'check_factor':
../Check/cholmod_check.c:1508:2: warning: variable 'ps2' set but not used [-Wunused-but-set-variable]
  ps2, psxend, ssize, xsize, maxcsize, maxesize, nsrow2, jj, ii, xtype ;
  ^
../Check/cholmod_check.c:1506:9: warning: variable 'precise' set but not used [-Wunused-but-set-variable]
  count, precise, init_print, ilast, lnz, head, tail, jprev, plast,
         ^
../Check/cholmod_check.c:1505:38: warning: variable 'ordering' set but not used [-Wunused-but-set-variable]
     Int n, nzmax, j, p, pend, i, nz, ordering, space, is_monotonic, minor,
                                      ^
../Check/cholmod_check.c: In function 'check_factor.constprop':
../Check/cholmod_check.c:86:2: warning: 'psxend' may be used uninitialized in this function [-Wmaybe-uninitialized]
  (Common->print_function) (format, arg) ; \
  ^
../Check/cholmod_check.c:1508:7: note: 'psxend' was declared here
  ps2, psxend, ssize, xsize, maxcsize, maxesize, nsrow2, jj, ii, xtype ;
       ^
../Check/cholmod_check.c:1507:55: warning: 'psx' may be used uninitialized in this function [-Wmaybe-uninitialized]
  jnext, examine_super, nsuper, s, k1, k2, psi, psend, psx, nsrow, nscol,
                                                       ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -DDLONG -c  ../Check/cholmod_read.c -o cholmod_l_read.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -DDLONG -c  ../Check/cholmod_write.c -o cholmod_l_write.o
../Check/cholmod_write.c: In function 'cholmod_l_write_sparse':
../Check/cholmod_write.c:365:33: warning: variable 'symmetry' set but not used [-Wunused-but-set-variable]
     Int nrow, ncol, is_complex, symmetry, i, j, q, iz, p, nz, is_binary, stype,
                                 ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -DDLONG -c  ../Cholesky/cholmod_amd.c -o cholmod_l_amd.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -DDLONG -c  ../Cholesky/cholmod_analyze.c -o cholmod_l_analyze.o
../Cholesky/cholmod_analyze.c: In function 'cholmod_l_analyze_p2':
../Cholesky/cholmod_analyze.c:422:69: warning: variable 'ncol' set but not used [-Wunused-but-set-variable]
     Int k, n, ordering, method, nmethods, status, default_strategy, ncol, uncol,
                                                                     ^
../Cholesky/cholmod_analyze.c:419:45: warning: variable 'CParent' set but not used [-Wunused-but-set-variable]
     Int *First, *Level, *Work4n, *Cmember, *CParent, *ColCount, *Lperm, *Parent,
                                             ^
../Cholesky/cholmod_analyze.c:419:35: warning: variable 'Cmember' set but not used [-Wunused-but-set-variable]
     Int *First, *Level, *Work4n, *Cmember, *CParent, *ColCount, *Lperm, *Parent,
                                   ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -DDLONG -c  ../Cholesky/cholmod_colamd.c -o cholmod_l_colamd.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -DDLONG -c  ../Cholesky/cholmod_etree.c -o cholmod_l_etree.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -DDLONG -c  ../Cholesky/cholmod_factorize.c -o cholmod_l_factorize.o
../Cholesky/cholmod_factorize.c: In function 'cholmod_l_factorize_p':
../Cholesky/cholmod_factorize.c:114:37: warning: variable 'n' set but not used [-Wunused-but-set-variable]
     Int nrow, ncol, stype, convert, n, nsuper, grow2, status ;
                                     ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -DDLONG -c  ../Cholesky/cholmod_postorder.c -o cholmod_l_postorder.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -DDLONG -c  ../Cholesky/cholmod_rcond.c -o cholmod_l_rcond.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -DDLONG -c  ../Cholesky/cholmod_resymbol.c -o cholmod_l_resymbol.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -DDLONG -c  ../Cholesky/cholmod_rowcolcounts.c -o cholmod_l_rowcolcounts.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -DDLONG -c  ../Cholesky/cholmod_rowfac.c -o cholmod_l_rowfac.o
In file included from ../Cholesky/cholmod_rowfac.c:164:0:
../Cholesky/t_cholmod_rowfac.c: In function 'r_cholmod_rowfac':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
  use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
                                              ^
../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                                ^
../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                      ^
../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                            ^
../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                  ^
In file included from ../Cholesky/cholmod_rowfac.c:166:0:
../Cholesky/t_cholmod_rowfac.c: In function 'c_cholmod_rowfac':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
  use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
                                              ^
../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                                ^
../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                      ^
../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                            ^
../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                  ^
In file included from ../Cholesky/cholmod_rowfac.c:168:0:
../Cholesky/t_cholmod_rowfac.c: In function 'z_cholmod_rowfac':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
  use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
                                              ^
In file included from ../Cholesky/cholmod_rowfac.c:172:0:
../Cholesky/t_cholmod_rowfac.c: In function 'r_cholmod_rowfac_mask':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
  use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
                                              ^
../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                                ^
../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                      ^
../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                            ^
../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                  ^
In file included from ../Cholesky/cholmod_rowfac.c:174:0:
../Cholesky/t_cholmod_rowfac.c: In function 'c_cholmod_rowfac_mask':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
  use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
                                              ^
../Cholesky/t_cholmod_rowfac.c:47:48: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                                ^
../Cholesky/t_cholmod_rowfac.c:47:38: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                                      ^
../Cholesky/t_cholmod_rowfac.c:47:28: warning: variable 'Lz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                            ^
../Cholesky/t_cholmod_rowfac.c:47:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Lx, *Lz, *Wx, *Wz, *Fx, *Fz ;
                  ^
In file included from ../Cholesky/cholmod_rowfac.c:176:0:
../Cholesky/t_cholmod_rowfac.c: In function 'z_cholmod_rowfac_mask':
../Cholesky/t_cholmod_rowfac.c:51:46: warning: variable 'nzmax' set but not used [-Wunused-but-set-variable]
  use_dbound, packed, stype, Fpacked, sorted, nzmax, len, parent ;
                                              ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -DDLONG -c  ../Cholesky/cholmod_solve.c -o cholmod_l_solve.o
In file included from ../Cholesky/cholmod_solve.c:66:0:
../Cholesky/t_cholmod_solve.c: In function 'r_ldl_dsolve':
../Cholesky/t_cholmod_solve.c:64:23: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
     double *Lx, *Yx, *Yz ;
                       ^
In file included from ../Cholesky/cholmod_solve.c:69:0:
../Cholesky/t_cholmod_solve.c: In function 'c_ldl_dsolve':
../Cholesky/t_cholmod_solve.c:64:23: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
     double *Lx, *Yx, *Yz ;
                       ^
../Cholesky/cholmod_solve.c: In function 'iperm':
../Cholesky/cholmod_solve.c:337:13: warning: variable 'nk' set but not used [-Wunused-but-set-variable]
     Int k2, nk, p, k, j, nrow, ncol, d, dj, j2 ;
             ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -DDLONG -c  ../Cholesky/cholmod_spsolve.c -o cholmod_l_spsolve.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -DDLONG -c  ../MatrixOps/cholmod_drop.c -o cholmod_l_drop.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -DDLONG -c  ../MatrixOps/cholmod_horzcat.c -o cholmod_l_horzcat.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -DDLONG -c  ../MatrixOps/cholmod_norm.c -o cholmod_l_norm.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -DDLONG -c  ../MatrixOps/cholmod_scale.c -o cholmod_l_scale.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -DDLONG -c  ../MatrixOps/cholmod_sdmult.c -o cholmod_l_sdmult.o
In file included from ../MatrixOps/cholmod_sdmult.c:46:0:
../MatrixOps/t_cholmod_sdmult.c: In function 'r_cholmod_sdmult':
../MatrixOps/t_cholmod_sdmult.c:55:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int packed, nrow, ncol, j, k, p, pend, kcol, i ;
                 ^
../MatrixOps/t_cholmod_sdmult.c:52:47: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                                               ^
../MatrixOps/t_cholmod_sdmult.c:52:38: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                                      ^
../MatrixOps/t_cholmod_sdmult.c:52:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                            ^
../MatrixOps/t_cholmod_sdmult.c:52:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                  ^
In file included from ../MatrixOps/cholmod_sdmult.c:48:0:
../MatrixOps/t_cholmod_sdmult.c: In function 'c_cholmod_sdmult':
../MatrixOps/t_cholmod_sdmult.c:55:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int packed, nrow, ncol, j, k, p, pend, kcol, i ;
                 ^
../MatrixOps/t_cholmod_sdmult.c:52:47: warning: variable 'Wz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                                               ^
../MatrixOps/t_cholmod_sdmult.c:52:38: warning: variable 'Yz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                                      ^
../MatrixOps/t_cholmod_sdmult.c:52:28: warning: variable 'Xz' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                            ^
../MatrixOps/t_cholmod_sdmult.c:52:18: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Ax, *Az, *Xx, *Xz, *Yx, *Yz, *w, *Wz ;
                  ^
In file included from ../MatrixOps/cholmod_sdmult.c:50:0:
../MatrixOps/t_cholmod_sdmult.c: In function 'z_cholmod_sdmult':
../MatrixOps/t_cholmod_sdmult.c:55:17: warning: variable 'nrow' set but not used [-Wunused-but-set-variable]
     Int packed, nrow, ncol, j, k, p, pend, kcol, i ;
                 ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -DDLONG -c  ../MatrixOps/cholmod_ssmult.c -o cholmod_l_ssmult.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -DDLONG -c  ../MatrixOps/cholmod_submatrix.c -o cholmod_l_submatrix.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -DDLONG -c  ../MatrixOps/cholmod_vertcat.c -o cholmod_l_vertcat.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -DDLONG -c  ../MatrixOps/cholmod_symmetry.c -o cholmod_l_symmetry.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -DDLONG -c  ../Modify/cholmod_rowadd.c -o cholmod_l_rowadd.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -DDLONG -c  ../Modify/cholmod_rowdel.c -o cholmod_l_rowdel.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -DDLONG -c  ../Modify/cholmod_updown.c -o cholmod_l_updown.o
../Modify/cholmod_updown.c: In function 'cholmod_l_updown_mask':
../Modify/cholmod_updown.c:410:33: warning: variable 'ps1' set but not used [-Wunused-but-set-variable]
  *Set_ps1 [32], *Set_ps2 [32], *ps1, *ps2 ;
                                 ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -DDLONG -c  ../Supernodal/cholmod_super_numeric.c -o cholmod_l_super_numeric.o
In file included from ../Supernodal/cholmod_super_numeric.c:78:0:
../Supernodal/t_cholmod_super_numeric.c: In function 'r_cholmod_super_numeric':
../Supernodal/t_cholmod_super_numeric.c:111:33: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
                                 ^
../Supernodal/t_cholmod_super_numeric.c:111:28: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
                            ^
In file included from ../Supernodal/cholmod_super_numeric.c:80:0:
../Supernodal/t_cholmod_super_numeric.c: In function 'c_cholmod_super_numeric':
../Supernodal/t_cholmod_super_numeric.c:111:33: warning: variable 'Fz' set but not used [-Wunused-but-set-variable]
     double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
                                 ^
../Supernodal/t_cholmod_super_numeric.c:111:28: warning: variable 'Az' set but not used [-Wunused-but-set-variable]
     double *Lx, *Ax, *Fx, *Az, *Fz, *C ;
                            ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -DDLONG -c  ../Supernodal/cholmod_super_solve.c -o cholmod_l_super_solve.o
In file included from ../Supernodal/cholmod_super_solve.c:28:0:
../Supernodal/t_cholmod_super_solve.c: In function 'r_cholmod_super_lsolve':
../Supernodal/t_cholmod_super_solve.c:33:10: warning: variable 'n' set but not used [-Wunused-but-set-variable]
  nsrow2, n, ps2, j, i, d, nrhs ;
          ^
../Supernodal/t_cholmod_super_solve.c: In function 'r_cholmod_super_ltsolve':
../Supernodal/t_cholmod_super_solve.c:241:10: warning: variable 'n' set but not used [-Wunused-but-set-variable]
  nsrow2, n, ps2, j, i, d, nrhs ;
          ^
In file included from ../Supernodal/cholmod_super_solve.c:30:0:
../Supernodal/t_cholmod_super_solve.c: In function 'c_cholmod_super_lsolve':
../Supernodal/t_cholmod_super_solve.c:33:10: warning: variable 'n' set but not used [-Wunused-but-set-variable]
  nsrow2, n, ps2, j, i, d, nrhs ;
          ^
../Supernodal/t_cholmod_super_solve.c: In function 'c_cholmod_super_ltsolve':
../Supernodal/t_cholmod_super_solve.c:241:10: warning: variable 'n' set but not used [-Wunused-but-set-variable]
  nsrow2, n, ps2, j, i, d, nrhs ;
          ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../../AMD/Include -I../../AMD/Source -I../../COLAMD/Include -I../Include -I../../SuiteSparse_config -DNPARTITION -DNPRINT    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -DDLONG -c  ../Supernodal/cholmod_super_symbolic.c -o cholmod_l_super_symbolic.o
../Supernodal/cholmod_super_symbolic.c: In function 'cholmod_l_super_symbolic2':
../Supernodal/cholmod_super_symbolic.c:455:7: warning: variable 'totsize' set but not used [-Wunused-but-set-variable]
   Int totsize ;
       ^
C:/Rtools/mingw_64/bin/ar -rucs ../../CHOLMOD.a cholmod_aat.o cholmod_add.o cholmod_band.o cholmod_change_factor.o cholmod_common.o cholmod_complex.o cholmod_copy.o cholmod_dense.o cholmod_error.o cholmod_factor.o cholmod_memory.o cholmod_sparse.o cholmod_transpose.o cholmod_triplet.o cholmod_version.o cholmod_check.o cholmod_read.o cholmod_write.o cholmod_amd.o cholmod_analyze.o cholmod_colamd.o cholmod_etree.o cholmod_factorize.o cholmod_postorder.o cholmod_rcond.o cholmod_resymbol.o cholmod_rowcolcounts.o cholmod_rowfac.o cholmod_solve.o cholmod_spsolve.o cholmod_drop.o cholmod_horzcat.o cholmod_norm.o cholmod_scale.o cholmod_sdmult.o cholmod_ssmult.o cholmod_submatrix.o cholmod_vertcat.o cholmod_symmetry.o cholmod_rowadd.o cholmod_rowdel.o cholmod_updown.o cholmod_super_numeric.o cholmod_super_solve.o cholmod_super_symbolic.o  cholmod_l_aat.o cholmod_l_add.o cholmod_l_band.o cholmod_l_change_factor.o cholmod_l_common.o cholmod_l_complex.o cholmod_l_copy.o cholmod_l_dense.o cholmod_l_error.o cholmod_l_factor.o cholmod_l_memory.o cholmod_l_sparse.o cholmod_l_transpose.o cholmod_l_triplet.o cholmod_l_version.o cholmod_l_check.o cholmod_l_read.o cholmod_l_write.o cholmod_l_amd.o cholmod_l_analyze.o cholmod_l_colamd.o cholmod_l_etree.o cholmod_l_factorize.o cholmod_l_postorder.o cholmod_l_rcond.o cholmod_l_resymbol.o cholmod_l_rowcolcounts.o cholmod_l_rowfac.o cholmod_l_solve.o cholmod_l_spsolve.o cholmod_l_drop.o cholmod_l_horzcat.o cholmod_l_norm.o cholmod_l_scale.o cholmod_l_sdmult.o cholmod_l_ssmult.o cholmod_l_submatrix.o cholmod_l_vertcat.o cholmod_l_symmetry.o cholmod_l_rowadd.o cholmod_l_rowdel.o cholmod_l_updown.o cholmod_l_super_numeric.o cholmod_l_super_solve.o cholmod_l_super_symbolic.o 
( cd Source ; /rtools/bin/make -f "C:/projects/BUILD/R-source-win64/etc/x64/Makeconf" -f Makefile lib )
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../Include -I../../SuiteSparse_config    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c colamd_global.c -o colamd_global.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../Include -I../../SuiteSparse_config    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c colamd.c -o colamd.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../Include -I../../SuiteSparse_config    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -I../Include -DDLONG -c colamd.c -o colamd_l.o
C:/Rtools/mingw_64/bin/ar -rucs ../../COLAMD.a colamd_global.o colamd.o colamd_l.o
( cd Source ; /rtools/bin/make -f "C:/projects/BUILD/R-source-win64/etc/x64/Makeconf" -f Makefile lib )
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../Include -I../../SuiteSparse_config    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -I../Include -DDINT -c amd_aat.c -o amd_i_aat.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../Include -I../../SuiteSparse_config    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -I../Include -DDLONG -c amd_aat.c -o amd_l_aat.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../Include -I../../SuiteSparse_config    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -I../Include -DDINT -c amd_1.c -o amd_i_1.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../Include -I../../SuiteSparse_config    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -I../Include -DDLONG -c amd_1.c -o amd_l_1.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../Include -I../../SuiteSparse_config    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -I../Include -DDINT -c amd_2.c -o amd_i_2.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../Include -I../../SuiteSparse_config    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -I../Include -DDLONG -c amd_2.c -o amd_l_2.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../Include -I../../SuiteSparse_config    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -I../Include -DDINT -c amd_postorder.c -o amd_i_postorder.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../Include -I../../SuiteSparse_config    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -I../Include -DDLONG -c amd_postorder.c -o amd_l_postorder.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../Include -I../../SuiteSparse_config    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -I../Include -DDINT -c amd_post_tree.c -o amd_i_post_tree.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../Include -I../../SuiteSparse_config    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -I../Include -DDLONG -c amd_post_tree.c -o amd_l_post_tree.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../Include -I../../SuiteSparse_config    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -I../Include -DDINT -c amd_defaults.c -o amd_i_defaults.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../Include -I../../SuiteSparse_config    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -I../Include -DDLONG -c amd_defaults.c -o amd_l_defaults.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../Include -I../../SuiteSparse_config    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -I../Include -DDINT -c amd_order.c -o amd_i_order.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../Include -I../../SuiteSparse_config    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -I../Include -DDLONG -c amd_order.c -o amd_l_order.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../Include -I../../SuiteSparse_config    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -I../Include -DDINT -c amd_control.c -o amd_i_control.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../Include -I../../SuiteSparse_config    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -I../Include -DDLONG -c amd_control.c -o amd_l_control.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../Include -I../../SuiteSparse_config    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -I../Include -DDINT -c amd_info.c -o amd_i_info.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../Include -I../../SuiteSparse_config    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -I../Include -DDLONG -c amd_info.c -o amd_l_info.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../Include -I../../SuiteSparse_config    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -I../Include -DDINT -c amd_valid.c -o amd_i_valid.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../Include -I../../SuiteSparse_config    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -I../Include -DDLONG -c amd_valid.c -o amd_l_valid.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../Include -I../../SuiteSparse_config    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -I../Include -DDINT -c amd_preprocess.c -o amd_i_preprocess.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../Include -I../../SuiteSparse_config    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -I../Include -DDLONG -c amd_preprocess.c -o amd_l_preprocess.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../Include -I../../SuiteSparse_config    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -I../Include -DDINT -c amd_dump.c -o amd_i_dump.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../Include -I../../SuiteSparse_config    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -I../Include -DDLONG -c amd_dump.c -o amd_l_dump.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../Include -I../../SuiteSparse_config    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -I../Include -DDINT -c amd_global.c -o amd_i_global.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -I../Include -I../../SuiteSparse_config    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -I../Include -DDLONG -c amd_global.c -o amd_l_global.o
C:/Rtools/mingw_64/bin/ar -rucs ../../AMD.a amd_i_aat.o amd_l_aat.o amd_i_1.o amd_l_1.o amd_i_2.o amd_l_2.o amd_i_postorder.o amd_l_postorder.o amd_i_post_tree.o amd_l_post_tree.o amd_i_defaults.o amd_l_defaults.o amd_i_order.o amd_l_order.o amd_i_control.o amd_l_control.o amd_i_info.o amd_l_info.o amd_i_valid.o amd_l_valid.o amd_i_preprocess.o amd_l_preprocess.o amd_i_dump.o amd_l_dump.o amd_i_global.o amd_l_global.o 
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG -DNTIMER    -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c SuiteSparse_config.c -o SuiteSparse_config.o
C:/Rtools/mingw_64/bin/ar -rucs ../SuiteSparse_config.a SuiteSparse_config.o
C:\Rtools\mingw_64\bin\nm.exe: 'sublibs': No such file
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o Matrix.dll tmp.def CHMfactor.o Csparse.o TMatrix_as.o Tsparse.o init.o Mutils.o chm_common.o cs.o cs_utils.o dense.o dgCMatrix.o dgTMatrix.o dgeMatrix.o dpoMatrix.o dppMatrix.o dsCMatrix.o dsyMatrix.o dspMatrix.o dtCMatrix.o dtTMatrix.o dtrMatrix.o dtpMatrix.o factorizations.o ldense.o lgCMatrix.o sparseQR.o abIndex.o CHOLMOD.a COLAMD.a AMD.a SuiteSparse_config.a -LC:/projects/BUILD/R-source-win64/bin/x64 -lRlapack -LC:/projects/BUILD/R-source-win64/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/projects/BUILD/R-source-win64/extsoft/lib/x64 -LC:/projects/BUILD/R-source-win64/extsoft/lib -LC:/projects/BUILD/R-source-win64/bin/x64 -lR
installing to C:/projects/BUILD/R-source-win64/library/Matrix/libs/x64
** R
** data
** inst
** tests
** byte-compile and prepare package for lazy loading
Creating a generic function for 'chol2inv' from 'base' in package 'Matrix'
    (from the saved implicit definition)
Creating a generic function for 'chol2inv' from package 'base' in package 'Matrix'
Creating a generic function for 'diag' from package 'base' in package 'Matrix'
Creating a generic function for 'drop' from package 'base' in package 'Matrix'
Creating a generic function for 'cov2cor' from package 'stats' in package 'Matrix'
Creating a generic function for 'unname' from package 'base' in package 'Matrix'
Creating a generic function for 'norm' from package 'base' in package 'Matrix'
Creating a generic function for 'rcond' from 'base' in package 'Matrix'
    (from the saved implicit definition)
Creating a generic function for 'rcond' from package 'base' in package 'Matrix'
in method for 'coerce' with signature '"matrix.csr","dgRMatrix"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"dgRMatrix","matrix.csr"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"matrix.csc","dgCMatrix"': no definition for class "matrix.csc"
in method for 'coerce' with signature '"dgCMatrix","matrix.csc"': no definition for class "matrix.csc"
in method for 'coerce' with signature '"matrix.coo","dgTMatrix"': no definition for class "matrix.coo"
in method for 'coerce' with signature '"dgTMatrix","matrix.coo"': no definition for class "matrix.coo"
in method for 'coerce' with signature '"dsparseMatrix","matrix.csr"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"matrix.csr","dgCMatrix"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"matrix.coo","dgCMatrix"': no definition for class "matrix.coo"
in method for 'coerce' with signature '"matrix.csr","RsparseMatrix"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"matrix.csc","CsparseMatrix"': no definition for class "matrix.csc"
in method for 'coerce' with signature '"matrix.coo","TsparseMatrix"': no definition for class "matrix.coo"
in method for 'coerce' with signature '"matrix.csr","CsparseMatrix"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"matrix.coo","CsparseMatrix"': no definition for class "matrix.coo"
in method for 'coerce' with signature '"matrix.csc","TsparseMatrix"': no definition for class "matrix.csc"
in method for 'coerce' with signature '"matrix.csr","TsparseMatrix"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"CsparseMatrix","matrix.csr"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"CsparseMatrix","matrix.coo"': no definition for class "matrix.coo"
in method for 'coerce' with signature '"CsparseMatrix","matrix.csc"': no definition for class "matrix.csc"
in method for 'coerce' with signature '"matrix.csr","Matrix"': no definition for class "matrix.csr"
in method for 'coerce' with signature '"matrix.coo","Matrix"': no definition for class "matrix.coo"
in method for 'coerce' with signature '"matrix.csc","Matrix"': no definition for class "matrix.csc"
Creating a generic function for 'colSums' from package 'base' in package 'Matrix'
Creating a generic function for 'colMeans' from package 'base' in package 'Matrix'
Creating a generic function for 'rowSums' from package 'base' in package 'Matrix'
Creating a generic function for 'rowMeans' from package 'base' in package 'Matrix'
in method for 'colSums' with signature 'x="igCMatrix"': no definition for class "igCMatrix"
in method for 'rowSums' with signature 'x="igCMatrix"': no definition for class "igCMatrix"
in method for 'colMeans' with signature 'x="igCMatrix"': no definition for class "igCMatrix"
in method for 'rowMeans' with signature 'x="igCMatrix"': no definition for class "igCMatrix"
Creating a generic function for 'zapsmall' from package 'base' in package 'Matrix'
Creating a generic function for 'diag<-' from package 'base' in package 'Matrix'
Creating a generic function for 'crossprod' from package 'base' in package 'Matrix'
Creating a generic function for 'tcrossprod' from package 'base' in package 'Matrix'
Creating a generic function for 'which' from package 'base' in package 'Matrix'
in method for 'coerce' with signature '"graphAM","sparseMatrix"': no definition for class "graphAM"
in method for 'coerce' with signature '"graph","CsparseMatrix"': no definition for class "graph"
in method for 'coerce' with signature '"graph","Matrix"': no definition for class "graph"
in method for 'coerce' with signature '"graphNEL","CsparseMatrix"': no definition for class "graphNEL"
in method for 'coerce' with signature '"graphNEL","TsparseMatrix"': no definition for class "graphNEL"
in method for 'coerce' with signature '"sparseMatrix","graph"': no definition for class "graph"
in method for 'coerce' with signature '"sparseMatrix","graphNEL"': no definition for class "graphNEL"
in method for 'coerce' with signature '"TsparseMatrix","graphNEL"': no definition for class "graphNEL"
Creating a generic function for 'qr.R' from package 'base' in package 'Matrix'
Creating a generic function for 'qr.Q' from package 'base' in package 'Matrix'
Creating a generic function for 'qr.qy' from package 'base' in package 'Matrix'
Creating a generic function for 'qr.qty' from package 'base' in package 'Matrix'
Creating a generic function for 'qr.coef' from package 'base' in package 'Matrix'
Creating a generic function for 'qr.resid' from package 'base' in package 'Matrix'
Creating a generic function for 'qr.fitted' from package 'base' in package 'Matrix'
Creating a generic function for 'toeplitz' from package 'stats' in package 'Matrix'
** help
*** installing help indices
  converting help for package 'Matrix'
    finding HTML links ... done
    BunchKaufman-methods                    html  
    CAex                                    html  
    CHMfactor-class                         html  
    Cholesky-class                          html  
    Cholesky                                html  
    CsparseMatrix-class                     html  
    Diagonal                                html  
    Hilbert                                 html  
    KNex                                    html  
    KhatriRao                               html  
    LU-class                                html  
    Matrix-class                            html  
    Matrix                                  html  
    MatrixClass                             html  
    MatrixFactorization-class               html  
    RsparseMatrix-class                     html  
    Schur-class                             html  
    Schur                                   html  
    SparseM-conv                            html  
    Subassign-methods                       html  
    TsparseMatrix-class                     html  
    USCounties                              html  
    Xtrct-methods                           html  
    abIndex-class                           html  
Rd warning: C:/Users/appveyor/AppData/Local/Temp/1/RtmpemPFZA/R.INSTALLb48799c1547/Matrix/man/abIndex-class.Rd:80: file link 'Ops' in package 'methods' does not exist and so has been treated as a topic
    abIseq                                  html  
    all-methods                             html  
    all.equal-methods                       html  
    atomicVector-class                      html  
    band                                    html  
    bandSparse                              html  
    bdiag                                   html  
    boolean-matprod                         html  
    cBind                                   html  
    chol                                    html  
    chol2inv-methods                        html  
    colSums                                 html  
    compMatrix-class                        html  
    condest                                 html  
    dMatrix-class                           html  
    ddenseMatrix-class                      html  
    ddiMatrix-class                         html  
    denseMatrix-class                       html  
    dgCMatrix-class                         html  
    dgRMatrix-class                         html  
    dgTMatrix-class                         html  
    dgeMatrix-class                         html  
    diagU2N                                 html  
    diagonalMatrix-class                    html  
    dpoMatrix-class                         html  
    drop0                                   html  
    dsCMatrix-class                         html  
    dsRMatrix-class                         html  
    dsparseMatrix-class                     html  
    dsyMatrix-class                         html  
    dtCMatrix-class                         html  
    dtRMatrix-class-def                     html  
    dtpMatrix-class                         html  
    dtrMatrix-class                         html  
    expand                                  html  
    expm                                    html  
    externalFormats                         html  
    facmul                                  html  
    forceSymmetric                          html  
    formatSparseM                           html  
    generalMatrix-class                     html  
    graph2T                                 html  
    image-methods                           html  
Rd warning: C:/Users/appveyor/AppData/Local/Temp/1/RtmpemPFZA/R.INSTALLb48799c1547/Matrix/man/image-methods.Rd:53: file link 'panel.levelplot.raster' in package 'lattice' does not exist and so has been treated as a topic
Rd warning: C:/Users/appveyor/AppData/Local/Temp/1/RtmpemPFZA/R.INSTALLb48799c1547/Matrix/man/image-methods.Rd:81: file link 'get.gpar' in package 'grid' does not exist and so has been treated as a topic
    indMatrix-class                         html  
    index-class                             html  
    invPerm                                 html  
    is.na-methods                           html  
    is.null.DN                              html  
    isSymmetric-methods                     html  
    isTriangular                            html  
    kronecker-methods                       html  
    ldenseMatrix-class                      html  
    ldiMatrix-class                         html  
    lgeMatrix-class                         html  
    lsparseMatrix-classes                   html  
    lsyMatrix-class                         html  
    ltrMatrix-class                         html  
    lu                                      html  
    matrix-products                         html  
Rd warning: C:/Users/appveyor/AppData/Local/Temp/1/RtmpemPFZA/R.INSTALLb48799c1547/Matrix/man/matrix-products.Rd:406: file link 'tcrossprod' in package 'base' does not exist and so has been treated as a topic
    nMatrix-class                           html  
    ndenseMatrix-class                      html  
    nearPD                                  html  
    ngeMatrix-class                         html  
    nnzero                                  html  
    norm                                    html  
    nsparseMatrix-classes                   html  
    nsyMatrix-class                         html  
    ntrMatrix-class                         html  
    number-class                            html  
    pMatrix-class                           html  
    printSpMatrix                           html  
    qr-methods                              html  
    rankMatrix                              html  
    rcond                                   html  
    rep2abI                                 html  
    replValue-class                         html  
    rleDiff-class                           html  
    rsparsematrix                           html  
    solve-methods                           html  
    spMatrix                                html  
    sparse.model.matrix                     html  
    sparseLU-class                          html  
    sparseMatrix-class                      html  
    sparseMatrix                            html  
    sparseQR-class                          html  
    sparseVector-class                      html  
    sparseVector                            html  
    symmetricMatrix-class                   html  
    symmpart                                html  
    triangularMatrix-class                  html  
    uniqTsparse                             html  
    unpack                                  html  
    unused-classes                          html  
    updown                                  html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Matrix)
Making 'packages.html' ... done

----- installing recommended package nlme
* installing *source* package 'nlme' ...
** package 'nlme' successfully unpacked and MD5 sums checked
** using non-staged installation
** libs
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c chol.f -o chol.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c corStruct.c -o corStruct.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c gnls.c -o gnls.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c init.c -o init.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c matrix.c -o matrix.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c nlOptimizer.c -o nlOptimizer.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c nlme.c -o nlme.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c nlmefit.c -o nlmefit.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c pdMat.c -o pdMat.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c pythag.c -o pythag.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c rs.f -o rs.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o nlme.dll tmp.def chol.o corStruct.o gnls.o init.o matrix.o nlOptimizer.o nlme.o nlmefit.o pdMat.o pythag.o rs.o -LC:/projects/BUILD/R-source-win64/extsoft/lib/x64 -LC:/projects/BUILD/R-source-win64/extsoft/lib -lgfortran -lm -lquadmath -LC:/projects/BUILD/R-source-win64/bin/x64 -lR
installing to C:/projects/BUILD/R-source-win64/library/nlme/libs/x64
** R
** data
*** moving datasets to lazyload DB
** inst
** tests
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'nlme'
    finding HTML links ... done
    ACF                                     html  
    ACF.gls                                 html  
    ACF.lme                                 html  
    Alfalfa                                 html  
    Assay                                   html  
    BodyWeight                              html  
    Cefamandole                             html  
    Coef                                    html  
    Covariate                               html  
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    Dialyzer                                html  
    Dim                                     html  
    Dim.corSpatial                          html  
    Dim.corStruct                           html  
    Dim.pdMat                               html  
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    Extract.pdMat                           html  
    Fatigue                                 html  
    Gasoline                                html  
    Glucose                                 html  
    Glucose2                                html  
    Gun                                     html  
    IGF                                     html  
    Initialize                              html  
    Initialize.corStruct                    html  
    Initialize.glsStruct                    html  
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    LDEsysMat                               html  
    Machines                                html  
    MathAchSchool                           html  
    MathAchieve                             html  
    Matrix                                  html  
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    RatPupWeight                            html  
    Relaxin                                 html  
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    Tetracycline1                           html  
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    VarCorr                                 html  
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    Variogram.corExp                        html  
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    Variogram.corRatio                      html  
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    Variogram.default                       html  
    Variogram.gls                           html  
    Variogram.lme                           html  
    Wafer                                   html  
    Wheat                                   html  
    Wheat2                                  html  
    allCoef                                 html  
    anova.gls                               html  
    anova.lme                               html  
    as.matrix.corStruct                     html  
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    asOneFormula                            html  
    asTable                                 html  
    augPred                                 html  
    balancedGrouped                         html  
    bdf                                     html  
    coef.corStruct                          html  
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    coef.lmList                             html  
    coef.lme                                html  
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    coef.pdMat                              html  
    coef.reStruct                           html  
    coef.varFunc                            html  
    collapse                                html  
    collapse.groupedData                    html  
    compareFits                             html  
    comparePred                             html  
    corAR1                                  html  
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    corCAR1                                 html  
    corClasses                              html  
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    corExp                                  html  
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    corFactor.corStruct                     html  
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    corMatrix.corStruct                     html  
    corMatrix.pdMat                         html  
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    corNatural                              html  
    corRatio                                html  
    corSpatial                              html  
    corSpher                                html  
    corSymm                                 html  
    ergoStool                               html  
    fdHess                                  html  
    fitted.glsStruct                        html  
    fitted.gnlsStruct                       html  
    fitted.lmList                           html  
    fitted.lme                              html  
    fitted.lmeStruct                        html  
    fitted.nlmeStruct                       html  
    fixed.effects                           html  
    fixef.lmList                            html  
    formula.pdBlocked                       html  
    formula.pdMat                           html  
    formula.reStruct                        html  
    gapply                                  html  
    getCovariate                            html  
    getCovariate.corStruct                  html  
    getCovariate.data.frame                 html  
    getCovariate.varFunc                    html  
    getCovariateFormula                     html  
    getData                                 html  
    getData.gls                             html  
    getData.lmList                          html  
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    getGroups                               html  
    getGroups.corStruct                     html  
    getGroups.data.frame                    html  
    getGroups.gls                           html  
    getGroups.lmList                        html  
    getGroups.lme                           html  
    getGroups.varFunc                       html  
    getGroupsFormula                        html  
    getResponse                             html  
    getResponseFormula                      html  
    getVarCov                               html  
    gls-internal                            html  
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    glsControl                              html  
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    gnls                                    html  
    gnlsControl                             html  
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    groupedData                             html  
    gsummary                                html  
    intervals                               html  
    intervals.gls                           html  
    intervals.lmList                        html  
    intervals.lme                           html  
    isBalanced                              html  
    isInitialized                           html  
    lmList                                  html  
    lmList.groupedData                      html  
    lme                                     html  
    lme.groupedData                         html  
    lme.lmList                              html  
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    logDet                                  html  
    logDet.corStruct                        html  
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    model.matrix.reStruct                   html  
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    needUpdate.modelStruct                  html  
    nlme                                    html  
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    nlsList                                 html  
    nlsList.selfStart                       html  
    pairs.compareFits                       html  
    pairs.lmList                            html  
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    pdBlocked                               html  
    pdClasses                               html  
    pdCompSymm                              html  
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    pdConstruct.pdBlocked                   html  
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    pdIdent                                 html  
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    pdMatrix.reStruct                       html  
    pdNatural                               html  
    pdSymm                                  html  
    phenoModel                              html  
    plot.ACF                                html  
    plot.Variogram                          html  
    plot.augPred                            html  
    plot.compareFits                        html  
    plot.gls                                html  
    plot.intervals.lmList                   html  
Rd warning: C:/Users/appveyor/AppData/Local/Temp/1/RtmpWEH4Cg/R.INSTALLa3828601b27/nlme/man/plot.intervals.lmList.Rd:34: file link 'dotplot' in package 'lattice' does not exist and so has been treated as a topic
Rd warning: C:/Users/appveyor/AppData/Local/Temp/1/RtmpWEH4Cg/R.INSTALLa3828601b27/nlme/man/plot.intervals.lmList.Rd:21: file link 'dotplot' in package 'lattice' does not exist and so has been treated as a topic
    plot.lmList                             html  
    plot.lme                                html  
    plot.nffGroupedData                     html  
    plot.nfnGroupedData                     html  
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    plot.ranef.lmList                       html  
    plot.ranef.lme                          html  
Rd warning: C:/Users/appveyor/AppData/Local/Temp/1/RtmpWEH4Cg/R.INSTALLa3828601b27/nlme/man/plot.ranef.lme.Rd:25: file link 'dotplot' in package 'lattice' does not exist and so has been treated as a topic
Rd warning: C:/Users/appveyor/AppData/Local/Temp/1/RtmpWEH4Cg/R.INSTALLa3828601b27/nlme/man/plot.ranef.lme.Rd:65: file link 'dotplot' in package 'lattice' does not exist and so has been treated as a topic
Rd warning: C:/Users/appveyor/AppData/Local/Temp/1/RtmpWEH4Cg/R.INSTALLa3828601b27/nlme/man/plot.ranef.lme.Rd:71: file link 'dotplot' in package 'lattice' does not exist and so has been treated as a topic
    pooledSD                                html  
    predict.gls                             html  
    predict.gnls                            html  
    predict.lmList                          html  
    predict.lme                             html  
    predict.nlme                            html  
    print.summary.pdMat                     html  
    print.varFunc                           html  
    qqnorm.gls                              html  
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    quinModel                               html  
    random.effects                          html  
    ranef.lmList                            html  
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    reStruct                                html  
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    recalc.corStruct                        html  
    recalc.modelStruct                      html  
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    recalc.varFunc                          html  
    residuals.gls                           html  
    residuals.glsStruct                     html  
    residuals.gnlsStruct                    html  
    residuals.lmList                        html  
    residuals.lme                           html  
    residuals.lmeStruct                     html  
    residuals.nlmeStruct                    html  
    simulate.lme                            html  
    solve.pdMat                             html  
    solve.reStruct                          html  
    splitFormula                            html  
    summary.corStruct                       html  
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    summary.lme                             html  
    summary.modelStruct                     html  
    summary.nlsList                         html  
    summary.pdMat                           html  
    summary.varFunc                         html  
    update.modelStruct                      html  
    update.varFunc                          html  
    varClasses                              html  
    varComb                                 html  
    varConstPower                           html  
    varExp                                  html  
    varFixed                                html  
    varFunc                                 html  
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    varPower                                html  
    varWeights                              html  
    varWeights.glsStruct                    html  
    varWeights.lmeStruct                    html  
** building package indices
** testing if installed package can be loaded
* DONE (nlme)
Making 'packages.html' ... done

----- installing recommended package survival
* installing *source* package 'survival' ...
** package 'survival' successfully unpacked and MD5 sums checked
** using non-staged installation
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c agexact.c -o agexact.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c agfit4.c -o agfit4.o
agfit4.c: In function 'agfit4':
agfit4.c:575:24: warning: 'dtime' may be used uninitialized in this function [-Wmaybe-uninitialized]
                     if (tstop[p] < dtime) break; /* no more to add */
                        ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c agfit5.c -o agfit5.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c agmart.c -o agmart.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c agmart2.c -o agmart2.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c agmart3.c -o agmart3.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c agscore.c -o agscore.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c agsurv3.c -o agsurv3.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c agsurv4.c -o agsurv4.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c agsurv5.c -o agsurv5.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c chinv2.c -o chinv2.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c chinv3.c -o chinv3.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c cholesky2.c -o cholesky2.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c cholesky3.c -o cholesky3.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c cholesky5.c -o cholesky5.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c chsolve2.c -o chsolve2.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c chsolve3.c -o chsolve3.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c chsolve5.c -o chsolve5.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c concordance1.c -o concordance1.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c concordance3.c -o concordance3.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c cox_Rcallback.c -o cox_Rcallback.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c coxcount1.c -o coxcount1.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c coxdetail.c -o coxdetail.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c coxexact.c -o coxexact.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c coxfit5.c -o coxfit5.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c coxfit6.c -o coxfit6.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c coxmart.c -o coxmart.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c coxmart2.c -o coxmart2.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c coxph_wtest.c -o coxph_wtest.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c coxsafe.c -o coxsafe.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c coxscho.c -o coxscho.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c coxscore.c -o coxscore.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c dmatrix.c -o dmatrix.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c doloop.c -o doloop.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c finegray.c -o finegray.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c gchol.c -o gchol.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c init.c -o init.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c norisk.c -o norisk.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c pyears1.c -o pyears1.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c pyears2.c -o pyears2.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c pyears3b.c -o pyears3b.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c pystep.c -o pystep.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c survConcordance.c -o survConcordance.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c survdiff2.c -o survdiff2.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c survfit4.c -o survfit4.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c survfitci.c -o survfitci.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c survfitkm.c -o survfitkm.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c survpenal.c -o survpenal.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c survreg6.c -o survreg6.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c survreg7.c -o survreg7.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c survregc1.c -o survregc1.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c survregc2.c -o survregc2.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c survsplit.c -o survsplit.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c tmerge.c -o tmerge.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o survival.dll tmp.def agexact.o agfit4.o agfit5.o agmart.o agmart2.o agmart3.o agscore.o agsurv3.o agsurv4.o agsurv5.o chinv2.o chinv3.o cholesky2.o cholesky3.o cholesky5.o chsolve2.o chsolve3.o chsolve5.o concordance1.o concordance3.o cox_Rcallback.o coxcount1.o coxdetail.o coxexact.o coxfit5.o coxfit6.o coxmart.o coxmart2.o coxph_wtest.o coxsafe.o coxscho.o coxscore.o dmatrix.o doloop.o finegray.o gchol.o init.o norisk.o pyears1.o pyears2.o pyears3b.o pystep.o survConcordance.o survdiff2.o survfit4.o survfitci.o survfitkm.o survpenal.o survreg6.o survreg7.o survregc1.o survregc2.o survsplit.o tmerge.o -LC:/projects/BUILD/R-source-win64/extsoft/lib/x64 -LC:/projects/BUILD/R-source-win64/extsoft/lib -LC:/projects/BUILD/R-source-win64/bin/x64 -lR
installing to C:/projects/BUILD/R-source-win64/library/survival/libs/x64
** R
** data
*** moving datasets to lazyload DB
** inst
** tests
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'survival'
    finding HTML links ... done
    Surv                                    html  
    Survmethods                             html  
    aareg                                   html  
    aeqSurv                                 html  
    agreg.fit                               html  
    aml                                     html  
    anova.coxph                             html  
    attrassign                              html  
    basehaz                                 html  
    bladder                                 html  
    cch                                     html  
    cgd                                     html  
    cgd0                                    html  
    cipoisson                               html  
Rd warning: C:/Users/appveyor/AppData/Local/Temp/1/RtmpYbm7zz/R.INSTALLb78f456d9c/survival/man/cipoisson.Rd:59: file link 'ppois' in package 'stats' does not exist and so has been treated as a topic
Rd warning: C:/Users/appveyor/AppData/Local/Temp/1/RtmpYbm7zz/R.INSTALLb78f456d9c/survival/man/cipoisson.Rd:59: file link 'qpois' in package 'stats' does not exist and so has been treated as a topic
    clogit                                  html  
    cluster                                 html  
    colon                                   html  
    concordance                             html  
    concordancefit                          html  
    cox.zph                                 html  
    coxph                                   html  
    coxph.control                           html  
    coxph.detail                            html  
    coxph.object                            html  
    coxph.wtest                             html  
    diabetic                                html  
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    finegray                                html  
    flchain                                 html  
    frailty                                 html  
    heart                                   html  
    is.ratetable                            html  
    kidney                                  html  
    levels.Surv                             html  
    lines.survfit                           html  
    logLik.coxph                            html  
    logan                                   html  
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    model.frame.coxph                       html  
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    plot.aareg                              html  
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    plot.survfit                            html  
    predict.coxph                           html  
    predict.survreg                         html  
    print.aareg                             html  
    print.summary.coxph                     html  
    print.summary.survexp                   html  
    print.summary.survfit                   html  
    print.survfit                           html  
    pspline                                 html  
    pyears                                  html  
    quantile.survfit                        html  
    ratetable                               html  
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    rats                                    html  
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    reliability                             html  
    residuals.coxph                         html  
    residuals.survreg                       html  
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    stanford2                               html  
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    strata                                  html  
    summary.aareg                           html  
    summary.coxph                           html  
    summary.pyears                          html  
    summary.survexp                         html  
    summary.survfit                         html  
    survConcordance-deprecated              html  
    survSplit                               html  
    survdiff                                html  
    survexp                                 html  
    survexp.fit                             html  
    survexp.object                          html  
    survexp.us                              html  
    survfit                                 html  
    survfit.coxph                           html  
    survfit.formula                         html  
    survfit.matrix                          html  
    survfit.object                          html  
    survfitcoxph.fit                        html  
    survival-internal                       html  
    survobrien                              html  
    survreg                                 html  
    survreg.control                         html  
    survreg.distributions                   html  
    survreg.object                          html  
    survregDtest                            html  
    tcut                                    html  
    tmerge                                  html  
    tobin                                   html  
    transplant                              html  
    udca                                    html  
    untangle.specials                       html  
    uspop2                                  html  
    vcov.coxph                              html  
    veteran                                 html  
    xtfrm.Surv                              html  
    yates                                   html  
    yates_setup                             html  
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (survival)
Making 'packages.html' ... done

----- installing recommended package boot
* installing *source* package 'boot' ...
** package 'boot' successfully unpacked and MD5 sums checked
** using non-staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** tests
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'boot'
    finding HTML links ... done
    EEF.profile                             html  
    Imp.Estimates                           html  
    abc.ci                                  html  
    acme                                    html  
    aids                                    html  
    aircondit                               html  
    amis                                    html  
    aml                                     html  
    beaver                                  html  
    bigcity                                 html  
    boot-practicals                         html  
    boot                                    html  
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    brambles                                html  
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    capability                              html  
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    freq.array                              html  
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    glm.diag                                html  
    glm.diag.plots                          html  
    gravity                                 html  
    hirose                                  html  
    imp.weights                             html  
    inv.logit                               html  
    islay                                   html  
    jack.after.boot                         html  
    k3.linear                               html  
    linear.approx                           html  
    lines.saddle.distn                      html  
    logit                                   html  
    manaus                                  html  
    melanoma                                html  
    motor                                   html  
    neuro                                   html  
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    nodal                                   html  
    norm.ci                                 html  
    nuclear                                 html  
    paulsen                                 html  
    plot.boot                               html  
    poisons                                 html  
    polar                                   html  
    print.boot                              html  
    print.bootci                            html  
    print.saddle.distn                      html  
    print.simplex                           html  
    remission                               html  
    saddle                                  html  
    saddle.distn                            html  
    saddle.distn.object                     html  
    salinity                                html  
    simplex                                 html  
    simplex.object                          html  
    smooth.f                                html  
    sunspot                                 html  
    survival                                html  
    tau                                     html  
    tilt.boot                               html  
    tsboot                                  html  
    tuna                                    html  
    urine                                   html  
    var.linear                              html  
    wool                                    html  
** building package indices
** testing if installed package can be loaded
* DONE (boot)
Making 'packages.html' ... done

----- installing recommended package cluster
* installing *source* package 'cluster' ...
** package 'cluster' successfully unpacked and MD5 sums checked
** using non-staged installation
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c clara.c -o clara.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c daisy.f -o daisy.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c dysta.f -o dysta.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c fanny.c -o fanny.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c init.c -o init.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c mona.c -o mona.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c pam.c -o pam.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c sildist.c -o sildist.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c spannel.c -o spannel.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c twins.c -o twins.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o cluster.dll tmp.def clara.o daisy.o dysta.o fanny.o init.o mona.o pam.o sildist.o spannel.o twins.o -LC:/projects/BUILD/R-source-win64/extsoft/lib/x64 -LC:/projects/BUILD/R-source-win64/extsoft/lib -lgfortran -lm -lquadmath -LC:/projects/BUILD/R-source-win64/bin/x64 -lR
installing to C:/projects/BUILD/R-source-win64/library/cluster/libs/x64
** R
** data
*** moving datasets to lazyload DB
** inst
** tests
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'cluster'
    finding HTML links ... done
    agnes                                   html  
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    animals                                 html  
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Rd warning: C:/Users/appveyor/AppData/Local/Temp/1/Rtmpophr7V/R.INSTALL9478ec1485/cluster/man/clusplot.default.Rd:212: file link 'cov.mve' in package 'MASS' does not exist and so has been treated as a topic
    clusplot.partition                      html  
    cluster-internal                        html  
    coef.hclust                             html  
    daisy                                   html  
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    dissimilarity.object                    html  
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Rd warning: C:/Users/appveyor/AppData/Local/Temp/1/Rtmpophr7V/R.INSTALL9478ec1485/cluster/man/ellipsoidhull.Rd:36: file link 'cov.mve' in package 'MASS' does not exist and so has been treated as a topic
Rd warning: C:/Users/appveyor/AppData/Local/Temp/1/Rtmpophr7V/R.INSTALL9478ec1485/cluster/man/ellipsoidhull.Rd:87: file link 'cov.mve' in package 'MASS' does not exist and so has been treated as a topic
    fanny                                   html  
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    lower.to.upper.tri.inds                 html  
    mona                                    html  
    mona.object                             html  
    pam                                     html  
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    partition.object                        html  
    plantTraits                             html  
    plot.agnes                              html  
Rd warning: C:/Users/appveyor/AppData/Local/Temp/1/Rtmpophr7V/R.INSTALL9478ec1485/cluster/man/plot.agnes.Rd:73: file link 'plot.dendrogram' in package 'stats' does not exist and so has been treated as a topic
    plot.diana                              html  
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    print.agnes                             html  
    print.clara                             html  
    print.diana                             html  
    print.dissimilarity                     html  
Rd warning: C:/Users/appveyor/AppData/Local/Temp/1/Rtmpophr7V/R.INSTALL9478ec1485/cluster/man/print.dissimilarity.Rd:27: file link 'print.dist' in package 'stats' does not exist and so has been treated as a topic
    print.fanny                             html  
    print.mona                              html  
    print.pam                               html  
    ruspini                                 html  
    silhouette                              html  
    sizeDiss                                html  
    summary.agnes                           html  
    summary.clara                           html  
    summary.diana                           html  
    summary.mona                            html  
    summary.pam                             html  
    twins.object                            html  
    volume.ellipsoid                        html  
    votes.repub                             html  
    xclara                                  html  
** building package indices
** testing if installed package can be loaded
* DONE (cluster)
Making 'packages.html' ... done

----- installing recommended package codetools
* installing *source* package 'codetools' ...
** package 'codetools' successfully unpacked and MD5 sums checked
** using non-staged installation
** R
** tests
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'codetools'
    finding HTML links ... done
    checkUsage                              html  
    codetools                               html  
    findGlobals                             html  
    showTree                                html  
** building package indices
** testing if installed package can be loaded
* DONE (codetools)
Making 'packages.html' ... done

----- installing recommended package foreign
* installing *source* package 'foreign' ...
** package 'foreign' successfully unpacked and MD5 sums checked
** using non-staged installation
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c R_systat.c -o R_systat.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c Rdbfread.c -o Rdbfread.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c Rdbfwrite.c -o Rdbfwrite.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c SASxport.c -o SASxport.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c avl.c -o avl.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c dbfopen.c -o dbfopen.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c file-handle.c -o file-handle.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c format.c -o format.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c init.c -o init.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c minitab.c -o minitab.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c pfm-read.c -o pfm-read.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c sfm-read.c -o sfm-read.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c spss.c -o spss.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c stataread.c -o stataread.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o foreign.dll tmp.def R_systat.o Rdbfread.o Rdbfwrite.o SASxport.o avl.o dbfopen.o file-handle.o format.o init.o minitab.o pfm-read.o sfm-read.o spss.o stataread.o -LC:/projects/BUILD/R-source-win64/extsoft/lib/x64 -LC:/projects/BUILD/R-source-win64/extsoft/lib -LC:/projects/BUILD/R-source-win64/bin/x64 -lR
installing to C:/projects/BUILD/R-source-win64/library/foreign/libs/x64
** R
** inst
** tests
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'foreign'
    finding HTML links ... done
    lookup.xport                            html  
    read.S                                  html  
    read.arff                               html  
    read.dbf                                html  
    read.dta                                html  
    read.epiinfo                            html  
    read.mtp                                html  
    read.octave                             html  
    read.spss                               html  
    read.ssd                                html  
    read.systat                             html  
    read.xport                              html  
    write.arff                              html  
    write.dbf                               html  
    write.dta                               html  
    write.foreign                           html  
** building package indices
** testing if installed package can be loaded
* DONE (foreign)
Making 'packages.html' ... done

----- installing recommended package KernSmooth
* installing *source* package 'KernSmooth' ...
** package 'KernSmooth' successfully unpacked and MD5 sums checked
** using non-staged installation
** libs
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c blkest.f -o blkest.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c cp.f -o cp.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c dgedi.f -o dgedi.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c dgefa.f -o dgefa.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c dgesl.f -o dgesl.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c init.c -o init.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c linbin.f -o linbin.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c linbin2D.f -o linbin2D.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c locpoly.f -o locpoly.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c rlbin.f -o rlbin.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c sdiag.f -o sdiag.o
C:/Rtools/mingw_64/bin/gfortran      -O2  -mtune=generic -c sstdiag.f -o sstdiag.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o KernSmooth.dll tmp.def blkest.o cp.o dgedi.o dgefa.o dgesl.o init.o linbin.o linbin2D.o locpoly.o rlbin.o sdiag.o sstdiag.o -LC:/projects/BUILD/R-source-win64/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/projects/BUILD/R-source-win64/extsoft/lib/x64 -LC:/projects/BUILD/R-source-win64/extsoft/lib -lgfortran -lm -lquadmath -LC:/projects/BUILD/R-source-win64/bin/x64 -lR
installing to C:/projects/BUILD/R-source-win64/library/KernSmooth/libs/x64
** R
** inst
** tests
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'KernSmooth'
    finding HTML links ... done
    bkde                                    html  
    bkde2D                                  html  
    bkfe                                    html  
    dpih                                    html  
    dpik                                    html  
    dpill                                   html  
    locpoly                                 html  
** building package indices
** testing if installed package can be loaded
* DONE (KernSmooth)
Making 'packages.html' ... done

----- installing recommended package rpart
* installing *source* package 'rpart' ...
** package 'rpart' successfully unpacked and MD5 sums checked
** using non-staged installation
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c anova.c -o anova.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c anovapred.c -o anovapred.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c branch.c -o branch.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c bsplit.c -o bsplit.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c choose_surg.c -o choose_surg.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c fix_cp.c -o fix_cp.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c free_tree.c -o free_tree.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c gini.c -o gini.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c graycode.c -o graycode.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c init.c -o init.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c insert_split.c -o insert_split.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c make_cp_list.c -o make_cp_list.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c make_cp_table.c -o make_cp_table.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c mysort.c -o mysort.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c nodesplit.c -o nodesplit.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c partition.c -o partition.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c poisson.c -o poisson.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c pred_rpart.c -o pred_rpart.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c print_tree.c -o print_tree.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c rpart.c -o rpart.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c rpart_callback.c -o rpart_callback.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c rpartexp.c -o rpartexp.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c rpartexp2.c -o rpartexp2.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c rpcountup.c -o rpcountup.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c rpmatrix.c -o rpmatrix.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c rundown.c -o rundown.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c rundown2.c -o rundown2.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c surrogate.c -o surrogate.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c usersplit.c -o usersplit.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c xpred.c -o xpred.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c xval.c -o xval.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o rpart.dll tmp.def anova.o anovapred.o branch.o bsplit.o choose_surg.o fix_cp.o free_tree.o gini.o graycode.o init.o insert_split.o make_cp_list.o make_cp_table.o mysort.o nodesplit.o partition.o poisson.o pred_rpart.o print_tree.o rpart.o rpart_callback.o rpartexp.o rpartexp2.o rpcountup.o rpmatrix.o rundown.o rundown2.o surrogate.o usersplit.o xpred.o xval.o -LC:/projects/BUILD/R-source-win64/extsoft/lib/x64 -LC:/projects/BUILD/R-source-win64/extsoft/lib -LC:/projects/BUILD/R-source-win64/bin/x64 -lR
installing to C:/projects/BUILD/R-source-win64/library/rpart/libs/x64
** R
** data
*** moving datasets to lazyload DB
** inst
** tests
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'rpart'
    finding HTML links ... done
    car.test.frame                          html  
    car90                                   html  
    cu.summary                              html  
    kyphosis                                html  
    labels.rpart                            html  
    meanvar.rpart                           html  
    na.rpart                                html  
    path.rpart                              html  
    plot.rpart                              html  
    plotcp                                  html  
    post.rpart                              html  
    predict.rpart                           html  
    print.rpart                             html  
    printcp                                 html  
    prune.rpart                             html  
    residuals.rpart                         html  
    rpart-internal                          html  
    rpart                                   html  
    rpart.control                           html  
    rpart.exp                               html  
    rpart.object                            html  
    rsq.rpart                               html  
    snip.rpart                              html  
    solder.balance                          html  
    stagec                                  html  
    summary.rpart                           html  
    text.rpart                              html  
    xpred.rpart                             html  
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (rpart)
Making 'packages.html' ... done

----- installing recommended package class
* installing *source* package 'class' ...
** package 'class' successfully unpacked and MD5 sums checked
** using non-staged installation
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c class.c -o class.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o class.dll tmp.def class.o -LC:/projects/BUILD/R-source-win64/extsoft/lib/x64 -LC:/projects/BUILD/R-source-win64/extsoft/lib -LC:/projects/BUILD/R-source-win64/bin/x64 -lR
installing to C:/projects/BUILD/R-source-win64/library/class/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'class'
    finding HTML links ... done
    SOM                                     html  
    batchSOM                                html  
    condense                                html  
    knn                                     html  
    knn.cv                                  html  
    knn1                                    html  
    lvq1                                    html  
    lvq2                                    html  
    lvq3                                    html  
    lvqinit                                 html  
    lvqtest                                 html  
    multiedit                               html  
    olvq1                                   html  
    reduce.nn                               html  
    somgrid                                 html  
** building package indices
** testing if installed package can be loaded
* DONE (class)
Making 'packages.html' ... done

----- installing recommended package nnet
* installing *source* package 'nnet' ...
** package 'nnet' successfully unpacked and MD5 sums checked
** using non-staged installation
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c nnet.c -o nnet.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o nnet.dll tmp.def nnet.o -LC:/projects/BUILD/R-source-win64/extsoft/lib/x64 -LC:/projects/BUILD/R-source-win64/extsoft/lib -LC:/projects/BUILD/R-source-win64/bin/x64 -lR
installing to C:/projects/BUILD/R-source-win64/library/nnet/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'nnet'
    finding HTML links ... done
    class.ind                               html  
    multinom                                html  
    nnet.Hess                               html  
    nnet                                    html  
    predict.nnet                            html  
    which.is.max                            html  
** building package indices
** testing if installed package can be loaded
* DONE (nnet)
Making 'packages.html' ... done

----- installing recommended package spatial
* installing *source* package 'spatial' ...
** package 'spatial' successfully unpacked and MD5 sums checked
** using non-staged installation
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c init.c -o init.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c krc.c -o krc.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c pps.c -o pps.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o spatial.dll tmp.def init.o krc.o pps.o -LC:/projects/BUILD/R-source-win64/extsoft/lib/x64 -LC:/projects/BUILD/R-source-win64/extsoft/lib -LC:/projects/BUILD/R-source-win64/bin/x64 -lR
installing to C:/projects/BUILD/R-source-win64/library/spatial/libs/x64
** R
** inst
** tests
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'spatial'
    finding HTML links ... done
    Kaver                                   html  
    Kenvl                                   html  
    Kfn                                     html  
    Psim                                    html  
    SSI                                     html  
    Strauss                                 html  
    anova.trls                              html  
    correlogram                             html  
    expcov                                  html  
    ppgetregion                             html  
    ppinit                                  html  
    pplik                                   html  
    ppregion                                html  
    predict.trls                            html  
    prmat                                   html  
    semat                                   html  
    surf.gls                                html  
    surf.ls                                 html  
    trls.influence                          html  
    trmat                                   html  
    variogram                               html  
** building package indices
** testing if installed package can be loaded
* DONE (spatial)
Making 'packages.html' ... done

----- installing recommended package mgcv
* installing *source* package 'mgcv' ...
** package 'mgcv' successfully unpacked and MD5 sums checked
** using non-staged installation
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=generic -c coxph.c -o coxph.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=generic -c discrete.c -o discrete.o
discrete.c: In function 'indReduce':
discrete.c:101:24: warning: 'wl' may be used uninitialized in this function [-Wmaybe-uninitialized]
  i=ka[l+1];j=kb[l];Wij = wl[l];
                        ^
discrete.c:99:31: warning: 'ws' may be used uninitialized in this function [-Wmaybe-uninitialized]
         i=ka[l];j=kb[l+1];Wij = ws[l];
                               ^
discrete.c: In function 'XWXijs':
discrete.c:834:9: warning: 'D' may be used uninitialized in this function [-Wmaybe-uninitialized]
     *C,*D,*W,*wb,*p0,*p1,*p2,*p3,*pw,*pw1,*pl,*ps,*wi,*wsi,*wli,*wo,*psi,*pwi,*pli;
         ^
discrete.c:834:6: warning: 'C' may be used uninitialized in this function [-Wmaybe-uninitialized]
     *C,*D,*W,*wb,*p0,*p1,*p2,*p3,*pw,*pw1,*pl,*ps,*wi,*wsi,*wli,*wo,*psi,*pwi,*pli;
      ^
discrete.c:1034:87: warning: 'W' may be used uninitialized in this function [-Wmaybe-uninitialized]
    } else for (Kik=Ki,Kjk=Kj,p0=w,p1=w+n;p0<p1;p0++,Kik++,Kjk++) W[*Kik + mim * *Kjk] += *p0;
                                                                                       ^
discrete.c:1152:19: warning: 'wl' may be used uninitialized in this function [-Wmaybe-uninitialized]
       Dq[*Kjk] += *pl  * Xi[*Kik1] + *pw * Xi[*Kik];
                   ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=generic -c gdi.c -o gdi.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=generic -c init.c -o init.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=generic -c magic.c -o magic.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=generic -c mat.c -o mat.o
mat.c: In function 'chol_down':
mat.c:1747:9: warning: unused variable 'j' [-Wunused-variable]
   int i,j,n1;
         ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=generic -c matrix.c -o matrix.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=generic -c mgcv.c -o mgcv.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=generic -c misc.c -o misc.o
misc.c: In function 'tweedious':
misc.c:401:10: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
       if (!ok) if (jal<jal_lim) { /* need to expand buffer storage*/
          ^
misc.c:485:10: warning: suggest explicit braces to avoid ambiguous 'else' [-Wparentheses]
       if (!ok) if (jal<jal_lim) { /* need to expand buffer storage*/
          ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=generic -c mvn.c -o mvn.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=generic -c qp.c -o qp.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=generic -c soap.c -o soap.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=generic -c sparse-smooth.c -o sparse-smooth.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/projects/BUILD/R-source-win64/include" -DNDEBUG     -I"C:/projects/BUILD/R-source-win64/extsoft/include"  -fopenmp   -O2 -Wall  -std=gnu99 -mtune=generic -c tprs.c -o tprs.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o mgcv.dll tmp.def coxph.o discrete.o gdi.o init.o magic.o mat.o matrix.o mgcv.o misc.o mvn.o qp.o soap.o sparse-smooth.o tprs.o -LC:/projects/BUILD/R-source-win64/bin/x64 -lRlapack -LC:/projects/BUILD/R-source-win64/bin/x64 -lRblas -lgfortran -lm -lquadmath -fopenmp -LC:/projects/BUILD/R-source-win64/extsoft/lib/x64 -LC:/projects/BUILD/R-source-win64/extsoft/lib -LC:/projects/BUILD/R-source-win64/bin/x64 -lR
installing to C:/projects/BUILD/R-source-win64/library/mgcv/libs/x64
** R
** data
** inst
** tests
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'mgcv'
    finding HTML links ... done
    Beta                                    html  
    FFdes                                   html  
    Predict.matrix                          html  
    Predict.matrix.cr.smooth                html  
    Predict.matrix.soap.film                html  
    Rrank                                   html  
    Sl.initial.repara                       html  
    Sl.repara                               html  
    Sl.setup                                html  
    Tweedie                                 html  
    anova.gam                               html  
    bam                                     html  
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** building package indices
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[]\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber \T1/zi4/m/n/10 x \T1
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\T1/zi4/m/n/10 ^ double.neg.ulp.digits) / 2\T1/ptm/m/n/10 . Nor-mally \T1/zi4/m
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[]\T1/ptm/m/n/10 character string, the pre-ferred set-ting for [][]\T1/zi4/m/n/
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[]\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T
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[]\T1/ptm/m/n/10 If the calls to \T1/zi4/m/n/10 FUN \T1/ptm/m/n/10 re-turn vec-
tors of dif-fer-ent lengths, \T1/zi4/m/n/10 apply \T1/ptm/m/n/10 re-turns a lis
t of length
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 []\T1/zi4/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen
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[]\T1/ptm/m/n/10 The val-ues of the splits can also be ob-tained (less ef-fi-ci
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[][][]\T1/zi4/m/n/10 apply[][][] \T1/ptm/m/n/10 al-ways sim-pli-fies com-mon le
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 []   \T1/zi4/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...)
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor, or an ob-ject that can be co-erced to c
har-ac-ter by
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 []\T1/zi4/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex
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[]\T1/ptm/m/n/10 character string, par-tially matched to \T1/zi4/m/n/10 c("defa
ult","internal","wininet","libcurl")\T1/ptm/m/n/10 : 
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[]\T1/ptm/m/n/10 A note on `\T1/zi4/m/n/10 file://\T1/ptm/m/n/10 ' URLs. The mo
st gen-eral form (from RFC1738) is
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[]\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.0.0 the en-cod-ing \
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\T1/ptm/m/n/10 ated by Mi-crosoft ap-pli-ca-tions). If a BOM is re-quired (it i
s not rec-om-mended) when

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\T1/ptm/m/n/10 writ-ing it should be writ-ten ex-plic-itly, e.g. by \T1/zi4/m/n
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[]\T1/ptm/m/n/10 A length-one log-i-cal vec-tor that is not \T1/zi4/m/n/10 NA\T
1/ptm/m/n/10 . Con-di-tions of length greater

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\T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the 
first el-e-
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\T1/zi4/m/n/10 status _ codes$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https
 : / / en . wikipedia . org / wiki / List _ of _ FTP _ server _ return _ codes$
[][]\T1/ptm/m/n/10 .
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[][][]\T1/zi4/m/n/10 split[][][] \T1/ptm/m/n/10 for split-ting a vari-able ac-c
ord-ing to a group fac-tor; [][]\T1/zi4/m/n/10 factor[][][]\T1/ptm/m/n/10 , [][
]\T1/zi4/m/n/10 tabulate[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 table[][][]\T
1/ptm/m/n/10 ,
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[][][]\T1/zi4/m/n/10 I[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 plot.data.frame
[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 print.data.frame[][][]\T1/ptm/m/n/10 
, [][]\T1/zi4/m/n/10 row.names[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 names[]
[][] \T1/ptm/m/n/10 (for the col-umn names),
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[]\T1/ptm/m/n/10 A few times have spe-cific is-sues. First, the leap sec-onds a
re ig-nored, and real times

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value is on those OSes also used as an er-ror code.
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[]\T1/ptm/m/n/10 If true, [][]\T1/zi4/m/n/10 list[][][]\T1/ptm/m/n/10 s and ato
mic vec-tors with non-[][]\T1/zi4/m/n/10 NA[][][] \T1/ptm/m/n/10 names (see [][
]\T1/zi4/m/n/10 names[][][]\T1/ptm/m/n/10 ) are de-
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\T1/zi4/m/n/10 754-[]2008$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/n/10 https : / / 
en . wikipedia . org / wiki / Double _ precision$[][]\T1/ptm/m/n/10 , [][]$\T1/
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\T1/zi4/m/n/10 duplicated \T1/ptm/m/n/10 and \T1/zi4/m/n/10 anyDuplicated\T1/pt
m/m/n/10 , \T1/zi4/m/n/10 anyDuplicated(x,...) \T1/ptm/m/n/10 is a ``gen-er-al-
ized'' short-cut for
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[169] [170] [171]
Underfull \hbox (badness 4569) in paragraph at lines 11926--11930
[]\T1/ptm/m/n/10 When eval-u-at-ing ex-pres-sions in a data frame that has been
 passed as an ar-gu-ment

Underfull \hbox (badness 2401) in paragraph at lines 11926--11930
\T1/ptm/m/n/10 to a func-tion, the rel-e-vant en-clo-sure is of-ten the caller'
s en-vi-ron-ment, i.e., one needs
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[184] [185] [186] [187] [188] [189] [190] [191] [192] [193] [194] [195]
Underfull \hbox (badness 2253) in paragraph at lines 13605--13607
[]\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is
 done: see
[196]
Underfull \hbox (badness 1565) in paragraph at lines 13678--13682
[][][]\T1/zi4/m/n/10 Sys.readlink[][][] \T1/ptm/m/n/10 to find out about sym-bo
lic links, [][]\T1/zi4/m/n/10 files[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 fi
le.access[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files[][][]\T1/ptm/m/n/
10 , and

Underfull \hbox (badness 4927) in paragraph at lines 13722--13724
[]\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as \T1/zi4/m
/n/10 PATH \T1/ptm/m/n/10 and \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 with \T1/zi4
/m/n/10 fsep =
[197] [198]
Underfull \hbox (badness 3148) in paragraph at lines 13815--13820
[][][]\T1/zi4/m/n/10 files[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files[
][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 help[][][]\T1/ptm/m/n/10 ; [][]\T1/zi4
/m/n/10 RShowDoc[][][] \T1/ptm/m/n/10 call \T1/zi4/m/n/10 file.show() \T1/ptm/m
/n/10 for \T1/zi4/m/n/10 type = "text"\T1/ptm/m/n/10 . Con-sider
[199]
Underfull \hbox (badness 1466) in paragraph at lines 13864--13868
[]\T1/ptm/m/n/10 character vec-tors, con-tain-ing file names or paths. For \T1/
zi4/m/n/10 file.copy \T1/ptm/m/n/10 and
[200]
Underfull \hbox (badness 2875) in paragraph at lines 13985--13996
[]\T1/ptm/m/n/10 A ver-sion of sym-bolic link-ing to files/directories was im-p
le-mented more re-cently, and
[201]
Underfull \hbox (badness 10000) in paragraph at lines 14028--14032
[][][]\T1/zi4/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 file.ac
cess[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [
][]\T1/zi4/m/n/10 file.show[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files
[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 unlink[][][]\T1/ptm/m/n/10 , [][]\T1/
zi4/m/n/10 basename[][][]\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 14039--14042
[][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][
] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik
i /
[202] [203] [204] [205]
Underfull \hbox (badness 3965) in paragraph at lines 14328--14332
[]\T1/ptm/m/n/10 This is the same com-pu-ta-tion as for the em-pir-i-cal dis-tr
i-bu-tion func-tion, and in-deed,
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Underfull \hbox (badness 4429) in paragraph at lines 15104--15107
[]\T1/ptm/m/n/10 an atomic nu-mer-i-cal or char-ac-ter ob-ject, pos-si-bly [][]
\T1/zi4/m/n/10 complex[][][] \T1/ptm/m/n/10 only for
[218]
Underfull \hbox (badness 10000) in paragraph at lines 15210--15212
[]\T1/ptm/m/n/10 This works via \T1/zi4/m/n/10 prettyNum()\T1/ptm/m/n/10 , whic
h calls

Underfull \hbox (badness 1215) in paragraph at lines 15210--15212
\T1/zi4/m/n/10 .format.zeros(*,replace=replace.zero) \T1/ptm/m/n/10 three times
 in this case, see

Underfull \hbox (badness 10000) in paragraph at lines 15232--15237
[]\T1/ptm/m/n/10 For num-bers, \T1/zi4/m/n/10 formatC() \T1/ptm/m/n/10 calls \T
1/zi4/m/n/10 prettyNum() \T1/ptm/m/n/10 when needed which it-self calls

Underfull \hbox (badness 1558) in paragraph at lines 15232--15237
\T1/zi4/m/n/10 .format.zeros(*,replace=replace.zero)\T1/ptm/m/n/10 . (\T1/ptm/m
/it/10 ``when needed''\T1/ptm/m/n/10 : when \T1/zi4/m/n/10 zero.print \T1/ptm/m
/n/10 is not

Underfull \hbox (badness 10000) in paragraph at lines 15244--15248
[]\T1/zi4/m/n/10 formatC \T1/ptm/m/n/10 does not nec-es-sar-ily align the num-b
ers on the dec-i-mal point, so

Underfull \hbox (badness 2426) in paragraph at lines 15244--15248
\T1/zi4/m/n/10 formatC(c(6.11,13.1),digits = 2,format = "fg") \T1/ptm/m/n/10 gi
ves \T1/zi4/m/n/10 c("6.1"," 13")\T1/ptm/m/n/10 . If you want
[219]
Underfull \hbox (badness 2035) in paragraph at lines 15283--15287
[]\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/n/10 decimal.mark \T1/ptm/m/n/10 in
 \T1/zi4/m/n/10 formatC() \T1/ptm/m/n/10 was changed in \T1/phv/m/n/10 R \T1/pt
m/m/n/10 3.2.0: for use within
[220]
Underfull \vbox (badness 10000) has occurred while \output is active [221]
[222] [223] [224] [225] [226] [227] [228]
Underfull \hbox (badness 2452) in paragraph at lines 15882--15886
[]\T1/zi4/m/n/10 gctorture2 \T1/ptm/m/n/10 can also be in-voked via en-vi-ron-m
ent vari-ables at the start of the \T1/phv/m/n/10 R \T1/ptm/m/n/10 ses-

Underfull \hbox (badness 1147) in paragraph at lines 15882--15886
\T1/ptm/m/n/10 sion. \T1/zi4/m/n/10 R_GCTORTURE \T1/ptm/m/n/10 cor-re-sponds to
 the \T1/zi4/m/n/10 step \T1/ptm/m/n/10 ar-gu-ment, \T1/zi4/m/n/10 R_GCTORTURE_
WAIT \T1/ptm/m/n/10 to \T1/zi4/m/n/10 wait\T1/ptm/m/n/10 , and
[229] [230]
Underfull \hbox (badness 1092) in paragraph at lines 16055--16060
[][]\T1/zi4/m/n/10 library.dynam[][][]\T1/ptm/m/n/10 , or can be found af-ter t
he DLL has been loaded us-ing
[231] [232] [233]
Underfull \hbox (badness 6741) in paragraph at lines 16305--16309
\T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing \
T1/zi4/m/n/10 CRoutine\T1/ptm/m/n/10 , \T1/zi4/m/n/10 CallRoutine\T1/ptm/m/n/10
 ,
[234] [235] [236] [237] [238] [239] [240] [241] [242]
Underfull \vbox (badness 10000) has occurred while \output is active [243]
[244] [245] [246] [247] [248] [249] [250] [251] [252]
Underfull \hbox (badness 1478) in paragraph at lines 17594--17597
[]\T1/ptm/m/n/10 A char-ac-ter vec-tor, or an ob-ject to be con-verted to a cha
r-ac-ter vec-tor
[253] [254] [255]
Underfull \hbox (badness 10000) in paragraph at lines 17849--17851
[]\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 http : / / www
 . unicode . org / reports / tr35 /
[256] [257] [258] [259] [260] [261] [262] [263] [264]
Underfull \hbox (badness 1442) in paragraph at lines 18447--18449
[]\T1/ptm/m/n/10 the choice of de-fault graph-ics de-vice launched when needed 
and by [][]\T1/zi4/m/n/10 dev.new[][][]\T1/ptm/m/n/10 : see
[265]
Underfull \hbox (badness 2452) in paragraph at lines 18539--18555
[][][]\T1/zi4/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.c
omplex[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.double[][][]\T1/ptm/m/n/10 ,
 [][]\T1/zi4/m/n/10 as.integer[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.logi
cal[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.raw[][][]\T1/ptm/m/n/10 , [][]\
T1/zi4/m/n/10 as.vector[][][]\T1/ptm/m/n/10 ,
[266] [267] [268] [269] [270] [271]
Underfull \hbox (badness 1248) in paragraph at lines 18958--18961
[]\T1/zi4/m/n/10 is.atomic \T1/ptm/m/n/10 is true for the [][]atomic[][][] type
s (\T1/zi4/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "integer"\T1/ptm/m/n
/10 , \T1/zi4/m/n/10 "numeric"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "complex"\T1/ptm/
m/n/10 ,
[272] [273] [274] [275]
Underfull \hbox (badness 4739) in paragraph at lines 19216--19218
[]\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere
d, see
[276] [277] [278] [279] [280] [281] [282]
Underfull \hbox (badness 1596) in paragraph at lines 19646--19651
\T1/ptm/m/n/10 trix or, if \T1/zi4/m/n/10 simplify = "array"\T1/ptm/m/n/10 , an
 ar-ray if ap-pro-pri-ate, by ap-ply-ing \T1/zi4/m/n/10 simplify2array()\T1/ptm
/m/n/10 .
[283] [284] [285] [286] [287] [288] [289] [290] [291]
Underfull \hbox (badness 2469) in paragraph at lines 20250--20255
[]\T1/ptm/m/n/10 In late 2017 a \T1/zi4/m/n/10 libcurl \T1/ptm/m/n/10 in-stal-l
a-tion was seen di-vided into two li-braries, \T1/zi4/m/n/10 libcurl \T1/ptm/m/
n/10 and
[292]
Underfull \hbox (badness 10000) in paragraph at lines 20264--20271
[][][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][]
 \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs /
[293] [294] [295]
Underfull \hbox (badness 1014) in paragraph at lines 20507--20512
[]\T1/ptm/m/n/10 Normally \T1/zi4/m/n/10 library \T1/ptm/m/n/10 re-turns (in-vi
s-i-bly) the list of at-tached pack-ages, but \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/1
0 or \T1/zi4/m/n/10 FALSE \T1/ptm/m/n/10 if
[296] [297] [298] [299] [300] [301] [302] [303] [304] [305] [306]
Underfull \hbox (badness 1264) in paragraph at lines 21309--21314
[]\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways 
be sup-ported:
[307]
Underfull \hbox (badness 4441) in paragraph at lines 21338--21341
[]\T1/ptm/m/n/10 Note that set-ting cat-e-gory \T1/zi4/m/n/10 "LC_ALL" \T1/ptm/
m/n/10 sets only cat-e-gories \T1/zi4/m/n/10 "LC_COLLATE"\T1/ptm/m/n/10 , \T1/z
i4/m/n/10 "LC_CTYPE"\T1/ptm/m/n/10 ,
[308] [309] [310] [311] [312] [313] [314] [315] [316] [317]
Underfull \hbox (badness 6047) in paragraph at lines 22085--22087
[]\T1/ptm/m/n/10 The al-go-rithm used by \T1/zi4/m/n/10 make.unique \T1/ptm/m/n
/10 has the prop-erty that \T1/zi4/m/n/10 make.unique(c(A,B)) ==
[318] [319] [320] [321] [322] [323] [324] [325] [326] [327] [328] [329]
[330] [331] [332] [333]
Underfull \hbox (badness 1077) in paragraph at lines 23126--23132
\T1/zi4/m/n/10 / / en . wikipedia . org / wiki / Bzip2$[][]\T1/ptm/m/n/10 , [][
]$\T1/zi4/m/n/10 http : / / tukaani . org / xz/$[][] \T1/ptm/m/n/10 and [][]$\T
1/zi4/m/n/10 https : / / en . wikipedia .
[334] [335] [336] [337] [338] [339] [340] [341]
Underfull \hbox (badness 2790) in paragraph at lines 23631--23634
[]\T1/zi4/m/n/10 packageStartupMessage \T1/ptm/m/n/10 is a vari-ant whose mes-s
ages can be sup-pressed sep-a-rately by

Underfull \hbox (badness 1571) in paragraph at lines 23631--23634
\T1/zi4/m/n/10 suppressPackageStartupMessages\T1/ptm/m/n/10 . (They are still m
es-sages, so can be sup-pressed by
[342] [343] [344] [345]
Underfull \hbox (badness 1194) in paragraph at lines 23913--23916
[]\T1/ptm/m/n/10 The de-fault method for \T1/zi4/m/n/10 anyNA \T1/ptm/m/n/10 ha
n-dles atomic vec-tors with-out a class and \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 .
 It calls
[346] [347]
Underfull \hbox (badness 2368) in paragraph at lines 24119--24125
[]\T1/ptm/m/n/10 For an [][]\T1/zi4/m/n/10 environment[][][] env\T1/ptm/m/n/10 
, \T1/zi4/m/n/10 names(env) \T1/ptm/m/n/10 gives the names of the cor-re-spond-
ing list, i.e.,

Underfull \hbox (badness 4981) in paragraph at lines 24119--24125
\T1/zi4/m/n/10 names(as.list(env,all.names = TRUE)) \T1/ptm/m/n/10 which are al
so given by [][]\T1/zi4/m/n/10 ls[][][](env,all.names =
[348] [349] [350] [351] [352] [353]
Underfull \hbox (badness 10000) in paragraph at lines 24504--24507
[]\T1/ptm/m/n/10 optional [][]\T1/zi4/m/n/10 logical[][][] \T1/ptm/m/n/10 even-
tu-ally to be passed to \T1/zi4/m/n/10 print()\T1/ptm/m/n/10 , used by
[354] [355] [356] [357] [358] [359] [360] [361] [362]
Underfull \hbox (badness 10000) in paragraph at lines 25113--25115
[]\T1/zi4/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m
ore ef-fi-cient than \T1/zi4/m/n/10 pkg %in%
[363] [364] [365] [366] [367] [368] [369] [370] [371] [372] [373] [374]
Underfull \hbox (badness 1038) in paragraph at lines 25953--25961
[]\T1/ptm/m/n/10 the pack-ages that are at-tached by de-fault when \T1/phv/m/n/
10 R \T1/ptm/m/n/10 starts up. Ini-tially

Underfull \hbox (badness 1735) in paragraph at lines 25953--25961
\T1/ptm/m/n/10 set from value of the en-vi-ron-ment vari-able \T1/zi4/m/n/10 R_
DEFAULT_PACKAGES\T1/ptm/m/n/10 , or if that is un-

Underfull \hbox (badness 1292) in paragraph at lines 25953--25961
\T1/ptm/m/n/10 set to \T1/zi4/m/n/10 c("datasets","utils","grDevices","graphics
","stats","methods")\T1/ptm/m/n/10 . (Set

Underfull \hbox (badness 1881) in paragraph at lines 25962--25965
[]\T1/ptm/m/n/10 integer value con-trol-ling the print-ing of lan-guage con-str
ucts which are

Underfull \hbox (badness 6220) in paragraph at lines 25981--25983
[]\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see

[375]
Underfull \hbox (badness 2142) in paragraph at lines 26122--26126
[]\T1/ptm/m/n/10 the de-fault pa-per for-mat used by [][]\T1/zi4/m/n/10 postscr
ipt[][][]\T1/ptm/m/n/10 ; set by en-vi-ron-ment vari-able
[376]
Underfull \hbox (badness 1968) in paragraph at lines 26172--26177
[]\T1/ptm/m/n/10 the com-mand used by [][]\T1/zi4/m/n/10 postscript[][][] \T1/p
tm/m/n/10 for print-ing; set by en-vi-ron-ment vari-able
[377] [378] [379]
Underfull \hbox (badness 10000) in paragraph at lines 26460--26466
[]\T1/ptm/m/n/10 The URL of a Bio-con-duc-tor mir-ror for use by [][]\T1/zi4/m/
n/10 setRepositories[][][]\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 26460--26466
\T1/ptm/m/n/10 e.g. the de-fault `\T1/zi4/m/n/10 "https://bioconductor.org"\T1/
ptm/m/n/10 ' or the Eu-ro-pean mir-ror

Underfull \hbox (badness 10000) in paragraph at lines 26460--26466
\T1/ptm/m/n/10 `\T1/zi4/m/n/10 "https://bioconductor.statistik.tu-dortmund.de"\
T1/ptm/m/n/10 '. Can be set by

Underfull \hbox (badness 10000) in paragraph at lines 26473--26476
[]\T1/ptm/m/n/10 default Cc: ad-dress used by [][]\T1/zi4/m/n/10 create.post[][
][] \T1/ptm/m/n/10 (and hence[][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/n/10
 and

Underfull \hbox (badness 2689) in paragraph at lines 26499--26501
[]\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na
l HTTP server, see
[380]
Underfull \hbox (badness 10000) in paragraph at lines 26534--26539
[]\T1/ptm/m/n/10 Used by [][]\T1/zi4/m/n/10 install.packages[][][] \T1/ptm/m/n/
10 (and in-di-rectly

Underfull \hbox (badness 2529) in paragraph at lines 26540--26551
\T1/ptm/m/n/10 in-di-rectly [][]\T1/zi4/m/n/10 update.packages[][][]\T1/ptm/m/n
/10 ) on plat-forms which sup-port bi-nary pack-ages. Pos-si-

Underfull \hbox (badness 2512) in paragraph at lines 26540--26551
\T1/ptm/m/n/10 ble val-ues are \T1/zi4/m/n/10 "never"\T1/ptm/m/n/10 , \T1/zi4/m
/n/10 "interactive" \T1/ptm/m/n/10 (which means ask in in-ter-ac-tive use and

Underfull \hbox (badness 7203) in paragraph at lines 26552--26555
[]\T1/ptm/m/n/10 default email-ing method used by [][]\T1/zi4/m/n/10 create.pos
t[][][] \T1/ptm/m/n/10 and hence [][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/
n/10 and

Underfull \hbox (badness 10000) in paragraph at lines 26576--26581
[]\T1/zi4/m/n/10 "source" \T1/ptm/m/n/10 (the de-fault ex-cept un-der a CRAN ma
-cOS build),

Underfull \hbox (badness 2057) in paragraph at lines 26576--26581
\T1/zi4/m/n/10 "mac.binary.el-capitan" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "both"
 \T1/ptm/m/n/10 (the de-fault for CRAN ma-cOS builds).
[381] [382] [383] [384] [385] [386] [387]
Underfull \hbox (badness 10000) in paragraph at lines 27094--27097
[]\T1/zi4/m/n/10 str2expression(s) \T1/ptm/m/n/10 and \T1/zi4/m/n/10 str2lang(s
) \T1/ptm/m/n/10 re-turn spe-cial ver-sions of
[388]
Underfull \hbox (badness 7925) in paragraph at lines 27173--27177
[]\T1/ptm/m/n/10 for a [][]\T1/zi4/m/n/10 character[][][] \T1/ptm/m/n/10 vec-to
r \T1/zi4/m/n/10 s\T1/ptm/m/n/10 , \T1/zi4/m/n/10 str2expression(s) \T1/ptm/m/n
/10 cor-re-sponds to

Underfull \hbox (badness 1622) in paragraph at lines 27173--27177
[][]\T1/zi4/m/n/10 parse[][][](text = s,keep.source=FALSE)\T1/ptm/m/n/10 , whic
h is al-ways of type ([][]\T1/zi4/m/n/10 typeof[][][]\T1/ptm/m/n/10 ) and [][]\
T1/zi4/m/n/10 class[][][]

Underfull \hbox (badness 6125) in paragraph at lines 27178--27187
[]\T1/ptm/m/n/10 for a [][]\T1/zi4/m/n/10 character[][][] \T1/ptm/m/n/10 string
 \T1/zi4/m/n/10 s\T1/ptm/m/n/10 , \T1/zi4/m/n/10 str2lang(s) \T1/ptm/m/n/10 cor
-re-sponds to [][]\T1/zi4/m/n/10 parse[][][](text =
[389] [390] [391] [392] [393] [394] [395] [396] [397] [398] [399]
Underfull \hbox (badness 2726) in paragraph at lines 27899--27902
[]\T1/ptm/m/n/10 character string (or \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 ) in-di
-cat-ing [][]\T1/zi4/m/n/10 NA[][][] \T1/ptm/m/n/10 val-ues in printed out-put,
 see
[400] [401] [402] [403] [404] [405] [406] [407] [408] [409] [410] [411]
[412] [413] [414] [415] [416] [417] [418] [419] [420] [421] [422] [423]
[424]
Underfull \hbox (badness 1533) in paragraph at lines 29593--29596
[]\T1/ptm/m/n/10 As with all com-piled code, mis-specifying these func-tions ca
n crash \T1/phv/m/n/10 R\T1/ptm/m/n/10 . Do in-clude the
[425] [426]
Underfull \hbox (badness 1163) in paragraph at lines 29756--29767
[]\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no \T1/zi4/m/n/10 NA\
T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in
[427] [428] [429] [430] [431] [432] [433] [434] [435] [436] [437] [438]
[439] [440] [441] [442] [443] [444] [445] [446] [447] [448]
Underfull \hbox (badness 10000) in paragraph at lines 31299--31303
[]\T1/zi4/m/n/10 regexpr \T1/ptm/m/n/10 and \T1/zi4/m/n/10 gregexpr \T1/ptm/m/n
/10 sup-port `named cap-ture'. If groups are named, e.g.,

Underfull \hbox (badness 1221) in paragraph at lines 31299--31303
\T1/zi4/m/n/10 "(?<first>[A-Z][a-z]+)" \T1/ptm/m/n/10 then the po-si-tions of t
he matches are also re-turned by name.
[449]
Underfull \hbox (badness 6188) in paragraph at lines 31321--31323
[]\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 http : / / p
ubs . opengroup . org / onlinepubs / 9699919799 /
[450] [451] [452] [453] [454] [455] [456] [457]
Underfull \hbox (badness 1655) in paragraph at lines 31877--31879
[]\T1/ptm/m/n/10 a vec-tor (atomic, not a list) for \T1/zi4/m/n/10 rle()\T1/ptm
/m/n/10 ; an ob-ject of class \T1/zi4/m/n/10 "rle" \T1/ptm/m/n/10 for
[458] [459] [460] [461] [462] [463] [464] [465] [466] [467] [468] [469]
[470] [471] [472] [473]
Underfull \hbox (badness 2261) in paragraph at lines 32999--33004
[]\T1/ptm/m/n/10 If \T1/zi4/m/n/10 strip.white \T1/ptm/m/n/10 is of length 1, i
t ap-plies to all fields; oth-er-wise, if
[474]
Underfull \hbox (badness 10000) in paragraph at lines 33026--33032
[]\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac-
ters

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\T1/ptm/m/n/10 `\T1/zi4/m/n/10 \a,\b,\f,\n,\r,\t,\v\T1/ptm/m/n/10 ' and oc-tal 
and hex-adec-i-mal rep-re-sen-ta-tions like
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[487] [488]
Underfull \hbox (badness 10000) in paragraph at lines 34026--34028
[]\T1/ptm/m/n/10 Encoded `\T1/zi4/m/n/10 file://\T1/ptm/m/n/10 ' URLs should be
 in the Win-dows stan-dard form,
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Underfull \hbox (badness 1072) in paragraph at lines 36270--36274
[]\T1/ptm/m/n/10 On front-ends which sup-port it, the com-mands his-tory is rea
d from the file spec-i-fied by

Underfull \hbox (badness 10000) in paragraph at lines 36275--36281
[]\T1/ptm/m/n/10 The command-line op-tion `\T1/zi4/m/n/10 --vanilla\T1/ptm/m/n/
10 ' im-plies `\T1/zi4/m/n/10 --no-site-file\T1/ptm/m/n/10 ', `\T1/zi4/m/n/10 -
-no-init-file\T1/ptm/m/n/10 ',

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\T1/ptm/m/n/10 `\T1/zi4/m/n/10 --no-environ\T1/ptm/m/n/10 ' and (ex-cept for \T
1/zi4/m/n/10 R CMD\T1/ptm/m/n/10 ) `\T1/zi4/m/n/10 --no-restore\T1/ptm/m/n/10 '
 Un-der Win-dows, it also im-plies
[520]
Underfull \hbox (badness 10000) in paragraph at lines 36305--36311
[]\T1/ptm/m/n/10 On sys-tems with sub-architectures (mainly Win-dows), the file
s `\T1/zi4/m/n/10 Renviron.site\T1/ptm/m/n/10 '

Underfull \hbox (badness 10000) in paragraph at lines 36305--36311
\T1/ptm/m/n/10 and `\T1/zi4/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' are looked for
 first in architecture-specific di-rec-to-ries,

Underfull \hbox (badness 1320) in paragraph at lines 36305--36311
\T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/n/10 /etc/i386/R
environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/zi4/m/n/10 .Renviron.i386\T1/ptm/m/
n/10 ' will be used in
[521] [522] [523] [524] [525]
Underfull \hbox (badness 1142) in paragraph at lines 36668--36674
[]\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the \T1/zi4/m/n/10 form
at \T1/ptm/m/n/10 meth-ods is \T1/zi4/m/n/10 "%Y-%m-%d
[526] [527] [528] [529] [530] [531] [532] [533] [534] [535] [536] [537]
[538] [539] [540] [541] [542] [543] [544]
Underfull \hbox (badness 1565) in paragraph at lines 37941--37943
[]\T1/ptm/m/n/10 integer code used in \T1/zi4/m/n/10 quantile(*,type=quantile.t
ype) \T1/ptm/m/n/10 for the de-fault
[545] [546] [547] [548] [549] [550] [551] [552] [553] [554]
Underfull \hbox (badness 1616) in paragraph at lines 38643--38648
\T1/zi4/m/n/10 system("id") \T1/ptm/m/n/10 is much more portable on Unix-alikes
, pro-vided only the POSIX op-tions
[555] [556] [557] [558] [559] [560] [561] [562]
Underfull \hbox (badness 1472) in paragraph at lines 39169--39172
[]\T1/ptm/m/n/10 logical. If \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , func-tions kee
p their source in-clud-ing com-ments, see
[563] [564] [565] [566] [567] [568] [569] [570] [571] [572] [573] [574]
[575] [576]
Underfull \hbox (badness 10000) in paragraph at lines 40107--40111
[]\T1/ptm/m/n/10 On 64-bit plat-forms \T1/zi4/m/n/10 bin \T1/ptm/m/n/10 can hav
e $\OT1/cmr/m/n/10 2[]$ \T1/ptm/m/n/10 or more el-e-ments (i.e., \T1/zi4/m/n/10
 length(bin) >
[577] [578] [579] [580]
Underfull \hbox (badness 10000) in paragraph at lines 40358--40361
[][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [
][]$https : / / developer . r-[]project . org /
[581] [582] [583]
Underfull \hbox (badness 10000) in paragraph at lines 40542--40546
[][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r
emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 taskCallbackManager[
][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer .
[584] [585] [586] [587] [588] [589] [590]
Underfull \hbox (badness 10000) in paragraph at lines 41117--41120
[][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][
] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / data . iana . org / time-[
]zones /
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[603]
Underfull \hbox (badness 1990) in paragraph at lines 42020--42028
[]\T1/zi4/m/n/10 try \T1/ptm/m/n/10 eval-u-ates an ex-pres-sion and traps any e
r-rors that oc-cur dur-ing the eval-u-a-tion. If

Underfull \hbox (badness 4846) in paragraph at lines 42020--42028
\T1/ptm/m/n/10 an er-ror oc-curs then the er-ror mes-sage is printed to the [][
]\T1/zi4/m/n/10 stderr[][][] \T1/ptm/m/n/10 con-nec-tion un-less
[604] [605] [606] [607] [608] [609] [610]
Underfull \hbox (badness 1917) in paragraph at lines 42509--42516
[]\T1/ptm/m/n/10 When a func-tion call-ing \T1/zi4/m/n/10 UseMethod("fun") \T1/
ptm/m/n/10 is ap-plied to an ob-ject with class at-tribute
[611] [612] [613] [614] [615] [616] [617] [618] [619] [620] [621]
Underfull \hbox (badness 3668) in paragraph at lines 43238--43240
[]\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di-
ately, even if
[622]
Underfull \hbox (badness 2401) in paragraph at lines 43366--43370
[]\T1/ptm/m/n/10 See the de-scrip-tion of [][]\T1/zi4/m/n/10 options[][][]("war
n") \T1/ptm/m/n/10 for the cir-cum-stances un-der which there is a
[623] [624] [625]
Underfull \hbox (badness 2111) in paragraph at lines 43555--43560
\T1/ptm/m/n/10 If [][]\T1/zi4/m/n/10 names[][][](.dimnames) \T1/ptm/m/n/10 is n
ot empty, these are used as col-umn names.

Underfull \hbox (badness 10000) in paragraph at lines 43576--43581
[]\T1/ptm/m/n/10 If \T1/zi4/m/n/10 arr.ind == TRUE \T1/ptm/m/n/10 and \T1/zi4/m
/n/10 x \T1/ptm/m/n/10 is an [][]\T1/zi4/m/n/10 array[][][] \T1/ptm/m/n/10 (has
 a [][]\T1/zi4/m/n/10 dim[][][] \T1/ptm/m/n/10 at-tribute), the re-sult is
[626] [627] [628] [629] [630] [631] [632] [633] [634]
Underfull \hbox (badness 5417) in paragraph at lines 44158--44162
[]\T1/zi4/m/n/10 .packages() \T1/ptm/m/n/10 re-turns the names of the cur-rentl
y at-tached pack-ages \T1/ptm/m/it/10 in-vis-i-bly \T1/ptm/m/n/10 whereas
[635]
Underfull \hbox (badness 10000) in paragraph at lines 44219--44223
[]\T1/zi4/m/n/10 .standard_regexps \T1/ptm/m/n/10 re-turns a list of `stan-dard
' reg-exps, in-clud-ing el-e-ments named
[636]) (compiler-pkg.tex
Chapter 2.
[637] [638] [639] [640]) (datasets-pkg.tex
Chapter 3.
[641] [642] [643] [644] [645] [646]
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[648] [649] [650] [651] [652] [653] [654] [655]
Underfull \hbox (badness 1097) in paragraph at lines 1031--1035
[]\T1/ptm/m/n/10 MacDonell, W.R. (1902). On crim-i-nal an-thro-pom-e-try and th
e iden-ti-fi-ca-tion of crim-i-nals.
[656] [657] [658] [659] [660] [661] [662] [663] [664] [665] [666] [667]
[668] [669] [670] [671] [672] [673] [674] [675] [676] [677]
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[700]
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[701] [702] [703] [704] [705] [706] [707] [708] [709] [710] [711] [712]
[713] [714] [715]) (grDevices-pkg.tex [716]
Chapter 4.
[717] [718] [719] [720]
Underfull \hbox (badness 3158) in paragraph at lines 282--286
[]\T1/ptm/m/n/10 numeric vec-tor of length 3, \T1/zi4/m/n/10 c(mi,ma,n.)\T1/ptm
/m/n/10 , with iden-ti-cal mean-ing to

Underfull \hbox (badness 10000) in paragraph at lines 298--303
[]\T1/ptm/m/n/10 Apart from that, [][]\T1/zi4/m/n/10 axisTicks[][][]() \T1/ptm/
m/n/10 just calls the C func-tion \T1/zi4/m/n/10 CreateAtVector() \T1/ptm/m/n/1
0 in

Underfull \hbox (badness 1852) in paragraph at lines 298--303
\T1/ptm/m/n/10 `\T1/zi4/m/n/10 <Rsrc>/src/main/plot.c\T1/ptm/m/n/10 ' which is 
also called by the base \T1/ptm/b/n/10 graph-ics \T1/ptm/m/n/10 pack-age func-t
ion
[721] [722] [723] [724] [725] [726] [727] [728] [729] [730] [731] [732]
[733]
Underfull \hbox (badness 5175) in paragraph at lines 1120--1122
[]\T1/ptm/m/n/10 There is cur-rently no doc-u-men-ta-tion about the al-go-rithm
. The source code is in
[734] [735] [736]
Underfull \hbox (badness 1852) in paragraph at lines 1322--1325
[]\T1/zi4/m/n/10 densCols \T1/ptm/m/n/10 com-putes and re-turns the set of col-
ors that will be used in plot-ting, call-ing
[737] [738] [739]
Underfull \hbox (badness 1490) in paragraph at lines 1528--1533
\T1/ptm/m/n/10 by [][]\T1/zi4/m/n/10 rasterImage[][][] \T1/ptm/m/n/10 and [][]\
T1/zi4/m/n/10 grid.raster[][][]\T1/ptm/m/n/10 ? Pos-si-ble val-ues \T1/zi4/m/n/
10 "no"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "yes" \T1/ptm/m/n/10 and
[740] [741] [742] [743] [744] [745]
Underfull \hbox (badness 1325) in paragraph at lines 1934--1944
\T1/zi4/m/n/10 "png48"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pngmono"\T1/ptm/m/n/10 ,
 \T1/zi4/m/n/10 "pnggray"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pngalpha"\T1/ptm/m/n/
10 , \T1/zi4/m/n/10 "bmp16"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "bmp16m" "bmp256"\T1
/ptm/m/n/10 , \T1/zi4/m/n/10 "bmp32b"\T1/ptm/m/n/10 ,
[746]
Underfull \hbox (badness 10000) in paragraph at lines 2046--2048
[]\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the 
set-ting of
[747] [748] [749]
Underfull \hbox (badness 6758) in paragraph at lines 2224--2227
[]\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript
 doc-u-men-ta-tion) are
[750] [751] [752] [753] [754] [755] [756] [757] [758]
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Underfull \hbox (badness 10000) in paragraph at lines 3384--3389
[]\T1/zi4/m/n/10 nclass.FD \T1/ptm/m/n/10 uses the Freedman-Diaconis choice bas
ed on the inter-quartile range
[767] [768] [769] [770] [771] [772]
Underfull \hbox (badness 10000) in paragraph at lines 3785--3788
[]\T1/ptm/m/n/10 For use with \T1/zi4/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv
e a C in-te-ger for-mat such as
[773] [774] [775] [776] [777] [778] [779] [780] [781] [782]
Underfull \hbox (badness 10000) in paragraph at lines 4514--4519
[][][]$\T1/zi4/m/n/10 https : / / www . adobe . com / content / dam / acom / en
 / devnet / actionscript / articles / PLRM . pdf$[][]

Underfull \hbox (badness 4181) in paragraph at lines 4514--4519
\T1/ptm/m/n/10 or PDF [][]$\T1/zi4/m/n/10 https : / / www . adobe . com / devne
t / acrobat / pdfs / pdf _ reference _ 1-[]7 . pdf$[][] \T1/ptm/m/n/10 and in
[783] [784] [785] [786]
Underfull \hbox (badness 3364) in paragraph at lines 4813--4815
[]\T1/ptm/m/n/10 The TIFF spec-i-fi-ca-tion, in-clud-ing ex-ten-sions, at [][]$
\T1/zi4/m/n/10 https : / / partners . adobe . com / public /
[787] [788]
Underfull \hbox (badness 1377) in paragraph at lines 4947--4952
[]\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently 
al-lowed val-ues
[789]
Underfull \hbox (badness 1418) in paragraph at lines 5023--5030
\T1/ptm/m/n/10 it is one of \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4
/m/n/10 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/
zi4/m/n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm
/m/n/10 ,

Underfull \hbox (badness 1755) in paragraph at lines 5041--5043
[]\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East 
Asian lan-guages -- see
[790] [791]
Underfull \hbox (badness 1377) in paragraph at lines 5152--5157
[]\T1/ptm/m/n/10 Color mod-els pro-vided for back-wards com-pat-i-bil-ity are \
T1/zi4/m/n/10 "rgb" \T1/ptm/m/n/10 (which is RGB+gray) and

Underfull \hbox (badness 7344) in paragraph at lines 5221--5223
[]\T1/ptm/m/n/10 Support for Com-puter Mod-ern fonts is based on a con-tri-bu-t
ion by Brian D'Urso
[792] [793] [794]
Underfull \hbox (badness 2035) in paragraph at lines 5356--5365
[]\T1/ptm/m/n/10 Mappings for a num-ber of stan-dard Adobe fonts (and URW equiv
-a-lents) are also pro-

Underfull \hbox (badness 10000) in paragraph at lines 5356--5365
\T1/ptm/m/n/10 vided: \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4/m/n/1
0 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/zi4/m/
n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/1
0 ,

Underfull \hbox (badness 10000) in paragraph at lines 5356--5365
\T1/zi4/m/n/10 "NewCenturySchoolbook"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Palatino"
 \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "Times"\T1/ptm/m/n/10 ; \T1/zi4/m/n/10 "URWG
othic"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "URWBookman"\T1/ptm/m/n/10 ,
[795]
Underfull \hbox (badness 10000) in paragraph at lines 5424--5431
[]\T1/zi4/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/zi4
/m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu /

Underfull \hbox (badness 2189) in paragraph at lines 5424--5431
\T1/zi4/m/n/10 chinese-[]fonts-[]truetype/$[][]\T1/ptm/m/n/10 . Ken Lunde's CJK
V re-sources are at [][]$\T1/zi4/m/n/10 ftp : / / ftp . oreilly .
[796] [797]
Underfull \hbox (badness 1546) in paragraph at lines 5566--5574
[]\T1/ptm/m/n/10 arguments \T1/zi4/m/n/10 onefile\T1/ptm/m/n/10 , \T1/zi4/m/n/1
0 family\T1/ptm/m/n/10 , \T1/zi4/m/n/10 title\T1/ptm/m/n/10 , \T1/zi4/m/n/10 fo
nts\T1/ptm/m/n/10 , \T1/zi4/m/n/10 encoding\T1/ptm/m/n/10 , \T1/zi4/m/n/10 bg\T
1/ptm/m/n/10 , \T1/zi4/m/n/10 fg\T1/ptm/m/n/10 , \T1/zi4/m/n/10 width\T1/ptm/m/
n/10 ,
[798] [799] [800] [801] [802] [803] [804] [805]
Underfull \hbox (badness 10000) in paragraph at lines 6101--6104
[]\T1/zi4/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red
/green/blue) into HSV space
[806] [807] [808] [809] [810] [811] [812] [813] [814] [815] [816] [817]
Underfull \hbox (badness 1189) in paragraph at lines 6937--6939
[]\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used
. One of
[818]
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[]\T1/zi4/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK 
lan-guages and
[819] [820] [821] [822] [823]
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[]\T1/ptm/m/n/10 the font fam-ily to be used. This must be one of \T1/zi4/m/n/1
0 "AvantGarde"\T1/ptm/m/n/10 ,
[824] [825]
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[]\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., \T1/zi4/m/n/10 n
umber[i] \T1/ptm/m/n/10 is the mul-ti-plic-ity of
[826] [827] [828]) (graphics-pkg.tex
Chapter 5.
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[][][]\T1/zi4/m/n/10 boxplot.default[][][] \T1/ptm/m/n/10 which al-ready works 
nowa-days with data.frames; [][]\T1/zi4/m/n/10 boxplot.formula[][][]\T1/ptm/m/n
/10 ,
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[862] [863] [864]
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\T1/ptm/m/n/10 be in as-cend-ing or-der. (The rest of this de-scrip-tion does n
ot ap-ply to
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[]\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing if log-a-rith-mic axes are 
to be used, see
[898] [899] [900] [901]
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[]\T1/ptm/b/it/10 R.O.\T1/ptm/m/n/10 ; size of de-fault char-ac-ter \T1/zi4/m/n
/10 (width,height) \T1/ptm/m/n/10 in user co-or-di-nate units.

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\T1/zi4/m/n/10 par("cxy") \T1/ptm/m/n/10 is \T1/zi4/m/n/10 par("cin")/par("pin"
) \T1/ptm/m/n/10 scaled to user co-or-di-nates. Note that
[902] [903]
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[904 <C:/projects/BUILD/R-source-win64/library/graphics/help/figures/mai.pdf>]
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[905 <C:/projects/BUILD/R-source-win64/library/graphics/help/figures/oma.pdf>]
[906]
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[]\T1/ptm/m/n/10 The five stan-dard dash-dot line types (\T1/zi4/m/n/10 lty = 2
:6\T1/ptm/m/n/10 ) cor-re-spond to
[907] [908] [909] [910] [911] [912] [913] [914] [915] [916] [917] [918]
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[][] 
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[]\T1/ptm/m/n/10 For each \T1/zi4/m/n/10 i\T1/ptm/m/n/10 , a line seg-ment is d
rawn be-tween the point \T1/zi4/m/n/10 (x0[i],y0[i]) \T1/ptm/m/n/10 and the poi
nt
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[]\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color

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[]\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color
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s}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.8915 \HeaderA{units}{Graphical Units}{units}
                                               [963] [964] [965] [966])
(grid-pkg.tex
Chapter 6.
[967] [968] [969] [970] [971] [972] [973] [974]
Underfull \hbox (badness 2680) in paragraph at lines 483--486
[]\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 preDrawDetails \T1/ptm/m/n/10 and \T1
/zi4/m/n/10 postDrawDetails \T1/ptm/m/n/10 are also called in the cal-cu-la-tio
n of
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[][][]\T1/ptm/m/n/10 Grid[][][], [][]\T1/zi4/m/n/10 pushViewport[][][]\T1/ptm/m
/n/10 , [][]\T1/zi4/m/n/10 popViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10
 downViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 seekViewport[][][]\T1/pt
m/m/n/10 , [][]\T1/zi4/m/n/10 upViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/
10 unit[][][]\T1/ptm/m/n/10 ,
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[1036]
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[]\T1/ptm/m/n/10 Both func-tions cre-ate a seg-ments grob (a graph-i-cal ob-jec
t de-scrib-ing seg-ments), but only
[1037] [1038] [1039] [1040]
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[]\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject
s are co-erced by
[1041] [1042] [1043] [1044] [1045] [1046] [1047] [1048] [1049] [1050] [1051]
[1052] [1053] [1054] [1055] [1056] [1057] [1058] [1059] [1060] [1061] [1062]
[1063] [1064] [1065] [1066] [1067] [1068]
Underfull \hbox (badness 1824) in paragraph at lines 6535--6538
[]\T1/ptm/m/n/10 This can be use-ful for re-turn-ing to your start-ing point by
 do-ing some-thing like \T1/zi4/m/n/10 depth
[1069] [1070] [1071] [1072]) (methods-pkg.tex
Chapter 7.
[1073] [1074] [1075] [1076] [1077] [1078] [1079] [1080]
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[]\T1/ptm/m/n/10 The class \T1/zi4/m/n/10 "className" \T1/ptm/m/n/10 ex-tends \
T1/zi4/m/n/10 "character" \T1/ptm/m/n/10 and has a slot \T1/zi4/m/n/10 "package
"\T1/ptm/m/n/10 , also of class
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[]\T1/ptm/m/n/10 Two vir-tual classes are sup-plied to test for ref-er-ence ob-
jects: \T1/zi4/m/n/10 is(x,"refClass") \T1/ptm/m/n/10 tests

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[]\T1/ptm/m/n/10 The ar-gu-ment to \T1/zi4/m/n/10 insertSource \T1/ptm/m/n/10 c
an be an ob-ject of class

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\T1/ptm/m/n/10 file name is passed to \T1/zi4/m/n/10 insertSource \T1/ptm/m/n/1
0 it calls \T1/zi4/m/n/10 evalSource \T1/ptm/m/n/10 to ob-tain the
[1099] [1100] [1101]
Underfull \hbox (badness 2213) in paragraph at lines 2214--2219
[]\T1/ptm/m/n/10 To re-strict the search to classes in a par-tic-u-lar pack-age
, use \T1/zi4/m/n/10 where =
[1102] [1103] [1104] [1105] [1106]
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[]\T1/ptm/m/n/10 As you might ex-pect [][]\T1/zi4/m/n/10 setGeneric[][][] \T1/p
tm/m/n/10 and [][]\T1/zi4/m/n/10 setGroupGeneric[][][] \T1/ptm/m/n/10 cre-ate o
b-jects of class
[1107] [1108]
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[]\T1/ptm/m/n/10 In \T1/zi4/m/n/10 getGenerics\T1/ptm/m/n/10 , if \T1/zi4/m/n/1
0 TRUE\T1/ptm/m/n/10 , the \T1/zi4/m/n/10 package \T1/ptm/m/n/10 slot of the re
-turned re-sult is in

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\T1/ptm/m/n/10 In ad-di-tion, \T1/zi4/m/n/10 removeGeneric \T1/ptm/m/n/10 re-mo
ves the func-tion it-self; \T1/zi4/m/n/10 removeMethods \T1/ptm/m/n/10 re-store
s the
[1109] [1110] [1111] [1112] [1113] [1114] [1115]
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[]\T1/zi4/m/n/10 getPackageName \T1/ptm/m/n/10 re-turns the character-string na
me of the pack-age (with-out the ex-tra-ne-ous
[1116] [1117] [1118] [1119] [1120]
Underfull \hbox (badness 10000) in paragraph at lines 3634--3639
[]\T1/ptm/m/n/10 The \T1/zi4/m/n/10 initialize \T1/ptm/m/n/10 method for these 
classes takes spe-cial ar-gu-ments

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[]\T1/ptm/m/n/10 The
[1121] [1122]
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[] \T1/zi4/m/n/10 Pos <-setClass("Pos",slots = c(latitude = "numeric",longitude
 = "numeric",altitude
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[]\T1/ptm/m/n/10 class [][]\T1/zi4/m/n/10 MethodsList[][][] \T1/ptm/m/n/10 for 
the ob-jects defin-ing sets of meth-ods as-so-ci-ated with a par-tic-u-lar

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\T1/zi4/m/n/10 MethodDefinition\T1/ptm/m/n/10 , or an ex-ten-sion. Class [][]\T
1/zi4/m/n/10 MethodWithNext[][][] \T1/ptm/m/n/10 for an ex-ten-sion used by
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[]\T1/ptm/m/n/10 Object of class \T1/zi4/m/n/10 "PossibleMethod" \T1/ptm/m/n/10
 the method to use in re-sponse to a
[1145]
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[]\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p
assed to
[1146] [1147] [1148]
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[]\T1/ptm/m/n/10 In ad-di-tion, the cur-rently avail-able gener-ics with meth-o
ds for this class are found (us-ing
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Underfull \hbox (badness 1675) in paragraph at lines 6451--6457
\T1/ptm/m/n/10 can be con-verted ex-plic-itly as \T1/zi4/m/n/10 externalRefMeth
od(f)\T1/ptm/m/n/10 , which re-turns an ob-ject of class
[1157] [1158] [1159] [1160]
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l.7234 \aliasA{Ops}{S4groupGeneric}{Ops}
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l.7235 \aliasA{Summary}{S4groupGeneric}{Summary}
                                                 [1167]
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[]\T1/ptm/m/n/10 The mem-bers of the group de-fined by a par-tic-u-lar generic 
can be ob-tained by call-ing
[1168] [1169]
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[]\T1/ptm/m/n/10 for \T1/zi4/m/n/10 .selectSuperClasses() \T1/ptm/m/n/10 only, 
a [][]\T1/zi4/m/n/10 list[][][] \T1/ptm/m/n/10 of class ex-ten-sions, typ-i-cal
ly
[1170] [1171] [1172] [1173] [1174] [1175] [1176] [1177] [1178] [1179] [1180]
[1181] [1182] [1183] [1184] [1185] [1186] [1187] [1188] [1189] [1190] [1191]
[1192] [1193] [1194] [1195] [1196] [1197] [1198] [1199] [1200] [1201] [1202]
Underfull \hbox (badness 1137) in paragraph at lines 10011--10019
[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/zi4/m/n/10 ne
w("signature",functionDef,...)\T1/ptm/m/n/10 . The
[1203] [1204] [1205] [1206] [1207] [1208] [1209]
Underfull \hbox (badness 1852) in paragraph at lines 10564--10568
[]\T1/ptm/m/n/10 Each of the classes ex-tends the cor-re-spond-ing un-traced cl
ass, from the data part; e.g.,
[1210] [1211] [1212]) (parallel-pkg.tex
Chapter 8.

Underfull \hbox (badness 5490) in paragraph at lines 14--16
[]\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `\T1/zi4
/m/n/10 "L\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 Ecuyer-CMRG"\T1/ptm/m/n/10 ' [][]RNG[
][][]: see
[1213] [1214] [1215] [1216] [1217] [1218] [1219] [1220]
Underfull \hbox (badness 3386) in paragraph at lines 595--598
[]\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by \T1/zi4/m/n/10 .R
andom.seed \T1/ptm/m/n/10 when the
[1221] [1222] [1223]) (splines-pkg.tex [1224]
Chapter 9.

Underfull \hbox (badness 10000) in paragraph at lines 22--24
[]\T1/ptm/m/n/10 Douglas M. Bates \T1/zi4/m/n/10 <bates@stat.wisc.edu> \T1/ptm/
m/n/10 and William N. Ven-ables
[1225] [1226] [1227] [1228] [1229] [1230] [1231] [1232] [1233] [1234] [1235]
[1236] [1237] [1238]) (stats-pkg.tex
Chapter 10.
[1239] [1240] [1241] [1242] [1243] [1244] [1245] [1246] [1247] [1248] [1249]
[1250] [1251]
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[]\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from \T1/zi4/m/n/10 lm 
\T1/ptm/m/n/10 or \T1/zi4/m/n/10 aov\T1/ptm/m/n/10 , or a for-mula for
[1252] [1253] [1254] [1255] [1256] [1257] [1258]
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[]\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of 
\T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 ,
[1259] [1260]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/zi4/m/n/10 c("aov","lm") \T1/ptm/m/n/1
0 or for mul-ti-ple re-sponses of class
[1261] [1262] [1263] [1264] [1265] [1266] [1267] [1268] [1269] [1270] [1271]
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[]\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of 
\T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 ,
[1289] [1290] [1291] [1292] [1293] [1294] [1295] [1296] [1297] [1298] [1299]
[1300] [1301] [1302]
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[]\T1/ptm/m/n/10 standardized resid-u-als, \T1/zi4/m/n/10 (observed -expected) 
/ sqrt(V)\T1/ptm/m/n/10 , where \T1/zi4/m/n/10 V \T1/ptm/m/n/10 is the
[1303] [1304] [1305] [1306] [1307]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor of length 2, equal to say $\OT1/cmr/m/n/10 
(\OML/cmm/m/it/10 g[]; g[]\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 , where $\OML/cmm/m/
it/10 g[] \OT1/cmr/m/n/10 =
[1308] [1309] [1310] [1311] [1312] [1313] [1314] [1315] [1316]
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[]\T1/ptm/m/n/10 character; par-tially matched to \T1/zi4/m/n/10 "circular"\T1/
ptm/m/n/10 , \T1/zi4/m/n/10 "open"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "filter"\T1/p
tm/m/n/10 . For

Underfull \hbox (badness 2932) in paragraph at lines 5334--5336
[]\T1/ptm/m/n/10 Note that the usual def-i-ni-tion of con-vo-lu-tion of two se-
quences \T1/zi4/m/n/10 x \T1/ptm/m/n/10 and \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is 
given by
[1317] [1318] [1319] [1320] [1321] [1322]
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[]\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of 
\T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 ,
[1323] [1324] [1325] [1326] [1327] [1328] [1329] [1330] [1331] [1332] [1333]
[1334] [1335]
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[]\T1/ptm/m/n/10 Objects of class \T1/zi4/m/n/10 "hclust" \T1/ptm/m/n/10 can be
 con-verted to class \T1/zi4/m/n/10 "dendrogram" \T1/ptm/m/n/10 us-ing method

Underfull \hbox (badness 10000) in paragraph at lines 6524--6526
[]\T1/zi4/m/n/10 rev.dendrogram \T1/ptm/m/n/10 sim-ply re-turns the den-dro-gra
m \T1/zi4/m/n/10 x \T1/ptm/m/n/10 with re-versed nodes, see also
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[1347]
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[]\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][]\T
1/zi4/m/n/10 dist[][][]()\T1/ptm/m/n/10 , the
[1348] [1349] [1350] [1351] [1352] [1353] [1354] [1355] [1356] [1357] [1358]
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[]\T1/ptm/m/n/10 Either \T1/zi4/m/n/10 "convolution" \T1/ptm/m/n/10 or \T1/zi4/
m/n/10 "recursive" \T1/ptm/m/n/10 (and can be ab-bre-vi-ated). If
[1373] [1374]
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[]\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of 
\T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 ,
[1375] [1376] [1377] [1378] [1379] [1380] [1381] [1382] [1383] [1384] [1385]
[1386] [1387] [1388] [1389] [1390] [1391] [1392] [1393]
Underfull \hbox (badness 4518) in paragraph at lines 10465--10470
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1394] [1395] [1396] [1397] [1398]
Underfull \hbox (badness 2142) in paragraph at lines 10825--10828
[]\T1/ptm/m/n/10 positive con-ver-gence tol-er-ance $\OML/cmm/m/it/10 $\T1/ptm
/m/n/10 ; the it-er-a-tions con-verge when $\OMS/cmsy/m/n/10 j\OML/cmm/m/it/10 
dev \OMS/cmsy/m/n/10 �

Underfull \hbox (badness 1253) in paragraph at lines 10844--10847
[]\T1/ptm/m/n/10 When \T1/zi4/m/n/10 trace \T1/ptm/m/n/10 is true, calls to [][
]\T1/zi4/m/n/10 cat[][][] \T1/ptm/m/n/10 pro-duce the out-put for each IWLS it-
er-a-tion. Hence,
[1399]
Underfull \hbox (badness 1708) in paragraph at lines 10906--10910
[]\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter-
na-tives are:
[1400] [1401] [1402] [1403] [1404]
Underfull \hbox (badness 1694) in paragraph at lines 11302--11305
[]\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these 
de-fault to
[1405] [1406] [1407] [1408] [1409] [1410]
Underfull \hbox (badness 10000) in paragraph at lines 11629--11632
[]\T1/ptm/m/n/10 If one of $\OML/cmm/m/it/10 m; n; k$\T1/ptm/m/n/10 , ex-ceeds 
[][]\T1/zi4/m/n/10 .Machine[][][]$integer.max\T1/ptm/m/n/10 , cur-rently the eq
uiv-a-lent of

Underfull \hbox (badness 1281) in paragraph at lines 11629--11632
\T1/zi4/m/n/10 qhyper(runif(nn),m,n,k) \T1/ptm/m/n/10 is used, when a bi-no-mia
l ap-prox-i-ma-tion may be con-sid-er-ably
[1411] [1412]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.hat}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.11783 \aliasA{hat}{influence.measures}{hat}
                                              [1413] [1414]
Underfull \hbox (badness 1484) in paragraph at lines 11918--11920
[]\T1/ptm/m/n/10 The func-tion \T1/zi4/m/n/10 hat() \T1/ptm/m/n/10 ex-ists main
ly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing
[1415] [1416] [1417] [1418] [1419] [1420] [1421] [1422] [1423]
Underfull \hbox (badness 10000) in paragraph at lines 12511--12513
[]\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][]\T1/zi4/m/n/10 solve.defa
ult[][][] \T1/ptm/m/n/10 when \T1/zi4/m/n/10 SSinit =
[1424] [1425] [1426] [1427] [1428]
Underfull \hbox (badness 2894) in paragraph at lines 12847--12851
[]\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f
ault method
[1429] [1430] [1431] [1432] [1433] [1434] [1435] [1436] [1437] [1438] [1439]
[1440]
Underfull \hbox (badness 4518) in paragraph at lines 13597--13602
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1441] [1442] [1443] [1444] [1445] [1446] [1447] [1448] [1449]
Underfull \hbox (badness 4518) in paragraph at lines 14249--14254
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1450] [1451]
Underfull \hbox (badness 8151) in paragraph at lines 14387--14391
[]\T1/ptm/m/n/10 Only for the (de-fault) case \T1/zi4/m/n/10 (surface = "interp
olate",statistics =

Underfull \hbox (badness 1199) in paragraph at lines 14394--14396
[]\T1/ptm/m/n/10 the num-ber of it-er-a-tions used in ro-bust fit-ting, i.e. on
ly if \T1/zi4/m/n/10 family \T1/ptm/m/n/10 is
[1452] [1453] [1454] [1455] [1456] [1457] [1458] [1459] [1460] [1461] [1462]
[1463] [1464] [1465] [1466] [1467] [1468]
Underfull \hbox (badness 2503) in paragraph at lines 15465--15469
[]\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of 
\T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 ,
[1469] [1470] [1471] [1472] [1473] [1474] [1475]
Underfull \hbox (badness 4621) in paragraph at lines 15977--15983
[]\T1/zi4/m/n/10 model.offset \T1/ptm/m/n/10 and \T1/zi4/m/n/10 model.response 
\T1/ptm/m/n/10 are equiv-a-lent to \T1/zi4/m/n/10 model.extract(,"offset") \T1/
ptm/m/n/10 and
[1476] [1477] [1478] [1479] [1480] [1481] [1482] [1483] [1484] [1485] [1486]
[1487] [1488] [1489] [1490] [1491] [1492] [1493] [1494] [1495] [1496] [1497]
[1498] [1499] [1500] [1501] [1502]
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[1515]
Underfull \hbox (badness 1377) in paragraph at lines 18576--18581
[]\T1/ptm/m/n/10 A vec-tor of scal-ing val-ues for the pa-ram-e-ters. Op-ti-miz
a-tion is per-formed on

Underfull \hbox (badness 1735) in paragraph at lines 18581--18584
[]\T1/ptm/m/n/10 A vec-tor of step sizes for the finite-difference ap-prox-i-ma
-tion to the gra-di-ent, on

Underfull \hbox (badness 2343) in paragraph at lines 18594--18598
[]\T1/ptm/m/n/10 Relative con-ver-gence tol-er-ance. The al-go-rithm stops if i
t is un-able to re-duce

Underfull \hbox (badness 3471) in paragraph at lines 18594--18598
\T1/ptm/m/n/10 the value by a fac-tor of \T1/zi4/m/n/10 reltol * (abs(val) + re
ltol) \T1/ptm/m/n/10 at a step. De-faults to
[1516]
Underfull \hbox (badness 2662) in paragraph at lines 18602--18606
[]\T1/ptm/m/n/10 The fre-quency of re-ports for the \T1/zi4/m/n/10 "BFGS"\T1/pt
m/m/n/10 , \T1/zi4/m/n/10 "L-BFGS-B" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "SANN" \
T1/ptm/m/n/10 meth-ods if
[1517] [1518]
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Overfull \hbox (15.73795pt too wide) in paragraph at lines 18827--18827
 []\T1/zi4/m/n/9 ## 1-D minimization: "Brent" or optimize() being preferred.. b
ut NM may be ok and "unavoidable",[] 

Overfull \hbox (3.75941pt too wide) in paragraph at lines 18830--18830
 []\T1/zi4/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list(
warn.1d.NelderMead = FALSE)))[] 
[1520] [1521] [1522] [1523] [1524] [1525]
Underfull \hbox (badness 1337) in paragraph at lines 19252--19255
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
[1526] [1527] [1528] [1529] [1530] [1531] [1532] [1533] [1534]
Underfull \hbox (badness 3049) in paragraph at lines 19748--19752
[]\T1/ptm/m/n/10 In the Cook's dis-tance vs leverage/(1-leverage) plot, con-tou
rs of stan-dard-ized resid-u-als
[1535] [1536] [1537] [1538]
Underfull \hbox (badness 1194) in paragraph at lines 20006--20009
[]\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting
 of the con-fi-dence
[1539] [1540] [1541] [1542] [1543]
Underfull \hbox (badness 2503) in paragraph at lines 20381--20384
[]\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of 
\T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 ,
[1544]
Underfull \hbox (badness 3919) in paragraph at lines 20408--20410
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Exact Poisson test" \T1
/ptm/m/n/10 or \T1/zi4/m/n/10 "Comparison of Poisson
[1545] [1546] [1547] [1548] [1549] [1550] [1551] [1552] [1553] [1554] [1555]
[1556] [1557] [1558] [1559] [1560]
Underfull \hbox (badness 10000) in paragraph at lines 21485--21491
[]\T1/ptm/m/n/10 For time-series pre-dic-tion, [][]\T1/zi4/m/n/10 predict.ar[][
][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 predict.Arima[][][]\T1/ptm/m/n/10 , [][]
\T1/zi4/m/n/10 predict.arima0[][][]\T1/ptm/m/n/10 ,
[1561] [1562] [1563] [1564] [1565] [1566] [1567] [1568] [1569] [1570] [1571]
[1572] [1573] [1574] [1575] [1576] [1577] [1578] [1579] [1580] [1581]
Underfull \hbox (badness 1337) in paragraph at lines 22834--22840
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
[1582] [1583] [1584] [1585] [1586] [1587] [1588] [1589] [1590]
Overfull \hbox (27.74408pt too wide) in paragraph at lines 23399--23399
 []  \T1/zi4/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty
p, ...), quantile(x, prob, type=1)))[] 
[1591] [1592] [1593]
Underfull \hbox (badness 10000) in paragraph at lines 23650--23653
[]\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by

Underfull \hbox (badness 4205) in paragraph at lines 23650--23653
\T1/zi4/m/n/10 cutree(hclust.obj,k = k)\T1/ptm/m/n/10 , can be spec-i-fied for 
ef-fi-ciency if al-ready
[1594] [1595] [1596] [1597] [1598] [1599] [1600] [1601] [1602]
Underfull \hbox (badness 10000) in paragraph at lines 24235--24238
[]\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult \T1/zi4/m/n/10 y = run
med(x,k) \T1/ptm/m/n/10 sim-ply has \T1/zi4/m/n/10 y[j] =
[1603]
Underfull \hbox (badness 3690) in paragraph at lines 24287--24291
[][][]\T1/zi4/m/n/10 smoothEnds[][][] \T1/ptm/m/n/10 which im-ple-ments Tukey's
 end point rule and is called by de-fault from
[1604] [1605] [1606] [1607] [1608] [1609]
Underfull \vbox (badness 10000) has occurred while \output is active [1610]
[1611]
Underfull \hbox (badness 2165) in paragraph at lines 24777--24782
[]\T1/ptm/m/n/10 Each of the fol-low-ing are \T1/zi4/m/n/10 "selfStart" \T1/ptm
/m/n/10 mod-els (with ex-am-ples) [][]\T1/zi4/m/n/10 SSasymp[][][]\T1/ptm/m/n/1
0 , [][]\T1/zi4/m/n/10 SSasympOff[][][]\T1/ptm/m/n/10 ,
[1612] [1613] [1614]
Underfull \hbox (badness 1867) in paragraph at lines 24982--24984
[]\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods. 
Passed to

Underfull \hbox (badness 10000) in paragraph at lines 24995--24999
\T1/ptm/m/n/10 where \T1/zi4/m/n/10 NN <-[][]nobs[][][](object,use.fallback = u
se.fallback) \T1/ptm/m/n/10 and \T1/zi4/m/n/10 PP
[1615] [1616] [1617] [1618] [1619] [1620] [1621] [1622] [1623] [1624] [1625]
[1626] [1627] [1628] [1629] [1630] [1631] [1632] [1633] [1634] [1635] [1636]
[1637]
Underfull \hbox (badness 3514) in paragraph at lines 26556--26561
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1638] [1639] [1640] [1641]
Overfull \hbox (2.23795pt too wide) in paragraph at lines 26790--26790
 []       \T1/zi4/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5]
 == frac(log(2), e^{phi[2]})}),[] 

Underfull \hbox (badness 3514) in paragraph at lines 26826--26832
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1642] [1643] [1644] [1645]
Underfull \hbox (badness 3514) in paragraph at lines 27040--27045
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1646]
Underfull \hbox (badness 3514) in paragraph at lines 27127--27132
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1647]
Underfull \hbox (badness 3514) in paragraph at lines 27192--27197
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1648] [1649]
Underfull \hbox (badness 3514) in paragraph at lines 27286--27291
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1650]
Underfull \hbox (badness 6691) in paragraph at lines 27378--27383
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 x\T1/p
tm/m/n/10 . It is the value of the ex-pres-sion
[1651] [1652] [1653] [1654] [1655] [1656] [1657] [1658]
Underfull \hbox (badness 4024) in paragraph at lines 27908--27911
[]\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex-trac-tion
, which
[1659] [1660] [1661] [1662] [1663] [1664] [1665] [1666] [1667] [1668]
Underfull \hbox (badness 5431) in paragraph at lines 28514--28516
[]\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/z
i4/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if
[1669] [1670] [1671]
Underfull \hbox (badness 5431) in paragraph at lines 28724--28727
[]\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/z
i4/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if
[1672] [1673] [1674] [1675] [1676]
Underfull \hbox (badness 1337) in paragraph at lines 29038--29042
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
[1677] [1678] [1679] [1680] [1681]
Underfull \hbox (badness 1616) in paragraph at lines 29340--29343
[]\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial
 resid-u-als, when
[1682] [1683] [1684] [1685] [1686] [1687] [1688] [1689] [1690] [1691] [1692]
[1693] [1694] [1695] [1696] [1697] [1698]
Underfull \hbox (badness 3557) in paragraph at lines 30470--30474
[]\T1/ptm/m/n/10 Setting \T1/zi4/m/n/10 extendInt \T1/ptm/m/n/10 to a non-\T1/z
i4/m/n/10 "no" \T1/ptm/m/n/10 string, means search-ing for the cor-rect \T1/zi4
/m/n/10 interval =
[1699] [1700] [1701] [1702] [1703] [1704]
Underfull \hbox (badness 1337) in paragraph at lines 30834--30838
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
[1705] [1706] [1707] [1708] [1709] [1710] [1711] [1712]
Underfull \hbox (badness 1337) in paragraph at lines 31361--31365
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
[1713] [1714] [1715] [1716] [1717] [1718] [1719] [1720] [1721]) (stats4-pkg.tex
[1722]
Chapter 11.
[1723] [1724] [1725] [1726] [1727] [1728]pdfTeX warning (ext4): destination wit
h the same identifier (name{Rfn.show.Rdash.methods}) has been already used, dup
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<to be read again> 
                   \relax 
l.407 ...Package \pkg{stats4}}{show.Rdash.methods}
                                                   [1729] [1730] [1731])
(tcltk-pkg.tex [1732]
Chapter 12.
[1733] [1734] [1735] [1736] [1737] [1738] [1739]
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Underfull \hbox (badness 1546) in paragraph at lines 660--667
[]\T1/zi4/m/n/10 tcl \T1/ptm/m/n/10 pro-vides a generic in-ter-face to call-ing
 any Tk or Tcl com-mand by sim-ply run-ning
[1741] [1742] [1743] [1744] [1745]
Underfull \vbox (badness 10000) has occurred while \output is active [1746]
[1747] [1748] [1749] [1750] [1751] [1752]) (tools-pkg.tex
Chapter 13.
[1753]

LaTeX Font Warning: Font shape `T1/zi4/m/it' undefined
(Font)              using `T1/zi4/m/n' instead on input line 72.

[1754]
Underfull \hbox (badness 3039) in paragraph at lines 164--167
[]\T1/zi4/m/n/10 assertWarning() \T1/ptm/m/n/10 as-serts that a warn-ing will b
e sig-nalled, but \T1/ptm/m/it/10 not \T1/ptm/m/n/10 an er-ror, whereas
[1755] [1756]
Underfull \hbox (badness 1308) in paragraph at lines 285--298
[]\T1/ptm/m/n/10 At a min-i-mum, the en-vi-ron-ment should con-tain rou-tines t
o ren-der each of the 12 types

Underfull \hbox (badness 4967) in paragraph at lines 285--298
\T1/ptm/m/n/10 of bib-li-o-graphic en-try sup-ported by [][]\T1/zi4/m/n/10 bibe
ntry[][][] \T1/ptm/m/n/10 as well as sev-eral other rou-tines de-

Underfull \hbox (badness 10000) in paragraph at lines 285--298
\T1/zi4/m/n/10 formatIncollection\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatInProcee
dings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatManual\T1/ptm/m/n/10 , \T1/zi4/m/n/1
0 formatMastersthesis\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 285--298
\T1/zi4/m/n/10 formatMisc\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatPhdthesis\T1/ptm
/m/n/10 , \T1/zi4/m/n/10 formatProceedings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 forma
tTechreport \T1/ptm/m/n/10 and
[1757]
Underfull \hbox (badness 3039) in paragraph at lines 389--391
[]\T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gine 
to use. Over-rides any
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[1765] [1766] [1767] [1768] [1769]
Underfull \hbox (badness 4441) in paragraph at lines 1139--1149
\T1/ptm/m/n/10 giv-ing the repos-i-to-ries to use for lo-cat-ing re-verse de-pe
n-den-cies (de-
[1770]
Underfull \hbox (badness 1014) in paragraph at lines 1163--1165
[]\T1/ptm/m/n/10 a log-i-cal in-di-cat-ing whether to also sum-ma-rize the re-v
erse de-pen-den-cies

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[]\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a 
pre-vi-ous

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[]\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us-ing


Overfull \hbox (15.52087pt too wide) in paragraph at lines 1206--1209
\T1/zi4/m/n/10 summarize_check_packages_in_dir_results \T1/ptm/m/n/10 and \T1/z
i4/m/n/10 summarize_check_packages_in_dir_timings\T1/ptm/m/n/10 ,
[1771] [1772] [1773] [1774] [1775]
Underfull \hbox (badness 2293) in paragraph at lines 1558--1560
[]\T1/zi4/m/n/10 CRAN_memtest_notes() \T1/ptm/m/n/10 is now dep-re-cated, with 
its func-tion-al-ity in-te-grated into that of
[1776] [1777]
Underfull \hbox (badness 7981) in paragraph at lines 1696--1701
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a
 sub-set of
[1778]
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor of \T1/phv/m/n/10 R \T1/ptm/m/n/10 li-br
ary trees, or \T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 for all known trees (see
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 []\T1/zi4/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl
ogo.svg}{options: width=100}",[] 
[1786] [1787] [1788]
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a
 sub-set of
[1789] [1790] [1791] [1792] [1793] [1794] [1795]

LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined
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[]\T1/zi4/m/sl/10 NULL \T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec-t
or of links, as re-turned by
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[]\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run
,
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[]\T1/ptm/m/n/10 Where sup-ported (\T1/zi4/m/sl/10 texi2dvi \T1/ptm/m/n/10 5.0 
and later; \T1/zi4/m/sl/10 texify.exe \T1/ptm/m/n/10 from MiK-TeX), op-tion
[1813]
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[]\T1/ptm/m/n/10 a ma-trix spec-i-fy-ing all pack-ages in-stalled on the lo-cal
 sys-tem, as from
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[]\T1/ptm/m/n/10 Users should ex-pect sig-nif-i-cantly smaller speedups over \T
1/zi4/m/sl/10 write_PACKAGES \T1/ptm/m/n/10 in the \T1/zi4/m/sl/10 type ==
[1819]
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[]\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/zi4/m/sl/10 p
o/\T1/ptm/m/sl/10 pkgname\T1/zi4/m/sl/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists.
 The

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\T1/ptm/m/n/10 `\T1/zi4/m/sl/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in 
the pack-age are ex-am-ined to cre-ate a file
[1820] [1821] [1822]
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[]\T1/ptm/m/n/10 The de-fault cor-re-sponds to the fields needed by [][]\T1/zi4
/m/sl/10 available.packages[][][]\T1/ptm/m/n/10 :
[1823]
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[]\T1/ptm/m/n/10 For a re-mote repos-i-tory there is a trade-off be-tween down-
load speed and time spent by
[1824] [1825] [1826]) (utils-pkg.tex
Chapter 14.

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[]\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T
1/zi4/m/sl/10 insertions\T1/ptm/m/n/10 ',
[1827] [1828] [1829] [1830] [1831]
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\T1/zi4/m/sl/10 c("vertical","horizontal","cascade","minimize","restore") \T1/p
tm/m/n/10 with
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[]\T1/ptm/m/n/10 Functions \T1/zi4/m/sl/10 aspell_package_Rd_files\T1/ptm/m/n/1
0 , \T1/zi4/m/sl/10 aspell_package_vignettes\T1/ptm/m/n/10 ,

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\T1/zi4/m/sl/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 aspel
l_package_C_files \T1/ptm/m/n/10 per-form spell check-ing on the
[1837] [1838]
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[]\T1/ptm/m/n/10 Argument \T1/zi4/m/sl/10 filters \T1/ptm/m/n/10 can be used to
 se-lect which of the pack-ages on the repos-i-to-

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\T1/ptm/m/n/10 ries are re-ported. It is called with its de-fault value (\T1/zi
4/m/sl/10 NULL\T1/ptm/m/n/10 ) by func-tions such as
[1839]
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[]\T1/ptm/m/n/10 Where pro-vided by the repos-i-tory, fields \T1/zi4/m/sl/10 "O
S_type"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "License"\T1/ptm/m/n/10 , \T1/zi4/m/sl/
10 "License_is_FOSS"\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 (\T1/ptm/m/it/10 deprecated\T1/ptm/m/n/10 , use \T1/zi4/m/sl/1
0 bibtex = T|F \T1/ptm/m/n/10 in-stead!) a num-ber, say $\OML/cmm/m/it/10 m$\T1
/ptm/m/n/10 , in-di-cat-

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\T1/ptm/m/n/10 ing that the bib-tex code should be given in ad-di-tion to the f
or-mat-

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\T1/ptm/m/n/10 ted tex \T1/ptm/m/it/10 when \T1/ptm/m/n/10 there are not more t
han $\OML/cmm/m/it/10 m$ \T1/ptm/m/n/10 en-tries. The de-fault is

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\T1/ptm/m/n/10 taken as [][]\T1/zi4/m/sl/10 getOption[][][]("citation.bibtex.ma
x",1) \T1/ptm/m/n/10 which is \T1/zi4/m/sl/10 1 \T1/ptm/m/n/10 typ-i-cally.

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\T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f
ault by

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[]\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing
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[]\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T
1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to
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[]\T1/ptm/m/n/10 None for \T1/zi4/m/sl/10 chooseCRANmirror()\T1/ptm/m/n/10 , th
is func-tion is in-voked for its side ef-fect of up-dat-ing
[1859] [1860] [1861] [1862] [1863]pdfTeX warning (ext4): destination with the s
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l.2566 ... the Clipboard in MS Windows}{clipboard}
                                                   [1864] [1865]
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[]\T1/ptm/m/n/10 A [][]\T1/zi4/m/sl/10 list[][][] \T1/ptm/m/n/10 or [][]\T1/zi4
/m/sl/10 array[][][]\T1/ptm/m/n/10 , see the \T1/zi4/m/sl/10 simplify \T1/ptm/m
/n/10 ar-gu-ment above. In the lat-ter case, the iden-tity
[1866] [1867] [1868] [1869] [1870] [1871]
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[]\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .tab\T1/ptm/m/n/10 ', `\T1/zi4/
m/sl/10 .txt\T1/ptm/m/n/10 ' or `\T1/zi4/m/sl/10 .TXT\T1/ptm/m/n/10 ' are read 
us-ing [][]\T1/zi4/m/sl/10 read.table[][][](...,header =

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[]\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .csv\T1/ptm/m/n/10 ' or `\T1/zi
4/m/sl/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/zi4/m/sl/10 read.table[]
[][](...,header = TRUE,sep =
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[]\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by
 the \T1/zi4/m/sl/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the
[1883]
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[]\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers 
via en-vi-ron-ment vari-able
[1884] [1885]
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[]\T1/ptm/m/n/10 additional ar-gu-ments to be passed to [][]\T1/zi4/m/sl/10 dow
nload.file[][][] \T1/ptm/m/n/10 and
[1886] [1887] [1888] [1889] [1890] [1891] [1892] [1893] [1894] [1895] [1896]pdf
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l.4850 ...mat Unordered and Ordered Lists}{format}
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l.4850 ...mat Unordered and Ordered Lists}{format}
                                                   [1897] [1898] [1899]
[1900] [1901] [1902] [1903] [1904]
Underfull \hbox (badness 1622) in paragraph at lines 5369--5373
[]\T1/ptm/m/n/10 This func-tion will search for Win-dows han-dles, for pass-ing
 to ex-ter-nal GUIs or to the
[1905] [1906] [1907] [1908] [1909] [1910] [1911] [1912] [1913]
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[]\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T
1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to
[1914]
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[]\T1/ptm/m/n/10 a char-ac-ter string to be matched in the help page `key-words
'. `Key-

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\T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are 
listed in file
[1915] [1916] [1917]
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[]\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de
x,
[1918]
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion 
to search. See
[1919]
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[]\T1/ptm/m/n/10 For de-tails of the lock-ing which is done, see the sec-tion `
Lock-ing' in the help for
[1920] [1921] [1922]
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[]\T1/ptm/m/n/10 a ma-trix as re-turned by [][]\T1/zi4/m/sl/10 available.packag
es[][][] \T1/ptm/m/n/10 list-ing pack-ages avail-able

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\T1/ptm/m/n/10 used if \T1/zi4/m/sl/10 repos = NULL\T1/ptm/m/n/10 . Can also be
 a char-ac-ter vec-tor, a sub-set of

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[]\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to
 be

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\T1/ptm/m/n/10 passed to \T1/zi4/m/sl/10 R CMD INSTALL \T1/ptm/m/n/10 for a sou
rce pack-age in-stall. E.g.,
[1923]
Underfull \hbox (badness 3219) in paragraph at lines 6786--6793
[]\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is \T1/zi4/m/sl/
10 "both" \T1/ptm/m/n/10 which means `use bi-nary if avail-

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\T1/ptm/m/n/10 able and cur-rent, oth-er-wise try source'. The ac-tion if there
 are source pack-ages

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\T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com
-piled is con-trolled by

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[][]\T1/zi4/m/sl/10 getOption[][][]("install.packages.compile.from.source")\T1/
ptm/m/n/10 . \T1/zi4/m/sl/10 type = "both" \T1/ptm/m/n/10 will be silently
[1924]
Underfull \hbox (badness 2932) in paragraph at lines 6794--6797
[]\T1/ptm/m/n/10 Using pack-ages with \T1/zi4/m/sl/10 type = "source" \T1/ptm/m
/n/10 al-ways works pro-vided the pack-age con-tains no
[1925]
Underfull \hbox (badness 10000) in paragraph at lines 6930--6935
[][][]\T1/zi4/m/sl/10 update.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10
 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 download.packages
[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 installed.packages[][][]\T1/ptm/m/n/
10 ,
[1926] [1927] [1928] [1929] [1930] [1931] [1932] [1933] [1934] [1935] [1936]
[1937] [1938] [1939] [1940] [1941] [1942] [1943] [1944] [1945] [1946] [1947]
[1948]
Underfull \hbox (badness 10000) in paragraph at lines 8431--8433
[]\T1/ptm/m/n/10 for \T1/zi4/m/sl/10 asDateBuilt()\T1/ptm/m/n/10 , a [][]\T1/zi
4/m/sl/10 character[][][] \T1/ptm/m/n/10 string as from
[1949]
Underfull \hbox (badness 2310) in paragraph at lines 8453--8458
[]\T1/ptm/m/n/10 If a `\T1/zi4/m/sl/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the
 given pack-age is found and can suc-cess-fully be read,
[1950] [1951] [1952] [1953] [1954] [1955] [1956]
Underfull \hbox (badness 1248) in paragraph at lines 8977--8981
[]\T1/zi4/m/sl/10 R CMD build \T1/ptm/m/n/10 builds \T1/phv/m/n/10 R \T1/ptm/m/
n/10 source tar-balls. The name(s) of the pack-ages are taken from the
[1957]
Underfull \hbox (badness 1789) in paragraph at lines 9055--9057
[]\T1/ptm/m/n/10 See `Writ-ing R Ex-ten-sions' and the `R for Win-dows FAQ' for
 more dis-cus-sion of the
[1958] [1959] [1960] [1961] [1962] [1963] [1964] [1965] [1966]
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[1968] [1969]
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[]\T1/ptm/m/n/10 The name \T1/zi4/m/sl/10 "clipboard" \T1/ptm/m/n/10 may also b
e used on Win-dows, in which case
[1970] [1971]
Underfull \hbox (badness 3000) in paragraph at lines 10028--10033
[][][]\T1/zi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 type.conve
rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for 
read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i
dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/zi4/m/sl/10 read.t
able[][][]\T1/ptm/m/n/10 ;
[1972] [1973] [1974] [1975] [1976] [1977] [1978] [1979]
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[][][]\T1/zi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 type.conve
rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for 
read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i
dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/zi4/m/sl/10 write.
table[][][]\T1/ptm/m/n/10 ;
[1980]
Underfull \hbox (badness 10000) in paragraph at lines 10667--10672
[]\T1/ptm/m/n/10 The `hive' con-tain-ing the key. The ab-bre-vi-a-tions are for


Underfull \hbox (badness 10000) in paragraph at lines 10667--10672
\T1/zi4/m/sl/10 HKEY_LOCAL_MACHINE\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 HKEY_CLASSES
_ROOT\T1/ptm/m/n/10 . \T1/zi4/m/sl/10 HKEY_CURRENT_USER\T1/ptm/m/n/10 ,
[1981] [1982] [1983] [1984] [1985] [1986] [1987]
Underfull \hbox (badness 2469) in paragraph at lines 11155--11159
[]\T1/ptm/m/n/10 Wikipedia con-trib-u-tors (2006). Ro-man nu-mer-als. Wikipedia
, The Free En-cy-clo-pe-dia.

Underfull \hbox (badness 3428) in paragraph at lines 11155--11159
[][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / w / index . php ? title
 = Roman _ numerals & oldid = 78252134$[][]\T1/ptm/m/n/10 . Ac-
[1988] [1989] [1990] [1991] [1992]
Underfull \hbox (badness 4060) in paragraph at lines 11486--11489
[]\T1/ptm/m/n/10 If `\T1/zi4/m/sl/10 --default-packages\T1/ptm/m/n/10 ' is not 
used, then \T1/zi4/m/sl/10 Rscript \T1/ptm/m/n/10 checks the en-vi-ron-ment var
i-able

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 []\T1/zi4/m/n/9 Rscript --default-packages=methods,datasets,utils,grDevices,gr
aphics,stats -e \TS1/zi4/m/n/9 '\T1/zi4/m/n/9 sessionInfo()\TS1/zi4/m/n/9 '[] 
[1993] [1994] [1995] [1996]
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[][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/
ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 https : / / www . gnu . org / software / emac
s / manual /
[1997] [1998] [1999]
Underfull \hbox (badness 10000) in paragraph at lines 11972--11976
[]\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/sl/10 stylepath \T1/ptm/m/n/10 is n
ow taken from the en-vi-ron-ment vari-able
[2000]
Underfull \hbox (badness 10000) in paragraph at lines 12003--12009
[]\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y
ou can add a
[2001] [2002]
Underfull \hbox (badness 1009) in paragraph at lines 12197--12209
[]\T1/ptm/m/n/10 Before each code chunk is eval-u-ated, zero or more hook func-
tions can be ex-e-cuted. If
[2003]
Underfull \hbox (badness 4779) in paragraph at lines 12234--12236
[]\T1/ptm/m/n/10 The file `\T1/zi4/m/sl/10 Rconsole\T1/ptm/m/n/10 ' con-fig-ure
s the R GUI (\T1/zi4/m/sl/10 Rgui\T1/ptm/m/n/10 ) con-sole un-der MS Win-dows a
nd

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\T1/ptm/m/n/10 (strip-ping any trail-ing slash), oth-er-wise to the Win-dows `p
er-sonal' di-rec-tory, oth-er-wise to
[2004] [2005] [2006] [2007] [2008] [2009]
Underfull \hbox (badness 3780) in paragraph at lines 12665--12669
[]\T1/ptm/m/n/10 A Bio-con-duc-tor mir-ror can be se-lected by set-ting [][]\T1
/zi4/m/sl/10 options[][][]("BioC_mirror")\T1/ptm/m/n/10 , e.g. via

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[]\T1/ptm/m/n/10 Repository `\T1/zi4/m/sl/10 CRAN\T1/ptm/m/n/10 ' is treated sp
e-cially: the value is taken from the cur-rent set-ting of
[2010] [2011] [2012]
Underfull \hbox (badness 2302) in paragraph at lines 12885--12887
[]\T1/ptm/m/n/10 Convert file paths to the short form. This is an in-ter-face t
o the Win-dows API call
[2013] [2014] [2015] [2016] [2017]
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[]\T1/ptm/m/n/10 logical; if \T1/zi4/m/sl/10 TRUE \T1/ptm/m/n/10 (de-fault), []
[]\T1/zi4/m/sl/10 deparse[][][](control = <S>) \T1/ptm/m/n/10 will not have

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[]\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t
ive
[2018]
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[2020] [2021] [2022] [2023]
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[]\T1/ptm/m/n/10 If \T1/zi4/m/sl/10 syntax = NULL \T1/ptm/m/n/10 (the de-fault)
 then the avail-able syn-tax ob-jects are con-sulted in turn,

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\T1/ptm/m/n/10 and se-lected if their \T1/zi4/m/sl/10 extension \T1/ptm/m/n/10 
com-po-nent matches (as a reg-exp) the file name. Ob-
[2024] [2025] [2026] [2027]
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[]\T1/ptm/m/n/10 When ar-gu-ment \T1/zi4/m/sl/10 tar \T1/ptm/m/n/10 is set to t
he com-mand \T1/zi4/m/sl/10 tar \T1/ptm/m/n/10 on ma-cOS, en-vi-ron-ment vari-a
ble

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[][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ 
format)$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 http : / / pubs . opengroup .
 org /

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\T1/zi4/m/sl/10 onlinepubs / 9699919799 / utilities / pax . html # tag _ 20 _ 9
2 _ 13 _ 06$[][] \T1/ptm/m/n/10 for the way the POSIX
[2028] [2029] [2030] [2031] [2032] [2033] [2034] [2035] [2036]
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[]\T1/ptm/m/n/10 Arguments such as \T1/zi4/m/sl/10 destdir \T1/ptm/m/n/10 and \
T1/zi4/m/sl/10 dependencies \T1/ptm/m/n/10 to be passed to

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[][]\T1/zi4/m/sl/10 install.packages[][][] \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 i
gnore_repo_cache\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 max_repo_cache_age \T1/ptm/m/n
/10 and
[2037]
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[]\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and
 in-stall. See

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[][][]\T1/zi4/m/sl/10 install.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/1
0 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 download.package
s[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 installed.packages[][][]\T1/ptm/m/n
/10 ,
[2038] [2039] [2040] [2041] [2042] [2043] [2044] [2045] [2046] [2047] [2048]
[2049]
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[]\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec-
tion e.g. \T1/zi4/m/sl/10 file =
[2050] [2051] [2052]) [2053] [2054] (KernSmooth-pkg.tex
Chapter 15.
[2055] [2056] [2057] [2058] [2059] [2060] [2061] [2062] [2063] [2064])
(MASS-pkg.tex
Chapter 16.
[2065] [2066] [2067] [2068] [2069] [2070] [2071] [2072] [2073] [2074] [2075]
[2076] [2077] [2078] [2079] [2080] [2081] [2082] [2083] [2084] [2085] [2086]
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[2098] [2099] [2100] [2101]
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[]\T1/ptm/m/n/10 further ar-gu-ments for \T1/zi4/m/sl/10 plot \T1/ptm/m/n/10 an
d graph-i-cal pa-ram-e-ters. Note that
[2102] [2103] [2104]
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\T1/zi4/m/sl/10 "geometric"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "log-normal"\T1/ptm
/m/n/10 , \T1/zi4/m/sl/10 "lognormal"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "logistic
"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "negative
[2105] [2106]
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[]\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i-
na-tor ex-ceeds
[2107] [2108] [2109] [2110] [2111] [2112] [2113] [2114] [2115] [2116] [2117]
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[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
rm \T1/zi4/m/sl/10 response ~
[2132]
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[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
rm \T1/zi4/m/sl/10 response ~
[2133] [2134] [2135] [2136] [2137] [2138] [2139] [2140] [2141] [2142] [2143]
[2144] [2145] [2146] [2147] [2148] [2149]pdfTeX warning (ext4): destination wit
h the same identifier (name{Rfn.npk}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.6111 ...sical N, P, K Factorial Experiment}{npk}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.npk.1}) has been already used, duplica
te ignored
<to be read again> 
                   \relax 
l.6111 ...sical N, P, K Factorial Experiment}{npk}
                                                   [2150] [2151] [2152]
[2153] [2154]
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[2156] [2157] [2158] [2159] [2160] [2161] [2162]
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[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
rm \T1/zi4/m/sl/10 response ~
[2163]
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[]\T1/ptm/m/n/10 The log-log and com-ple-men-tary log-log links are the in-crea
s-ing func-tions $\OML/cmm/m/it/10 F[]\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 p\OT1/c
mr/m/n/10 ) =
[2164] [2165] [2166]
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\T1/ptm/m/n/10 only the first \T1/zi4/m/sl/10 dimen \T1/ptm/m/n/10 dis-crim-i-n
ant com-po-nents are used (ex-cept for
[2167] [2168] [2169] [2170] [2171] [2172] [2173] [2174] [2175]
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[]\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i-
na-tor ex-ceeds
[2176] [2177] [2178] [2179] [2180] [2181] [2182] [2183] [2184] [2185] [2186]
[2187] [2188] [2189] [2190] [2191] [2192] [2193] [2194] [2195] [2196] [2197]
[2198] [2199] [2200] [2201] [2202] [2203] [2204] [2205] [2206] [2207] [2208]
[2209] [2210] [2211] [2212]) (Matrix-pkg.tex
Chapter 17.

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[]\T1/ptm/m/n/10 Note that the cur-rent im-ple-men-ta-tion de-tails are sub-jec
t to change, and if you

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\T1/ptm/m/n/10 con-sider work-ing with these classes, please con-tact the pack-
age main-tain-ers
[2213]
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[]\T1/ptm/m/n/10 This is cur-rently ex-per-i-men-tal and not yet used for our o
wn code. Please con-tact us
[2214] [2215] [2216] [2217]
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[]\T1/ptm/m/n/10 logical; if true the re-sult will be sym-met-ric (in-her-it-in
g from class
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[]\T1/ptm/m/n/10 The value of \T1/zi4/m/sl/10 bdiag() \T1/ptm/m/n/10 in-heris f
rom class [][]\T1/zi4/m/sl/10 CsparseMatrix[][][]\T1/ptm/m/n/10 , whereas \T1/z
i4/m/sl/10 .bdiag() \T1/ptm/m/n/10 re-turns a
[2220] [2221] [2222] [2223] [2224]
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[]\T1/zi4/m/sl/10 signature(from = "CHMfactor",to = "sparseMatrix") \T1/ptm/m/n
/10 (or equiv-a-lently, \T1/zi4/m/sl/10 to =
[2225] [2226]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.chol}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1134 ...- 'Matrix' S4 Generic and Methods}{chol}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.chol.1}) has been already used, duplic
ate ignored
<to be read again> 
                   \relax 
l.1134 ...- 'Matrix' S4 Generic and Methods}{chol}
                                                  
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\T1/ptm/m/n/10 sider [][]\T1/zi4/m/sl/10 Cholesky[][][]() \T1/ptm/m/n/10 in suc
h sit-u-a-tions, since \T1/zi4/m/sl/10 chol(x,pivot=TRUE) \T1/ptm/m/n/10 uses t
he same al-go-rithm
[2227pdfTeX warning (ext4): destination with the same identifier (name{Rfn.chol
,dsCMatrix.Rdash.method}) has been already used, duplicate ignored

\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.1209 \item[chol]
                   \code{signature(x = "dgeMatrix")}: works viapdfTeX warning (
ext4): destination with the same identifier (name{Rfn.chol,lsCMatrix.Rdash.meth
od}) has been already used, duplicate ignored

\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.1209 \item[chol]
                   \code{signature(x = "dgeMatrix")}: works viapdfTeX warning (
ext4): destination with the same identifier (name{Rfn.chol,nsCMatrix.Rdash.meth
od}) has been already used, duplicate ignored

\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.1209 \item[chol]
                   \code{signature(x = "dgeMatrix")}: works via] [2228]
[2229]
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[]\T1/ptm/m/n/10 This is a generic func-tion with spe-cial meth-ods for dif-fer
-ent types of ma-tri-ces. Use
[2230] [2231]
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[]\T1/ptm/m/n/10 Class \T1/zi4/m/sl/10 "MatrixFactorization" \T1/ptm/m/n/10 and
 \T1/zi4/m/sl/10 "dtrMatrix"\T1/ptm/m/n/10 , di-rectly. Class \T1/zi4/m/sl/10 "
dgeMatrix"\T1/ptm/m/n/10 , by class

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[]\T1/ptm/m/n/10 Both these fac-tor-iza-tions can \T1/ptm/m/it/10 di-rectly \T1
/ptm/m/n/10 be treated as (tri-an-gu-lar) ma-tri-ces, as they ex-tend
[2232]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.col
Sums}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1623 ... Row and Column Sums and Means}{colSums}
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ation with the same identifier (name{Rfn.colSums.1}) has been already used, dup
licate ignored
<to be read again> 
                   \relax 
l.1623 ... Row and Column Sums and Means}{colSums}
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ation with the same identifier (name{Rfn.colMeans}) has been already used, dupl
icate ignored
<to be read again> 
                   \relax 
l.1624 \aliasA{colMeans}{colSums}{colMeans}
                                           pdfTeX warning (ext4): destination w
ith the same identifier (name{Rfn.rowMeans}) has been already used, duplicate i
gnored
<to be read again> 
                   \relax 
l.1645 \aliasA{rowMeans}{colSums}{rowMeans}
                                           pdfTeX warning (ext4): destination w
ith the same identifier (name{Rfn.rowSums}) has been already used, duplicate ig
nored
<to be read again> 
                   \relax 
l.1656 \aliasA{rowSums}{colSums}{rowSums}
                                          [2233] [2234] [2235]
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[]\T1/ptm/m/n/10 a num-ber $\OML/cmm/m/it/10 > \OT1/cmr/m/n/10 0$\T1/ptm/m/n/10
 , the es-ti-mated (1-norm) con-di-tion num-ber $[]$; when
[2236] [2237] [2238] [2239] [2240]
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[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/zi4/m/sl/10 n
ew("dgCMatrix",...)\T1/ptm/m/n/10 , more typ-i-cally via
[2241] [2242] [2243] [2244]
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[]\T1/ptm/m/n/10 However this means that a ma-trix typ-i-cally can tbe stored i
n more than one pos-si-ble
[2245] [2246]
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[]\T1/zi4/m/sl/10 Diagonal() \T1/ptm/m/n/10 re-turns an ob-ject of class [][]\T
1/zi4/m/sl/10 ddiMatrix[][][] \T1/ptm/m/n/10 or [][]\T1/zi4/m/sl/10 ldiMatrix[]
[][] \T1/ptm/m/n/10 (with ``su-per-class''
[2247]
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[]\T1/zi4/m/sl/10 signature(x = "diagonalMatrix")\T1/ptm/m/n/10 : all these gro
up meth-ods re-turn a
[2248] [2249] [2250]
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[]\T1/zi4/m/sl/10 signature(x = "dMatrix",digits = "numeric")\T1/ptm/m/n/10 : t
his group con-tains [][]\T1/zi4/m/sl/10 round[][][]() \T1/ptm/m/n/10 and

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[][][]\T1/zi4/m/sl/10 drop0[][][](x,tol=1e-10) \T1/ptm/m/n/10 is some-times pre
fer-able to (and more ef-fi-cient than)
[2251] [2252]
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[]\T1/ptm/m/n/10 a Ma-trix like \T1/zi4/m/sl/10 x \T1/ptm/m/n/10 but with no ex
-plicit ze-ros, i.e., \T1/zi4/m/sl/10 !any(x@x == 0)\T1/ptm/m/n/10 , al-ways in
-her-it-ing from
[2253] [2254] [2255] [2256] [2257]
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[]\T1/zi4/m/sl/10 signature(x = "dspMatrix",type = "character")\T1/ptm/m/n/10 ,
 or \T1/zi4/m/sl/10 x = "dsyMatrix" \T1/ptm/m/n/10 or \T1/zi4/m/sl/10 type =

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[]\T1/zi4/m/sl/10 signature(x = "dspMatrix",type = "character")\T1/ptm/m/n/10 ,
 or \T1/zi4/m/sl/10 x = "dsyMatrix" \T1/ptm/m/n/10 or \T1/zi4/m/sl/10 type =
[2258] [2259]
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[]\T1/ptm/m/n/10 Class \T1/zi4/m/sl/10 "dgCMatrix"\T1/ptm/m/n/10 , di-rectly. C
lass \T1/zi4/m/sl/10 "triangularMatrix"\T1/ptm/m/n/10 , di-rectly. Class \T1/zi
4/m/sl/10 "dMatrix"\T1/ptm/m/n/10 ,
[2260] [2261]
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[]\T1/zi4/m/sl/10 signature(x = "dtpMatrix",logarithm = "logical")\T1/ptm/m/n/1
0 : the [][]\T1/zi4/m/sl/10 determinant[][][](x)
[2262] [2263] [2264] [2265] [2266] [2267]
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 [] \T1/zi4/m/n/9 readHB(gzcon(url("http://www.cise.ufl.edu/research/sparse/RB/
Boeing/msc00726.tar.gz"))))[] 

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 [] \T1/zi4/m/n/9 readMM(gzcon(url("ftp://math.nist.gov/pub/MatrixMarket2/Harwe
ll-Boeing/counterx/jgl009.mtx.gz"))))[] 
[2268] [2269]
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[]\T1/ptm/m/n/10 a string spec-i-fy-ing how the \T1/zi4/m/sl/10 zero.print \T1/
ptm/m/n/10 codes should be aligned, see
[2270] [2271] [2272] [2273] [2274]
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[]\T1/ptm/m/n/10 color for the bor-der of each rect-an-gle. \T1/zi4/m/sl/10 NA 
\T1/ptm/m/n/10 means no bor-der is drawn.

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\T1/ptm/m/n/10 When \T1/zi4/m/sl/10 NULL \T1/ptm/m/n/10 as by de-fault, \T1/zi4
/m/sl/10 border.col <-if(lwd < .01) NA else NULL \T1/ptm/m/n/10 is

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[]\T1/ptm/m/n/10 All meth-ods cur-rently end up call-ing the method for the [][
]\T1/zi4/m/sl/10 dgTMatrix[][][] \T1/ptm/m/n/10 class. Use
[2275]
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 []\T1/zi4/m/n/9 image(USCounties, c(1,100), c(1,100), useAbs=FALSE, lwd=3, bor
der.col = adjustcolor("skyblue", 1/2))[] 
[2276]
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[]\T1/ptm/m/n/10 While ``row-indexing'' (of more than one row \T1/ptm/m/it/10 o
r \T1/ptm/m/n/10 us-ing \T1/zi4/m/sl/10 drop=FALSE\T1/ptm/m/n/10 ) stays within
 the

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[]\T1/zi4/m/sl/10 signature(x = "matrix",y = "indMatrix") \T1/ptm/m/n/10 and ot
her sig-na-tures (use
[2277]
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[]\T1/zi4/m/sl/10 signature(from = "numeric",to = "indMatrix")\T1/ptm/m/n/10 : 
a user con-ve-nience, to al-low

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[]\T1/zi4/m/sl/10 signature(from = "indMatrix",to = "matrix")\T1/ptm/m/n/10 : c
o-er-cion to a tra-di-tional
[2278] [2279] [2280] [2281] [2282]
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[]\T1/zi4/m/sl/10 isTriangular(M) \T1/ptm/m/n/10 re-turns a [][]\T1/zi4/m/sl/10
 logical[][][] \T1/ptm/m/n/10 in-di-cat-ing if \T1/zi4/m/sl/10 M \T1/ptm/m/n/10
 is a tri-an-gu-lar ma-trix. Anal-o-gously,
[2283] [2284] [2285] [2286]
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[]\T1/zi4/m/sl/10 signature(x = "ndenseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally
 equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2287]
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[]\T1/ptm/m/n/10 Class \T1/zi4/m/sl/10 "ldenseMatrix"\T1/ptm/m/n/10 , di-rectly
. Class \T1/zi4/m/sl/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/zi4/m/sl/10 "lde
nseMatrix"\T1/ptm/m/n/10 . Class
[2288]
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[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/zi4/m/sl/10 t[][][]() \T1/ptm/m/n/10
 and co-er-cion meth-ods (for [][]\T1/zi4/m/sl/10 as[][][](.)\T1/ptm/m/n/10 ); 
use, e.g.,
[2289]
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[]\T1/zi4/m/sl/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-call
y equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2290]
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[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/zi4/m/sl/10 t[][][]() \T1/ptm/m/n/10
 and co-er-cion meth-ods (for [][]\T1/zi4/m/sl/10 as[][][](.)\T1/ptm/m/n/10 ; u
se, e.g.,
[2291]
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[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/zi4/m/sl/10 t[][][]() \T1/ptm/m/n/10
 and co-er-cion meth-ods (for [][]\T1/zi4/m/sl/10 as[][][](.)\T1/ptm/m/n/10 ; u
se, e.g.,
[2292]
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[]\T1/zi4/m/sl/10 lu() \T1/ptm/m/n/10 is a generic func-tion with spe-cial meth
-ods for dif-fer-ent types of ma-tri-ces. Use
[2293] [2294] [2295]
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[]\T1/ptm/m/n/10 Note that when the re-sult-ing ma-trix is di-ag-o-nal (``math-
e-mat-i-cally''),
[2296]
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[]\T1/ptm/m/n/10 Most of the time, the func-tion works via a tra-di-tional (\T1
/ptm/m/it/10 full\T1/ptm/m/n/10 ) [][]\T1/zi4/m/sl/10 matrix[][][]\T1/ptm/m/n/1
0 . How-ever,
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[]\T1/zi4/m/sl/10 signature(x = "Matrix")\T1/ptm/m/n/10 : sim-ply de-fined as \
T1/zi4/m/sl/10 prod(dim(x)) \T1/ptm/m/n/10 (and hence of mode

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[]\T1/zi4/m/sl/10 signature(object = "Matrix")\T1/ptm/m/n/10 : draws an [][]\T1
/zi4/m/sl/10 image[][][] \T1/ptm/m/n/10 of the ma-trix en-tries, us-ing

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l.7044 ...*\%}{matrix-products}{.Rpcent.*.Rpcent.}
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l.7152 ...A{crossprod}{matrix-products}{crossprod}
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l.7252 ...tcrossprod}{matrix-products}{tcrossprod}
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\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
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[]\T1/zi4/m/sl/10 signature(x = "dtrMatrix",y = "matrix") \T1/ptm/m/n/10 and ot
her sig-na-tures (use

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\T1/zi4/m/sl/10 showMethods("%*%",class="dtrMatrix")\T1/ptm/m/n/10 ): ma-trix m
ul-ti-pli-ca-tion. Mul-ti-pli-ca-tion of

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[]\T1/zi4/m/sl/10 signature(x = "CsparseMatrix",y = "missing") \T1/ptm/m/n/10 r
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[]\T1/zi4/m/sl/10 signature(x = "TsparseMatrix",y = "missing") \T1/ptm/m/n/10 r
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[]\T1/zi4/m/sl/10 signature(x = "dtrMatrix",y = "matrix") \T1/ptm/m/n/10 and ot
her sig-na-tures, see
[2301] [2302]
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[]\T1/ptm/m/n/10 classes in-her-it-ing from \T1/zi4/m/sl/10 "MatrixFactorizatio
n"\T1/ptm/m/n/10 , such as [][]\T1/zi4/m/sl/10 LU[][][]\T1/ptm/m/n/10 , [][]\T1
/zi4/m/sl/10 Cholesky[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 CHMfactor[][][]
\T1/ptm/m/n/10 , and
[2303]
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[]\T1/zi4/m/sl/10 signature(x = "ndenseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally
 equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2304]
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[]\T1/ptm/m/n/10 logical in-di-cat-ing if \T1/zi4/m/sl/10 X <-(X + t(X))/2 \T1/
ptm/m/n/10 should be done, af-ter \T1/zi4/m/sl/10 X
[2305] [2306]
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[]\T1/ptm/m/n/10 Class \T1/zi4/m/sl/10 "ndenseMatrix"\T1/ptm/m/n/10 , di-rectly
. Class \T1/zi4/m/sl/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/zi4/m/sl/10 "nde
nseMatrix"\T1/ptm/m/n/10 . Class

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[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/zi4/m/sl/10 t[][][]() \T1/ptm/m/n/10
 and co-er-cion meth-ods (for [][]\T1/zi4/m/sl/10 as[][][](.)\T1/ptm/m/n/10 ); 
use, e.g.,
[2308] [2309]
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[]\T1/ptm/m/n/10 fast sim-ple meth-ods
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l.8154 \HeaderA{norm}{Matrix Norms}{norm}
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[]\T1/zi4/m/sl/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-call
y equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2313]
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[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/zi4/m/sl/10 t[][][]() \T1/ptm/m/n/10
 and co-er-cion meth-ods (for [][]\T1/zi4/m/sl/10 as[][][](.)\T1/ptm/m/n/10 ; u
se, e.g.,
[2314]
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[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/zi4/m/sl/10 t[][][]() \T1/ptm/m/n/10
 and co-er-cion meth-ods (for [][]\T1/zi4/m/sl/10 as[][][](.)\T1/ptm/m/n/10 ; u
se, e.g.,
[2315]
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[]\T1/zi4/m/sl/10 signature(x = "matrix",y = "pMatrix") \T1/ptm/m/n/10 and othe
r sig-na-tures (use

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[]\T1/zi4/m/sl/10 signature(from = "numeric",to = "pMatrix")\T1/ptm/m/n/10 : a 
user con-ve-nience, to al-low
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                   \relax 
l.8956 \aliasA{qr}{qr-methods}{qr}
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l.9252 ... the Reciprocal Condition Number}{rcond}
                                                   [2325] [2326] [2327]
[2328]
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[]\T1/ptm/m/n/10 The al-go-rithm first sam-ples ``en-coded'' $\OT1/cmr/m/n/10 (
\OML/cmm/m/it/10 i; j\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 s with-out re-place-ment,
 via one di-men-sional

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\T1/ptm/m/n/10 in-dices, if not \T1/zi4/m/sl/10 symmetric [][]sample.int[][][](
nrow*ncol,nnz)\T1/ptm/m/n/10 , then---if \T1/zi4/m/sl/10 rand.x \T1/ptm/m/n/10 
is not \T1/zi4/m/sl/10 NULL\T1/ptm/m/n/10 ---

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\T1/ptm/m/n/10 gets \T1/zi4/m/sl/10 x <-rand.x(nnz) \T1/ptm/m/n/10 and calls []
[]\T1/zi4/m/sl/10 sparseMatrix[][][](i=i,j=j,x=x,..)\T1/ptm/m/n/10 . When \T1/z
i4/m/sl/10 rand.x=NULL\T1/ptm/m/n/10 ,
[2329] [2330] [2331] [2332]pdfTeX warning (ext4): destination with the same ide
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                                            [2333]
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[]\T1/ptm/m/n/10 with ex-tra ar-gu-ment list \T1/zi4/m/sl/10 ( sparse =
[2334]
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[]\T1/ptm/m/n/10 , and sim-i-lar \T1/zi4/m/sl/10 b\T1/ptm/m/n/10 , in-clud-ing 
\T1/zi4/m/sl/10 "missing"\T1/ptm/m/n/10 , and

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[]\T1/ptm/m/n/10 Construct a sparse model or ``de-sign'' ma-trix, form a for-mu
la and data frame
[2335]
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[]\T1/ptm/m/n/10 character string or \T1/zi4/m/sl/10 NULL \T1/ptm/m/n/10 or (co
-er-ca-ble to)

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[]\T1/ptm/m/n/10 should fac-tors have un-used lev-els dropped? The de-fault for

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[]\T1/zi4/m/sl/10 signature(from = "factor",to = "sparseMatrix")\T1/ptm/m/n/10 
: Co-er-cion of a fac-tor to

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\T1/zi4/m/sl/10 "sparseMatrix" \T1/ptm/m/n/10 pro-duces the ma-trix of in-di-ca
-tor \T1/ptm/b/n/10 rows \T1/ptm/m/n/10 stored as an ob-ject of class
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                                            [2345] [2346]
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[]\T1/ptm/m/n/10 vector of the non zero en-tries; may be miss-ing in which case
 a
[2347] [2348]
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[]\T1/zi4/m/sl/10 signature(x = "sparseVector") \T1/ptm/m/n/10 re-peat \T1/zi4/
m/sl/10 x\T1/ptm/m/n/10 , with the same ar-gu-ment list
[2349]
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[2351] [2352]
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[]\T1/ptm/m/n/10 The va-lid-ity checks do not re-quire a sym-met-ric \T1/zi4/m/
sl/10 Dimnames \T1/ptm/m/n/10 slot, so it can be
[2353]
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[]\T1/ptm/m/n/10 These are generic func-tions with sev-eral meth-ods for dif-fe
r-ent ma-trix classes, use e.g.,
[2354] [2355]
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[]\T1/ptm/m/n/10 For con-ve-nience, meth-ods for some op-er-a-tions such as \T1
/zi4/m/sl/10 %*% \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 crossprod \T1/ptm/m/n/10 ar
e de-fined
[2356]
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[]\T1/ptm/m/n/10 Note that \T1/zi4/m/sl/10 new(.)\T1/ptm/m/n/10 , [][]\T1/zi4/m
/sl/10 spMatrix[][][] \T1/ptm/m/n/10 or [][]\T1/zi4/m/sl/10 sparseMatrix[][][] 
\T1/ptm/m/n/10 con-struc-tors for \T1/zi4/m/sl/10 "dgTMatrix" \T1/ptm/m/n/10 (a
nd other
[2357] [2358] [2359] [2360] [2361] [2362]
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[]\T1/ptm/m/n/10 is cur-rently a sim-ple fall-back
[2363] [2364] [2365]) (boot-pkg.tex [2366]
Chapter 18.
[2367] [2368] [2369] [2370] [2371] [2372] [2373] [2374] [2375] [2376]
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[]\T1/ptm/m/n/10 Where random-number gen-er-a-tion is done in the worker pro-ce
sses, the de-fault be-haviour
[2377]
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[]\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi
-cient boot-strap sim-u-la-tion.
[2378]
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[2380]
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[]\T1/ptm/m/n/10 A vec-tor of char-ac-ter strings rep-re-sent-ing the type of i
n-ter-

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\T1/ptm/m/n/10 vals re-quired. The value should be any sub-set of the val-ues

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\T1/zi4/m/sl/10 c("norm","basic","stud","perc","bca") \T1/ptm/m/n/10 or sim-ply
 \T1/zi4/m/sl/10 "all" \T1/ptm/m/n/10 which will
[2381]
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[]\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est. The de-fa
ult value is
[2382] [2383] [2384] [2385]
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[]\T1/ptm/m/n/10 Rawlings, J.O. (1988) \T1/ptm/m/it/10 Ap-plied Re-gres-sion An
al-y-sis\T1/ptm/m/n/10 . Wadsworth and Brooks/Cole Statis-
[2386] [2387] [2388] [2389] [2390] [2391]
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[]\T1/ptm/m/n/10 The sim-u-la-tion type. Pos-si-ble types are \T1/zi4/m/sl/10 "
ordinary" \T1/ptm/m/n/10 (case re-sam-pling),
[2392] [2393]
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[]\T1/ptm/m/n/10 The length of time (in months) that the res-i-dent spent at Ch
an-ning House.
[2395] [2396] [2397] [2398]
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[]\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est on the ori
g-i-nal data set
[2399]
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[]\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi
-cient boot-strap sim-u-la-tion.
[2400] [2401]
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[]\T1/ptm/m/n/10 The un-bi-ased es-ti-ma-tor uses a mul-ti-plier of \T1/zi4/m/s
l/10 n/((n-1)*(n-2)) \T1/ptm/m/n/10 where \T1/zi4/m/sl/10 n \T1/ptm/m/n/10 is t
he sam-ple

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\T1/ptm/m/n/10 size, if \T1/zi4/m/sl/10 unbiased \T1/ptm/m/n/10 is \T1/zi4/m/sl
/10 FALSE \T1/ptm/m/n/10 then a mul-ti-plier of \T1/zi4/m/sl/10 1/n \T1/ptm/m/n
/10 is used. This is mul-ti-plied by
[2402] [2403] [2404] [2405] [2406] [2407] [2408] [2409] [2410] [2411] [2412]
[2413] [2414] [2415] [2416] [2417] [2418] [2419] [2420] [2421] [2422] [2423]
[2424]
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[]\T1/ptm/m/n/10 The quan-tiles at which the plots are re-quired. The de-fault 
is
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[]\T1/ptm/m/n/10 The in-dex of the statis-tic of in-ter-est within the out-put 
of a call to
[2436] [2437] [2438] [2439]
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[]\T1/ptm/m/n/10 An in-te-ger giv-ing the num-ber of classes to be used in the 
boot-strap

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\T1/ptm/m/n/10 his-togram. The de-fault is the in-te-ger be-tween 10 and 100 cl
os-est to
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[]\T1/ptm/m/n/10 The re-turned value is an ob-ject of class \T1/zi4/m/sl/10 "sa
ddle.distn"\T1/ptm/m/n/10 . See the help file for
[2451] [2452] [2453] [2454] [2455] [2456] [2457] [2458] [2459]
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[]\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sec-ond ar-gu-m
ent ex-pected by
[2460] [2461] [2462] [2463] [2464] [2465] [2466] [2467] [2468] [2469])
(class-pkg.tex [2470]
Chapter 19.
[2471] [2472] [2473] [2474] [2475] [2476] [2477] [2478] [2479] [2480] [2481]
[2482] [2483] [2484] [2485] [2486]) (cluster-pkg.tex
Chapter 20.
[2487] [2488] [2489] [2490] [2491]
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[2493] [2494] [2495] [2496]
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[]\T1/ptm/m/n/10 Setting this to \T1/zi4/m/sl/10 FALSE \T1/ptm/m/n/10 saves mem
-ory (and hence time), but dis-ables
[2497]
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[]\T1/ptm/m/n/10 Kaufman and Rousseeuw (see [][]\T1/zi4/m/sl/10 agnes[][][]\T1/
ptm/m/n/10 ), orig-i-nally. Met-ric \T1/zi4/m/sl/10 "jaccard"\T1/ptm/m/n/10 : K
amil Ko-zlowski
[2498] [2499]
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[]\T1/ptm/m/n/10 list with sil-hou-ette width in-for-ma-tion for the best sam-p
le, see
[2500] [2501]
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[]\T1/ptm/m/n/10 simply cor-re-sponds to the global max-i-mum, i.e., is

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[]\T1/ptm/m/n/10 This, the de-fault, has been pro-posed by Mar-tin Maech-ler in
 2012,
[2502] [2503] [2504]
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[]\T1/ptm/m/n/10 when \T1/zi4/m/sl/10 x \T1/ptm/m/n/10 does not have a \T1/zi4/
m/sl/10 diss \T1/ptm/m/n/10 nor a \T1/zi4/m/sl/10 data \T1/ptm/m/n/10 com-po-ne
nt, e.g., for
[2505] [2506] [2507]
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[2508] [2509]
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[]\T1/ptm/m/n/10 an ob-ject of class \T1/zi4/m/sl/10 "hclust" \T1/ptm/m/n/10 or
 \T1/zi4/m/sl/10 "twins"\T1/ptm/m/n/10 , i.e., typ-i-cally the re-sult of
[2510] [2511] [2512] [2513] [2514] [2515] [2516] [2517]
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[][][]\T1/zi4/m/sl/10 predict.ellipsoid[][][] \T1/ptm/m/n/10 which is also the 
[][]\T1/zi4/m/sl/10 predict[][][] \T1/ptm/m/n/10 method for \T1/zi4/m/sl/10 ell
ipsoid \T1/ptm/m/n/10 ob-jects.
[2518] [2519] [2520] [2521]
Underfull \hbox (badness 6675) in paragraph at lines 2411--2413
[]\T1/ptm/m/n/10 list with sil-hou-ette in-for-ma-tion of the near-est crisp cl
us-ter-ing, see
[2522] [2523] [2524] [2525] [2526] [2527] [2528]
Underfull \hbox (badness 2980) in paragraph at lines 2902--2906
[][][]\T1/zi4/m/sl/10 agnes[][][] \T1/ptm/m/n/10 for back-ground and ref-er-enc
es; [][]\T1/zi4/m/sl/10 pam.object[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 cl
ara[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 daisy[][][]\T1/ptm/m/n/10 , [][]\
T1/zi4/m/sl/10 partition.object[][][]\T1/ptm/m/n/10 ,
[2529] [2530] [2531] [2532] [2533]
Underfull \hbox (badness 1142) in paragraph at lines 3243--3246
[]\T1/ptm/m/n/10 graphical pa-ram-e-ters (see [][]\T1/zi4/m/sl/10 par[][][]\T1/
ptm/m/n/10 ) may also be sup-plied and are passed to
[2534] [2535]
Underfull \hbox (badness 1142) in paragraph at lines 3362--3365
[]\T1/ptm/m/n/10 graphical pa-ram-e-ters (see [][]\T1/zi4/m/sl/10 par[][][]\T1/
ptm/m/n/10 ) may also be sup-plied and are passed to
[2536] [2537] [2538] [2539]
Underfull \hbox (badness 2582) in paragraph at lines 3585--3590
[][][]\T1/zi4/m/sl/10 partition.object[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/1
0 clusplot.partition[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 clusplot.default
[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 pam[][][]\T1/ptm/m/n/10 , [][]\T1/zi
4/m/sl/10 pam.object[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 clara[][][]\T1/p
tm/m/n/10 ,
[2540]
Underfull \hbox (badness 3209) in paragraph at lines 3647--3652
[]\T1/ptm/m/n/10 Note that cur-rently the method func-tion sim-ply calls \T1/zi
4/m/sl/10 plot([][]as.hclust[][][](x),...)\T1/ptm/m/n/10 , which

Underfull \hbox (badness 8019) in paragraph at lines 3647--3652
\T1/ptm/m/n/10 dis-patches to [][]\T1/zi4/m/sl/10 plot.hclust[][][](..)\T1/ptm/
m/n/10 . If more flex-i-ble plots are needed, con-sider \T1/zi4/m/sl/10 xx
[2541] [2542] [2543] [2544]
Underfull \hbox (badness 10000) in paragraph at lines 3939--3941
[]\T1/ptm/m/n/10 a \T1/zi4/m/sl/10 dissimilarity \T1/ptm/m/n/10 ob-ject or a \T
1/zi4/m/sl/10 summary.dissimilarity \T1/ptm/m/n/10 one for
[2545] [2546] [2547] [2548]
Underfull \hbox (badness 2626) in paragraph at lines 4163--4168
[]\T1/ptm/m/n/10 arguments passed [][]\T1/zi4/m/sl/10 barplot[][][]()\T1/ptm/m/
n/10 ; note that the de-fault used to be \T1/zi4/m/sl/10 col =
[2549]
Underfull \hbox (badness 1383) in paragraph at lines 4241--4246
[]\T1/ptm/m/n/10 While \T1/zi4/m/sl/10 silhouette() \T1/ptm/m/n/10 is \T1/ptm/m
/it/10 in-trin-sic \T1/ptm/m/n/10 to the [][]\T1/zi4/m/sl/10 partition[][][] \T
1/ptm/m/n/10 clus-ter-ings, and hence has a (triv-ial)
[2550] [2551] [2552] [2553] [2554] [2555] [2556]
Underfull \hbox (badness 10000) in paragraph at lines 4684--4686
[]\T1/ptm/m/n/10 Sample data set ac-com-pa-ny-ing the ref-er-ence be-low (file 
`\T1/zi4/m/sl/10 xclara.dat\T1/ptm/m/n/10 ' in side
[2557] [2558]) (codetools-pkg.tex
Chapter 21.
[2559] [2560] [2561] [2562] [2563]) (foreign-pkg.tex [2564]
Chapter 22.
[2565] [2566] [2567] [2568] [2569] [2570] [2571] [2572]
Underfull \hbox (badness 10000) in paragraph at lines 506--515
[]\T1/ptm/m/n/10 character: what to do with du-pli-cated value la-bels for dif-
fer-

Underfull \hbox (badness 10000) in paragraph at lines 506--515
\T1/ptm/m/n/10 ent lev-els. For \T1/zi4/m/sl/10 "append" \T1/ptm/m/n/10 (the de
-fault), the first orig-i-nal value

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\T1/ptm/m/n/10 la-bel is kept while fur-ther du-pli-cated la-bels are re-named 
to
[2573]
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 []\T1/zi4/m/n/9 ### Expect lots of warnings as value labels (corresponding to 
R factor labels) are uncomplete,[] 
[2574] [2575] [2576]
Underfull \hbox (badness 10000) in paragraph at lines 813--814

[2577] [2578] [2579] [2580] [2581] [2582] [2583]
Underfull \hbox (badness 10000) in paragraph at lines 1267--1273
[]\T1/ptm/m/n/10 The work for this func-tion is done by \T1/zi4/m/sl/10 foreign
:::writeForeignStata\T1/ptm/m/n/10 ,
[2584] [2585]) (lattice-pkg.tex [2586]
Chapter 23.
[2587] [2588] [2589] [2590] [2591] [2592] [2593] [2594] [2595] [2596] [2597]
[2598] [2599] [2600] [2601] [2602]
Underfull \hbox (badness 1062) in paragraph at lines 1398--1402
\T1/ptm/m/n/10 no-ta-tion for the x and y axes re-spec-tively. See doc-u-men-ta
-tion for
[2603]
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Underfull \hbox (badness 1803) in paragraph at lines 1566--1583
[][][]\T1/zi4/m/sl/10 Lattice[][][] \T1/ptm/m/n/10 for an overview of the pack-
age, as well as [][]\T1/zi4/m/sl/10 barchart.table[][][]\T1/ptm/m/n/10 , [][]\T
1/zi4/m/sl/10 print.trellis[][][]\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 1566--1583
[][]\T1/zi4/m/sl/10 panel.stripplot[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 p
anel.superpose[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 panel.loess[][][]\T1/p
tm/m/n/10 , [][]\T1/zi4/m/sl/10 panel.average[][][]\T1/ptm/m/n/10 , [][]\T1/zi4
/m/sl/10 strip.default[][][]\T1/ptm/m/n/10 ,
[2605] [2606] [2607]
Underfull \hbox (badness 3009) in paragraph at lines 1725--1727
[]\T1/ptm/m/n/10 additional ar-gu-ments passed to [][]\T1/zi4/m/sl/10 xyplot[][
][]\T1/ptm/m/n/10 , which may pass them on to

Underfull \hbox (badness 6808) in paragraph at lines 1755--1759
[]\T1/ptm/m/n/10 graphical ar-gu-ments, which are pro-cessed and even-tu-ally p
assed to
[2608] [2609] [2610] [2611] [2612]
Underfull \hbox (badness 10000) in paragraph at lines 2141--2144
[]\T1/ptm/m/n/10 When \T1/zi4/m/sl/10 breaks \T1/ptm/m/n/10 is un-spec-i-fied, 
the value of
[2613] [2614] [2615] [2616] [2617] [2618] [2619] [2620] [2621] [2622]
Underfull \hbox (badness 2781) in paragraph at lines 2848--2850
[]\T1/ptm/m/n/10 A color ramp spec-i-fi-ca-tion, as in the \T1/zi4/m/sl/10 col.
regions \T1/ptm/m/n/10 ar-gu-ment in
[2623]
Underfull \hbox (badness 2486) in paragraph at lines 2959--2963
[]\T1/ptm/m/n/10 Other use-ful ar-gu-ments are men-tioned in the help page for 
the de-fault panel func-tion
[2624] [2625] [2626] [2627] [2628] [2629] [2630]pdfTeX warning (ext4): destinat
ion with the same identifier (name{Rfn.parallel}) has been already used, duplic
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<to be read again> 
                   \relax 
l.3431 \aliasA{parallel}{B\_08\_splom}{parallel}
                                                 [2631] [2632] [2633] [2634]
[2635] [2636] [2637]
Underfull \hbox (badness 5696) in paragraph at lines 3922--3926
[]\T1/ptm/m/n/10 A pos-si-ble use of this ar-gu-ment is to change the de-fault 
set-tings

Underfull \hbox (badness 10000) in paragraph at lines 3922--3926
\T1/ptm/m/n/10 by spec-i-fy-ing \T1/zi4/m/sl/10 lattice.options(default.theme =
 "col.whitebg")\T1/ptm/m/n/10 .

Underfull \hbox (badness 2435) in paragraph at lines 3922--3926
\T1/ptm/m/n/10 For back-compatibility, this is ini-tially (when lat-tice is loa
ded) set to
[2638] [2639]
Underfull \hbox (badness 1173) in paragraph at lines 4061--4065
[]\T1/ptm/m/n/10 A char-ac-ter string giv-ing the name of a com-po-nent. If un-
spec-i-fied in

Underfull \hbox (badness 3219) in paragraph at lines 4088--4090
[]\T1/ptm/m/n/10 A log-i-cal flag, in-di-cat-ing whether a warn-ing should be i
s-sued when
[2640] [2641] [2642]
Underfull \hbox (badness 3492) in paragraph at lines 4284--4294
[]\T1/ptm/m/n/10 A color spec-i-fi-ca-tion. \T1/zi4/m/sl/10 col \T1/ptm/m/n/10 
is used for com-po-nents \T1/zi4/m/sl/10 "plot.symbol"\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 4309--4312
[]\T1/ptm/m/n/10 fill color, ap-pli-ca-ble for com-po-nents \T1/zi4/m/sl/10 plo
t.symbol\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 plot.polygon\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 4312--4314
[]\T1/ptm/m/n/10 border color, ap-pli-ca-ble for com-po-nents \T1/zi4/m/sl/10 p
lot.polygon \T1/ptm/m/n/10 and
[2643] [2644] [2645] [2646] [2647] [2648] [2649] [2650] [2651] [2652]
Underfull \hbox (badness 6157) in paragraph at lines 5035--5038
[]\T1/zi4/m/sl/10 plot.shingle \T1/ptm/m/n/10 dis-plays the ranges of shin-gles
 via rect-an-gles. \T1/zi4/m/sl/10 print.shingle \T1/ptm/m/n/10 and
[2653] [2654] [2655] [2656] [2657] [2658]
Underfull \hbox (badness 10000) in paragraph at lines 5486--5489
[]\T1/ptm/m/n/10 logical, spec-i-fy-ing whether the la-bels etc should be hor-i
-zon-tal.

Underfull \hbox (badness 5592) in paragraph at lines 5486--5489
\T1/zi4/m/sl/10 horizontal=FALSE \T1/ptm/m/n/10 is use-ful for strips on the le
ft of pan-els us-ing
[2659] [2660] [2661] [2662] [2663]
Underfull \hbox (badness 4805) in paragraph at lines 5846--5850
[]\T1/ptm/m/n/10 logical, whether the view-port be-ing as-signed fo-cus should 
be high-

Underfull \hbox (badness 10000) in paragraph at lines 5857--5864
[]\T1/ptm/m/n/10 For \T1/zi4/m/sl/10 panel.identify.qqmath\T1/ptm/m/n/10 , ex-t
ra pa-ram-e-ters are passed on to

Underfull \hbox (badness 1226) in paragraph at lines 5857--5864
\T1/zi4/m/sl/10 panel.identify\T1/ptm/m/n/10 . For \T1/zi4/m/sl/10 panel.identi
fy\T1/ptm/m/n/10 , ex-tra ar-gu-ments are treated as

Underfull \hbox (badness 2418) in paragraph at lines 5857--5864
\T1/ptm/m/n/10 graph-i-cal pa-ram-e-ters and are used for la-belling. For \T1/z
i4/m/sl/10 trellis.focus

Underfull \hbox (badness 10000) in paragraph at lines 5857--5864
\T1/ptm/m/n/10 and \T1/zi4/m/sl/10 trellis.switchFocus\T1/ptm/m/n/10 , these ar
e used (in com-bi-na-tion with

Underfull \hbox (badness 1259) in paragraph at lines 5857--5864
[][]\T1/zi4/m/sl/10 lattice.options[][][]\T1/ptm/m/n/10 ) for high-light-ing th
e cho-sen view-port if so re-quested.
[2664] [2665] [2666] [2667]
Underfull \hbox (badness 4242) in paragraph at lines 6157--6162
[]\T1/ptm/m/n/10 Graphical pa-ram-e-ters for the bars. By de-fault, the trel-li
s pa-ram-e-

Underfull \hbox (badness 2529) in paragraph at lines 6157--6162
\T1/ptm/m/n/10 ter \T1/zi4/m/sl/10 plot.polygon \T1/ptm/m/n/10 is used if there
 is no group-ing vari-able, oth-er-wise
[2668] [2669]
Underfull \hbox (badness 2310) in paragraph at lines 6273--6278
[]\T1/ptm/m/n/10 Creates Box and Whisker plot of \T1/zi4/m/sl/10 x \T1/ptm/m/n/
10 for ev-ery level of \T1/zi4/m/sl/10 y \T1/ptm/m/n/10 (or the other way round
 if
[2670] [2671] [2672] [2673] [2674] [2675] [2676] [2677] [2678] [2679] [2680]
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\T1/ptm/m/n/10 to know what ar-gu-ments this func-tion is passed when called. U
se
[2681] [2682] [2683] [2684]
Underfull \hbox (badness 2012) in paragraph at lines 7326--7329
[]\T1/ptm/m/n/10 Further ar-gu-ments, of-ten graph-i-cal pa-ram-e-ters, even-tu
-ally passed on to
[2685] [2686]
Underfull \hbox (badness 3333) in paragraph at lines 7498--7500
[]\T1/ptm/m/n/10 default colours are ob-tained from \T1/zi4/m/sl/10 plot.symbol
 \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 plot.line \T1/ptm/m/n/10 us-ing
[2687] [2688] [2689]
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[2691] [2692]
Underfull \hbox (badness 1436) in paragraph at lines 7912--7918
[]\T1/ptm/m/n/10 A log-i-cal flag de-ter-min-ing whether the de-fault graph-i-c
al pa-ram-e-ters for
[2693] [2694] [2695] [2696] [2697] [2698] [2699] [2700]
Underfull \hbox (badness 10000) in paragraph at lines 8470--8473
[]\T1/ptm/m/n/10 Extra ar-gu-ments. Passed down to \T1/zi4/m/sl/10 panel.superp
ose \T1/ptm/m/n/10 from
[2701]
Underfull \hbox (badness 1092) in paragraph at lines 8516--8518
[]\T1/ptm/m/n/10 Deepayan Sarkar \T1/zi4/m/sl/10 <Deepayan.Sarkar@R-project.org
> \T1/ptm/m/n/10 (\T1/zi4/m/sl/10 panel.superpose.2 \T1/ptm/m/n/10 orig-i-nally
 con-
[2702] [2703]
Underfull \hbox (badness 3895) in paragraph at lines 8677--8680
[]\T1/ptm/m/n/10 details of his-togram cal-cu-la-tions. \T1/zi4/m/sl/10 type \T
1/ptm/m/n/10 has a dif-fer-ent mean-ing in
[2704]
Underfull \hbox (badness 1515) in paragraph at lines 8753--8757
[]\T1/ptm/m/n/10 numeric vec-tor of length two, rep-re-sent-ing prob-a-bil-i-ti
es. If used with
[2705] [2706]
Underfull \hbox (badness 6316) in paragraph at lines 8859--8864
[]\T1/ptm/m/n/10 which packet (counted ac-cord-ing to the packet or-der, de-scr
ibed in

Underfull \hbox (badness 5908) in paragraph at lines 8876--8879
[]\T1/ptm/m/n/10 list, sim-i-lar to those pro-duced by \T1/zi4/m/sl/10 xscale.c
omponents.default \T1/ptm/m/n/10 and
[2707] [2708] [2709] [2710]
Overfull \hbox (1.94879pt too wide) in paragraph at lines 9164--9168
[]\T1/ptm/m/n/10 returns a list with sev-eral com-po-nents, in-clud-ing \T1/zi4
/m/sl/10 left,right,left.name,right.name,condition
[2711] [2712] [2713] [2714] [2715] [2716] [2717]
Underfull \hbox (badness 2310) in paragraph at lines 9622--9626
[]\T1/ptm/m/n/10 Factor with lev-els \T1/zi4/m/sl/10 "Svansota"\T1/ptm/m/n/10 ,
 \T1/zi4/m/sl/10 "No. 462"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "Manchuria"\T1/ptm/m
/n/10 , \T1/zi4/m/sl/10 "No. 475"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "Velvet"\T1/p
tm/m/n/10 ,

Underfull \hbox (badness 3701) in paragraph at lines 9627--9630
[]\T1/ptm/m/n/10 Factor with 6 lev-els: \T1/zi4/m/sl/10 "Grand Rapids"\T1/ptm/m
/n/10 , \T1/zi4/m/sl/10 "Duluth"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "University Fa
rm"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "Morris"\T1/ptm/m/n/10 ,
[2718] [2719] [2720]pdfTeX warning (ext4): destination with the same identifier
 (name{Rfn.melanoma}) has been already used, duplicate ignored
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                   \relax 
l.9853 \aliasA{melanoma}{H\_melanoma}{melanoma}
                                                [2721] [2722] [2723]
Underfull \hbox (badness 4144) in paragraph at lines 10077--10080
[]\T1/ptm/m/n/10 Rural Health Re-form Pol-icy Re-search Cen-ter. _Ex-plor-ing R
u-ral and Ur-ban Mor-tal-

Underfull \hbox (badness 1509) in paragraph at lines 10077--10080
\T1/ptm/m/n/10 ity Dif-fer-ences_, Au-gust 2015 Bethesda, MD. [][]$\T1/zi4/m/sl
/10 https : / / ruralhealth . und . edu / projects /
[2724] [2725]) (mgcv-pkg.tex [2726]
Chapter 24.
[2727] [2728] [2729]
Underfull \hbox (badness 1142) in paragraph at lines 171--175
\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from

Underfull \hbox (badness 1043) in paragraph at lines 196--201
\T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known 
scale.
[2730] [2731] [2732] [2733]
Underfull \hbox (badness 10000) in paragraph at lines 365--372
[][][]\T1/zi4/m/sl/10 mgcv.parallel[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 m
gcv-package[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 gamObject[][][]\T1/ptm/m/
n/10 , [][]\T1/zi4/m/sl/10 gam.models[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10
 smooth.terms[][][]\T1/ptm/m/n/10 ,

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[][]\T1/zi4/m/sl/10 linear.functional.terms[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m
/sl/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 te[][][] [][]predict.gam[][]
[]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 plot.gam[][][]\T1/ptm/m/n/10 , [][]\T1/z
i4/m/sl/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 gam.side[][][]
\T1/ptm/m/n/10 ,
[2734] [2735] [2736] [2737] [2738] [2739] [2740]
Underfull \hbox (badness 1158) in paragraph at lines 753--755
[]\T1/ptm/m/n/10 Choosing the ba-sis di-men-sion, and check-ing the choice, whe
n us-ing pe-nal-ized re-gres-sion
[2741]
Underfull \hbox (badness 1259) in paragraph at lines 816--817
[]\T1/ptm/m/n/10 Wood, S.N. (2017) Gen-er-al-ized Ad-di-tive Mod-els: An In-tro
-duc-tion with R (2nd edi-tion).
[2742]
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[2744] [2745] [2746] [2747] [2748] [2749] [2750] [2751] [2752] [2753] [2754]
[2755] [2756] [2757] [2758] [2759] [2760] [2761] [2762] [2763] [2764] [2765]
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\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
[2766]
Underfull \hbox (badness 1043) in paragraph at lines 2265--2270
\T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known 
scale.
[2767] [2768] [2769] [2770] [2771]
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[2786] [2787]
Underfull \hbox (badness 10000) in paragraph at lines 3584--3588
[]\T1/ptm/m/n/10 Random ef-fects can be added to \T1/zi4/m/sl/10 gam \T1/ptm/m/
n/10 mod-els us-ing \T1/zi4/m/sl/10 s(...,bs="re") \T1/ptm/m/n/10 terms (see
[2788] [2789]
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[2791] [2792]
Underfull \hbox (badness 1184) in paragraph at lines 3870--3874
[]\T1/ptm/m/n/10 list of the square root penal-ties: last en-try is root of fix
ed penalty, if
[2793] [2794] [2795] [2796] [2797] [2798] [2799] [2800] [2801] [2802] [2803]
[2804]
Underfull \hbox (badness 1142) in paragraph at lines 4591--4595
\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
[2805]
Underfull \hbox (badness 1231) in paragraph at lines 4692--4694
[]\T1/zi4/m/sl/10 gamm \T1/ptm/m/n/10 per-forms poorly with bi-nary data, since
 it uses PQL. It is bet-ter to use \T1/zi4/m/sl/10 gam \T1/ptm/m/n/10 with
[2806] [2807] [2808]
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[2810] [2811]
Underfull \hbox (badness 2181) in paragraph at lines 5064--5065
[]\T1/ptm/m/n/10 one sided for-mula con-tain-ing vari-ables needed for pre-dic-
tion, used by
[2812] [2813] [2814] [2815] [2816] [2817] [2818]
Underfull \hbox (badness 10000) in paragraph at lines 5453--5454
[]\T1/ptm/m/n/10 A pre-fit gam ob-ject, as pro-duced by \T1/zi4/m/sl/10 gam(...
,fit=FALSE) \T1/ptm/m/n/10 or
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[2822] [2823] [2824] [2825] [2826] [2827]
Underfull \hbox (badness 1142) in paragraph at lines 5956--5960
\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
[2828] [2829] [2830]
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[2832] [2833] [2834]
Underfull \hbox (badness 1087) in paragraph at lines 6326--6327
[]\T1/ptm/m/n/10 If \T1/zi4/m/sl/10 rho \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 thet
a \T1/ptm/m/n/10 were sup-plied then deriva-tives are w.r.t. these. In this cas
e, and if
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Underfull \vbox (badness 10000) has occurred while \output is active [2839]
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Underfull \hbox (badness 1242) in paragraph at lines 7272--7273
[]\T1/ptm/m/n/10 Development of mgcv ver-sion 1.8 was part funded by EP-SRC gra
nts EP/K005251/1 and
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Underfull \hbox (badness 6001) in paragraph at lines 7912--7914
[]\T1/ptm/m/n/10 Simon N. Wood \T1/zi4/m/sl/10 <simon.wood@r-project.org> \T1/p
tm/m/n/10 mod-i-fied from Ven-ables and Rip-ley's
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Underfull \hbox (badness 1038) in paragraph at lines 8661--8664
[]\T1/ptm/m/n/10 The fol-low-ing func-tions are pro-vided: \T1/zi4/m/sl/10 Dim.
pdIndot\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 coef.pdIdnot\T1/ptm/m/n/10 , \T1/zi4/m/
sl/10 corMatrix.pdIdnot\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 8661--8664
\T1/zi4/m/sl/10 logDet.pdIdnot\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 pdConstruct.pdId
not\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 pdFactor.pdIdnot\T1/ptm/m/n/10 , \T1/zi4/m/
sl/10 pdMatrix.pdIdnot\T1/ptm/m/n/10 ,
[2874]
Underfull \hbox (badness 10000) in paragraph at lines 8717--8720
[]\T1/ptm/m/n/10 These func-tions (\T1/zi4/m/sl/10 pdTens\T1/ptm/m/n/10 , \T1/z
i4/m/sl/10 pdConstruct.pdTens\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 pdFactor.pdTens\T
1/ptm/m/n/10 , \T1/zi4/m/sl/10 pdMatrix.pdTens\T1/ptm/m/n/10 ,
[2875] [2876] [2877] [2878] [2879] [2880] [2881] [2882] [2883] [2884] [2885]
Underfull \hbox (badness 1852) in paragraph at lines 9387--9390
[]\T1/ptm/m/n/10 To fa-cil-i-tate plot-ting with [][]\T1/zi4/m/sl/10 termplot[]
[][]\T1/ptm/m/n/10 , if \T1/zi4/m/sl/10 object \T1/ptm/m/n/10 pos-sesses an at-
tribute \T1/zi4/m/sl/10 "para.only" \T1/ptm/m/n/10 and
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Underfull \hbox (badness 1852) in paragraph at lines 9551--9554
[]\T1/ptm/m/n/10 To fa-cil-i-tate plot-ting with [][]\T1/zi4/m/sl/10 termplot[]
[][]\T1/ptm/m/n/10 , if \T1/zi4/m/sl/10 object \T1/ptm/m/n/10 pos-sesses an at-
tribute \T1/zi4/m/sl/10 "para.only" \T1/ptm/m/n/10 and
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[2892]
Underfull \hbox (badness 1205) in paragraph at lines 9780--9782
[]\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a
tes at which

Underfull \hbox (badness 2689) in paragraph at lines 9780--9782
\T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are 
as for

Underfull \hbox (badness 1975) in paragraph at lines 9786--9791
[]\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f
i-ca-tion ob-jects of class
[2893]
Underfull \hbox (badness 1205) in paragraph at lines 9870--9872
[]\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a
tes at which

Underfull \hbox (badness 2689) in paragraph at lines 9870--9872
\T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are 
as for
[2894] [2895] [2896]
Underfull \hbox (badness 1253) in paragraph at lines 10069--10071
[]\T1/ptm/m/n/10 Note that the op-ti-mized smooth-ing pa-ram-e-ter se-lec-tion 
cri-te-rion re-ported is one of GCV,
[2897] [2898] [2899] [2900]
Underfull \hbox (badness 4792) in paragraph at lines 10255--10258
[]\T1/ptm/m/n/10 Alternatively, but less straight-for-wardly, the \T1/zi4/m/sl/
10 paraPen \T1/ptm/m/n/10 ar-gu-ment to [][]\T1/zi4/m/sl/10 gam[][][] \T1/ptm/m
/n/10 can be used:

Underfull \hbox (badness 10000) in paragraph at lines 10255--10258
\T1/ptm/m/n/10 see [][]\T1/zi4/m/sl/10 gam.models[][][]\T1/ptm/m/n/10 . If smoo
th-ing pa-ram-e-ter es-ti-ma-tion is by ML or REML (e.g.
[2901]
Underfull \hbox (badness 10000) in paragraph at lines 10350--10353
[]\T1/ptm/m/n/10 the type of resid-u-als wanted. Usu-ally one of \T1/zi4/m/sl/1
0 "deviance"\T1/ptm/m/n/10 ,
[2902] [2903] [2904] [2905] [2906] [2907] [2908] [2909] [2910] [2911] [2912]
Underfull \hbox (badness 3861) in paragraph at lines 10978--10981
[]\T1/ptm/m/n/10 INTERNAL rou-tine to ap-ply ini-tial Sl re-parameterization to
 model ma-trix X, or, if
[2913] [2914]
Underfull \hbox (badness 1320) in paragraph at lines 11084--11089
\T1/ptm/m/n/10 and \T1/zi4/m/sl/10 b.orig = D*b.repara \T1/ptm/m/n/10 (where \T
1/zi4/m/sl/10 b.orig \T1/ptm/m/n/10 is the orig-i-nal pa-ram-e-ter vec-tor). If
 ma-
[2915] [2916]
Underfull \hbox (badness 1975) in paragraph at lines 11190--11195
[]\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f
i-ca-tion ob-jects of class
[2917]
Underfull \hbox (badness 1762) in paragraph at lines 11279--11291
\T1/ptm/m/n/10 plate re-gres-sion splines: see [][]\T1/zi4/m/sl/10 tprs[][][]\T
1/ptm/m/n/10 ); \T1/zi4/m/sl/10 ts.smooth.spec \T1/ptm/m/n/10 (thin plate re-gr
es-sion splines with
[2918] [2919] [2920]
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Underfull \hbox (badness 7667) in paragraph at lines 11491--11497
[][][]\T1/zi4/m/sl/10 gam[][][] \T1/ptm/m/n/10 can use adap-tive smooths of one
 or two vari-ables, spec-i-fied via terms like

Underfull \hbox (badness 10000) in paragraph at lines 11532--11533
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2922] [2923] [2924] [2925] [2926] [2927]
Underfull \hbox (badness 10000) in paragraph at lines 11808--11810
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2928] [2929]
Underfull \hbox (badness 10000) in paragraph at lines 11936--11937
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2930] [2931]
Underfull \hbox (badness 1436) in paragraph at lines 12074--12081
\T1/ptm/m/n/10 nest-ing of the smooth within the fac-tor. Note how-ever that: i
) \T1/zi4/m/sl/10 gamm \T1/ptm/m/n/10 only al-lows one
[2932] [2933]
Underfull \hbox (badness 10000) in paragraph at lines 12168--12169
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2934] [2935] [2936] [2937] [2938] [2939] [2940] [2941] [2942] [2943]
Underfull \hbox (badness 10000) in paragraph at lines 12754--12760
[]\T1/ptm/m/n/10 A smooth spec-i-fi-ca-tion ob-ject as pro-duced by a

Underfull \hbox (badness 1292) in paragraph at lines 12754--12760
\T1/zi4/m/sl/10 s(...,bs="so",xt=list(bnd=bnd,...)) \T1/ptm/m/n/10 term in a \T
1/zi4/m/sl/10 gam \T1/ptm/m/n/10 for-mula. Note
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Underfull \vbox (badness 10000) has occurred while \output is active [2948]
[2949]
Underfull \hbox (badness 10000) in paragraph at lines 13097--13098
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2950] [2951] [2952] [2953]
Underfull \hbox (badness 3895) in paragraph at lines 13358--13361
[][][]\T1/zi4/m/sl/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths of any
 num-ber of vari-ables, spec-i-fied via terms like
[2954]
Underfull \hbox (badness 10000) in paragraph at lines 13403--13405
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2955] [2956] [2957] [2958]
Underfull \hbox (badness 1371) in paragraph at lines 13620--13626
[]\T1/zi4/m/sl/10 bs="ad" \T1/ptm/m/n/10 Uni-vari-ate and bi-vari-ate adap-tive
 smooths are avail-able (see

Underfull \hbox (badness 10000) in paragraph at lines 13660--13664
[][][]\T1/zi4/m/sl/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 te[][][]\T1/p
tm/m/n/10 , [][]\T1/zi4/m/sl/10 t2[][][] [][]tprs[][][]\T1/ptm/m/n/10 ,[][]\T1/
zi4/m/sl/10 Duchon.spline[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 cubic.regre
ssion.spline[][][]\T1/ptm/m/n/10 ,[][]\T1/zi4/m/sl/10 p.spline[][][]\T1/ptm/m/n
/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 13660--13664
[][]\T1/zi4/m/sl/10 mrf[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 soap[][][]\T1
/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 Spherical.Spline[][][]\T1/ptm/m/n/10 , [][]\T
1/zi4/m/sl/10 adaptive.smooth[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 user.de
fined.smooth[][][]\T1/ptm/m/n/10 ,

Overfull \hbox (46.8009pt too wide) in paragraph at lines 13660--13664
[][]\T1/zi4/m/sl/10 smooth.construct.re.smooth.spec[][][]\T1/ptm/m/n/10 , [][]\
T1/zi4/m/sl/10 smooth.construct.gp.smooth.spec[][][]\T1/ptm/m/n/10 ,[][]\T1/zi4
/m/sl/10 factor.smooth.interaction[][][] 
[2959] [2960] [2961] [2962]
Underfull \hbox (badness 2326) in paragraph at lines 13865--13872
[]\T1/ptm/m/n/10 These wrap-per func-tions ex-ist to al-low smooths spec-i-fied
 us-ing [][]\T1/zi4/m/sl/10 smooth.construct[][][] \T1/ptm/m/n/10 and
[2963]
Underfull \hbox (badness 2158) in paragraph at lines 13950--13950
[]\T1/ptm/m/it/10 Extract smooth-ing pa-ram-e-ter es-ti-ma-tor co-vari-ance ma-
trix from
[2964] [2965] [2966] [2967] [2968] [2969] [2970] [2971] [2972] [2973] [2974]
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[2976] [2977] [2978] [2979] [2980] [2981] [2982] [2983] [2984] [2985] [2986]
[2987] [2988] [2989] [2990]
Underfull \hbox (badness 1796) in paragraph at lines 15594--15597
[]\T1/ptm/m/n/10 other op-tions to pass on to [][]\T1/zi4/m/sl/10 persp[][][]\T
1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 image[][][] \T1/ptm/m/n/10 or [][]\T1/zi4/m/
sl/10 contour[][][]\T1/ptm/m/n/10 . In par-tic-u-lar
[2991] [2992] [2993] [2994] [2995] [2996]) (nlme-pkg.tex
Chapter 25.
[2997] [2998] [2999] [3000] [3001] [3002] [3003] [3004] [3005] [3006] [3007]
[3008] [3009] [3010] [3011] [3012] [3013] [3014] [3015] [3016] [3017] [3018]
[3019] [3020] [3021] [3022] [3023] [3024] [3025] [3026]
Underfull \hbox (badness 2875) in paragraph at lines 1994--2000
[]\T1/ptm/m/n/10 an op-tional log-i-cal value or one-sided for-mula, in-di-cat-
ing a co-vari-ate

Underfull \hbox (badness 1466) in paragraph at lines 1994--2000
\T1/ptm/m/n/10 that is in-ner to the \T1/zi4/m/sl/10 displayLevel \T1/ptm/m/n/1
0 group-ing fac-tor. If equal to \T1/zi4/m/sl/10 TRUE\T1/ptm/m/n/10 ,
[3027] [3028] [3029] [3030]
Underfull \hbox (badness 10000) in paragraph at lines 2256--2262
[][][]\T1/zi4/m/sl/10 ACF.lme[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 corARMA
[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 corClasses[][][]\T1/ptm/m/n/10 , [][
]\T1/zi4/m/sl/10 Dim.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 Initi
alize.corStruct[][][]\T1/ptm/m/n/10 ,
[3031] [3032] [3033] [3034] [3035] [3036] [3037] [3038] [3039] [3040] [3041]
[3042] [3043] [3044] [3045] [3046] [3047] [3048] [3049] [3050] [3051] [3052]
[3053] [3054] [3055] [3056] [3057] [3058] [3059] [3060] [3061] [3062] [3063]
Underfull \hbox (badness 1067) in paragraph at lines 4414--4419
\T1/ptm/m/n/10 ma-trix), \T1/zi4/m/sl/10 fitted \T1/ptm/m/n/10 (fit-ted val-ues
), and \T1/zi4/m/sl/10 residuals \T1/ptm/m/n/10 (resid-u-als). De-faults to
[3064] [3065] [3066] [3067] [3068] [3069] [3070] [3071] [3072] [3073] [3074]
[3075]
Underfull \hbox (badness 10000) in paragraph at lines 5160--5164
[][][]\T1/zi4/m/sl/10 getCovariate.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/
m/sl/10 getCovariate.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 getCo
variate.varFunc[][][]\T1/ptm/m/n/10 ,
[3076] [3077] [3078] [3079] [3080] [3081] [3082]
Underfull \hbox (badness 10000) in paragraph at lines 5592--5595
[][][]\T1/zi4/m/sl/10 getGroupsFormula[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/1
0 getGroups.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 getGroups.gls[
][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 getGroups.lmList[][][]\T1/ptm/m/n/10 
,
[3083] [3084] [3085] [3086] [3087] [3088] [3089]
Underfull \hbox (badness 10000) in paragraph at lines 5973--5978
[][][]\T1/zi4/m/sl/10 getGroupsFormula.gls[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/
sl/10 getGroupsFormula.lmList[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 getGrou
psFormula.lme[][][]\T1/ptm/m/n/10 ,
[3090] [3091] [3092] [3093]
Underfull \hbox (badness 1490) in paragraph at lines 6243--6254
[][][]\T1/zi4/m/sl/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 glsC
ontrol[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 glsObject[][][]\T1/ptm/m/n/10 
, [][]\T1/zi4/m/sl/10 glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 plot.
gls[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 predict.gls[][][]\T1/ptm/m/n/10 ,
 [][]\T1/zi4/m/sl/10 qqnorm.gls[][][]\T1/ptm/m/n/10 ,
[3094]
Underfull \hbox (badness 10000) in paragraph at lines 6307--6309
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
[3095] [3096] [3097] [3098] [3099] [3100]
Underfull \hbox (badness 10000) in paragraph at lines 6721--6723
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
[3101] [3102] [3103] [3104]
Underfull \hbox (badness 10000) in paragraph at lines 6994--7001
[][][]\T1/zi4/m/sl/10 formula[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 gapply[
][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 gsummary[][][]\T1/ptm/m/n/10 , [][]\T
1/zi4/m/sl/10 lme[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 plot.nffGroupedData
[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 plot.nfnGroupedData[][][]\T1/ptm/m/n
/10 ,
[3105] [3106] [3107] [3108]
Underfull \hbox (badness 10000) in paragraph at lines 7254--7259
[][][]\T1/zi4/m/sl/10 Initialize.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/
sl/10 Initialize.lmeStruct[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 Initialize
.glsStruct[][][]\T1/ptm/m/n/10 ,
[3109] [3110] [3111] [3112] [3113] [3114] [3115] [3116] [3117] [3118] [3119]
[3120] [3121] [3122] [3123] [3124] [3125] [3126] [3127]
Underfull \hbox (badness 10000) in paragraph at lines 8521--8523
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
[3128]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sig
ma}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.8572 \aliasA{sigma}{lmeObject}{sigma}
                                        [3129] [3130] [3131] [3132]
Underfull \hbox (badness 10000) in paragraph at lines 8802--8809
[][][]\T1/zi4/m/sl/10 lm[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 lme.lmList[]
[][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 plot.lmList[][][]\T1/ptm/m/n/10 , [][]
\T1/zi4/m/sl/10 pooledSD[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 predict.lmLi
st[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 residuals.lmList[][][]\T1/ptm/m/n/
10 ,
[3133] [3134] [3135] [3136] [3137] [3138] [3139] [3140]
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[][][]\T1/zi4/m/sl/10 lme[][][]\T1/ptm/m/n/10 ,[][]\T1/zi4/m/sl/10 gls[][][]\T1
/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 logLik.corStruct[][][]\T1/ptm/m/n/10 , [][]\T
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.lmeStruct[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 logLik.lmList[][][]\T1/ptm
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[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a two-sided for-mula o
f the form
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e.nlsList[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 nlmeObject[][][]\T1/ptm/m/n
/10 , [][]\T1/zi4/m/sl/10 nlsList[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 nlm
eStruct[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 pdClasses[][][]\T1/ptm/m/n/10
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[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
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[]\T1/ptm/m/n/10 an op-tional nu-meric vec-tor with the lim-its for the y-axis.
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\T1/ptm/m/n/10 ma-trix), \T1/zi4/m/sl/10 fitted \T1/ptm/m/n/10 (fit-ted val-ues
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\T1/zi4/m/sl/10 Symmetry" \T1/ptm/m/n/10 for \T1/zi4/m/sl/10 pdCompSymm\T1/ptm/
m/n/10 , \T1/zi4/m/sl/10 "Diagonal" \T1/ptm/m/n/10 for \T1/zi4/m/sl/10 pdDiag\T
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stant plus power of covariate" \T1/ptm/m/n/10 for \T1/zi4/m/sl/10 varConstPower
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[][][]\T1/zi4/m/sl/10 Variogram.corExp[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/1
0 Variogram.corGaus[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 Variogram.corLin[
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[][]\T1/zi4/m/sl/10 Variogram.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl
/10 Variogram.corSpher[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 Variogram.defa
ult[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 Variogram.gls[][][]\T1/ptm/m/n/10
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[][][]\T1/zi4/m/sl/10 corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 Vari
ogram[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 Variogram.default[][][]\T1/ptm/
m/n/10 , [][]\T1/zi4/m/sl/10 Variogram.corExp[][][]\T1/ptm/m/n/10 , [][]\T1/zi4
/m/sl/10 Variogram.corGaus[][][]\T1/ptm/m/n/10 ,
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l.326 ... Myelogenous Leukemia survival data}{aml}
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[]\T1/ptm/m/n/10 F.J. Anscombe (1949). Trans-for-ma-tions of Pois-son, bi-no-mi
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fbeta"\T1/ptm/m/n/10 ,
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l.5866 ...ata from a soldering experiment}{solder}
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[]\T1/ptm/m/n/10 survival times, for time de-pen-dent pre-dic-tion. It gives th
e time range
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("C:\Program Files\MiKTeX 2.9\tex/latex/inconsolata\t1zi4.fd") [1] [2] [3]
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[50] [1] [2] (base-pkg.tex
Chapter 1.
[3] [4]
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[]\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber \T1/zi4/m/n/10 x \T1
/ptm/m/n/10 such that \T1/zi4/m/n/10 1 -x != 1\T1/ptm/m/n/10 . It

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\T1/ptm/m/n/10 equals \T1/zi4/m/n/10 double.base ^ double.neg.ulp.digits \T1/pt
m/m/n/10 if \T1/zi4/m/n/10 double.base

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\T1/ptm/m/n/10 is 2 or \T1/zi4/m/n/10 double.rounding \T1/ptm/m/n/10 is 0; oth-
er-wise, it is \T1/zi4/m/n/10 (double.base

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\T1/zi4/m/n/10 ^ double.neg.ulp.digits) / 2\T1/ptm/m/n/10 . Nor-mally \T1/zi4/m
/n/10 1.110223e-16\T1/ptm/m/n/10 . As

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\T1/zi4/m/n/10 double.neg.ulp.digits \T1/ptm/m/n/10 is bounded be-low by \T1/zi
4/m/n/10 -(double.digits + 3)\T1/ptm/m/n/10 ,
[5] [6]
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[]\T1/ptm/m/n/10 character string, the pre-ferred set-ting for [][]\T1/zi4/m/n/
10 options[][][]("pkgType")\T1/ptm/m/n/10 . Val-ues
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[]\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T
1/zi4/m/n/10 insertions\T1/ptm/m/n/10 ',
[11] [12] ("C:\Program Files\MiKTeX 2.9\tex/latex/inconsolata\ts1zi4.fd")
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[]\T1/ptm/m/n/10 If the calls to \T1/zi4/m/n/10 FUN \T1/ptm/m/n/10 re-turn vec-
tors of dif-fer-ent lengths, \T1/zi4/m/n/10 apply \T1/ptm/m/n/10 re-turns a lis
t of length
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 []\T1/zi4/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen
t-date-and-times-in-MATLAB.html)[] 
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[]\T1/ptm/m/n/10 The val-ues of the splits can also be ob-tained (less ef-fi-ci
ently) by

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[][][]\T1/zi4/m/n/10 apply[][][] \T1/ptm/m/n/10 al-ways sim-pli-fies com-mon le
ngth re-sults, so at-tempt-ing to split via

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\T1/zi4/m/n/10 apply(x,MARGIN,identity) \T1/ptm/m/n/10 does not work (as it sim
-ply gives \T1/zi4/m/n/10 x\T1/ptm/m/n/10 ). By chain-ing \T1/zi4/m/n/10 asplit

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[]\T1/ptm/m/n/10 The num-ber of lines printed for the de-parsed call can be lim
-ited by set-ting
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 []   \T1/zi4/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...)
, recursive=recursive) 
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor, or an ob-ject that can be co-erced to c
har-ac-ter by
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 []\T1/zi4/m/n/9 stopifnot(is.na(NpNA), is.na(NA_complex_), is.na(Re(NA_complex
_)), is.na(Im(NA_complex_)))[] 
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Overfull \hbox (46.35893pt too wide) in paragraph at lines 6574--6576
[]\T1/ptm/m/n/10 character string, par-tially matched to \T1/zi4/m/n/10 c("defa
ult","internal","wininet","libcurl")\T1/ptm/m/n/10 : 
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[]\T1/ptm/m/n/10 A note on `\T1/zi4/m/n/10 file://\T1/ptm/m/n/10 ' URLs. The mo
st gen-eral form (from RFC1738) is
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[]\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.0.0 the en-cod-ing \
T1/zi4/m/n/10 "UTF-8-BOM" \T1/ptm/m/n/10 is ac-cepted for read-ing and will re-


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\T1/ptm/m/n/10 move a Byte Or-der Mark if present (which it of-ten is for files
 and web-pages gen-er-

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\T1/ptm/m/n/10 ated by Mi-crosoft ap-pli-ca-tions). If a BOM is re-quired (it i
s not rec-om-mended) when

Underfull \hbox (badness 1831) in paragraph at lines 6904--6910
\T1/ptm/m/n/10 writ-ing it should be writ-ten ex-plic-itly, e.g. by \T1/zi4/m/n
/10 writeChar("\ufeff",con,eos = NULL) \T1/ptm/m/n/10 or
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Underfull \hbox (badness 1077) in paragraph at lines 7242--7248
[]\T1/ptm/m/n/10 A length-one log-i-cal vec-tor that is not \T1/zi4/m/n/10 NA\T
1/ptm/m/n/10 . Con-di-tions of length greater

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\T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the 
first el-e-
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Underfull \hbox (badness 2096) in paragraph at lines 7583--7587
\T1/zi4/m/n/10 status _ codes$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https
 : / / en . wikipedia . org / wiki / List _ of _ FTP _ server _ return _ codes$
[][]\T1/ptm/m/n/10 .
[111] [112]
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[][][]\T1/zi4/m/n/10 split[][][] \T1/ptm/m/n/10 for split-ting a vari-able ac-c
ord-ing to a group fac-tor; [][]\T1/zi4/m/n/10 factor[][][]\T1/ptm/m/n/10 , [][
]\T1/zi4/m/n/10 tabulate[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 table[][][]\T
1/ptm/m/n/10 ,
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[][][]\T1/zi4/m/n/10 I[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 plot.data.frame
[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 print.data.frame[][][]\T1/ptm/m/n/10 
, [][]\T1/zi4/m/n/10 row.names[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 names[]
[][] \T1/ptm/m/n/10 (for the col-umn names),
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[]\T1/ptm/m/n/10 A few times have spe-cific is-sues. First, the leap sec-onds a
re ig-nored, and real times

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\T1/ptm/m/n/10 there is a prob-lem in the POSIX/C99 stan-dard with \T1/zi4/m/n/
10 "1969-12-31 23:59:59 UTC"\T1/ptm/m/n/10 , which

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\T1/ptm/m/n/10 is \T1/zi4/m/n/10 -1 \T1/ptm/m/n/10 in cal-en-dar time and that 
value is on those OSes also used as an er-ror code.
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[]\T1/ptm/m/n/10 If true, [][]\T1/zi4/m/n/10 list[][][]\T1/ptm/m/n/10 s and ato
mic vec-tors with non-[][]\T1/zi4/m/n/10 NA[][][] \T1/ptm/m/n/10 names (see [][
]\T1/zi4/m/n/10 names[][][]\T1/ptm/m/n/10 ) are de-
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\T1/zi4/m/n/10 754-[]2008$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/n/10 https : / / 
en . wikipedia . org / wiki / Double _ precision$[][]\T1/ptm/m/n/10 , [][]$\T1/
zi4/m/n/10 https : / / en . wikipedia .
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[]\T1/ptm/m/n/10 For the de-fault meth-ods, and when-ever there are equiv-a-len
t method def-i-ni-tions for

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\T1/zi4/m/n/10 duplicated \T1/ptm/m/n/10 and \T1/zi4/m/n/10 anyDuplicated\T1/pt
m/m/n/10 , \T1/zi4/m/n/10 anyDuplicated(x,...) \T1/ptm/m/n/10 is a ``gen-er-al-
ized'' short-cut for
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[]\T1/ptm/m/n/10 When eval-u-at-ing ex-pres-sions in a data frame that has been
 passed as an ar-gu-ment

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\T1/ptm/m/n/10 to a func-tion, the rel-e-vant en-clo-sure is of-ten the caller'
s en-vi-ron-ment, i.e., one needs
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[]\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is
 done: see
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[][][]\T1/zi4/m/n/10 Sys.readlink[][][] \T1/ptm/m/n/10 to find out about sym-bo
lic links, [][]\T1/zi4/m/n/10 files[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 fi
le.access[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files[][][]\T1/ptm/m/n/
10 , and

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[]\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as \T1/zi4/m
/n/10 PATH \T1/ptm/m/n/10 and \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 with \T1/zi4
/m/n/10 fsep =
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[][][]\T1/zi4/m/n/10 files[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files[
][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 help[][][]\T1/ptm/m/n/10 ; [][]\T1/zi4
/m/n/10 RShowDoc[][][] \T1/ptm/m/n/10 call \T1/zi4/m/n/10 file.show() \T1/ptm/m
/n/10 for \T1/zi4/m/n/10 type = "text"\T1/ptm/m/n/10 . Con-sider
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[]\T1/ptm/m/n/10 character vec-tors, con-tain-ing file names or paths. For \T1/
zi4/m/n/10 file.copy \T1/ptm/m/n/10 and
[200]
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[]\T1/ptm/m/n/10 A ver-sion of sym-bolic link-ing to files/directories was im-p
le-mented more re-cently, and
[201]
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[][][]\T1/zi4/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 file.ac
cess[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [
][]\T1/zi4/m/n/10 file.show[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files
[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 unlink[][][]\T1/ptm/m/n/10 , [][]\T1/
zi4/m/n/10 basename[][][]\T1/ptm/m/n/10 ,

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[][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][
] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik
i /
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[]\T1/ptm/m/n/10 This is the same com-pu-ta-tion as for the em-pir-i-cal dis-tr
i-bu-tion func-tion, and in-deed,
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[]\T1/ptm/m/n/10 an atomic nu-mer-i-cal or char-ac-ter ob-ject, pos-si-bly [][]
\T1/zi4/m/n/10 complex[][][] \T1/ptm/m/n/10 only for
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[]\T1/ptm/m/n/10 This works via \T1/zi4/m/n/10 prettyNum()\T1/ptm/m/n/10 , whic
h calls

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\T1/zi4/m/n/10 .format.zeros(*,replace=replace.zero) \T1/ptm/m/n/10 three times
 in this case, see

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[]\T1/ptm/m/n/10 For num-bers, \T1/zi4/m/n/10 formatC() \T1/ptm/m/n/10 calls \T
1/zi4/m/n/10 prettyNum() \T1/ptm/m/n/10 when needed which it-self calls

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\T1/zi4/m/n/10 .format.zeros(*,replace=replace.zero)\T1/ptm/m/n/10 . (\T1/ptm/m
/it/10 ``when needed''\T1/ptm/m/n/10 : when \T1/zi4/m/n/10 zero.print \T1/ptm/m
/n/10 is not

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[]\T1/zi4/m/n/10 formatC \T1/ptm/m/n/10 does not nec-es-sar-ily align the num-b
ers on the dec-i-mal point, so

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\T1/zi4/m/n/10 formatC(c(6.11,13.1),digits = 2,format = "fg") \T1/ptm/m/n/10 gi
ves \T1/zi4/m/n/10 c("6.1"," 13")\T1/ptm/m/n/10 . If you want
[219]
Underfull \hbox (badness 2035) in paragraph at lines 15283--15287
[]\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/n/10 decimal.mark \T1/ptm/m/n/10 in
 \T1/zi4/m/n/10 formatC() \T1/ptm/m/n/10 was changed in \T1/phv/m/n/10 R \T1/pt
m/m/n/10 3.2.0: for use within
[220]
Underfull \vbox (badness 10000) has occurred while \output is active [221]
[222] [223] [224] [225] [226] [227] [228]
Underfull \hbox (badness 2452) in paragraph at lines 15882--15886
[]\T1/zi4/m/n/10 gctorture2 \T1/ptm/m/n/10 can also be in-voked via en-vi-ron-m
ent vari-ables at the start of the \T1/phv/m/n/10 R \T1/ptm/m/n/10 ses-

Underfull \hbox (badness 1147) in paragraph at lines 15882--15886
\T1/ptm/m/n/10 sion. \T1/zi4/m/n/10 R_GCTORTURE \T1/ptm/m/n/10 cor-re-sponds to
 the \T1/zi4/m/n/10 step \T1/ptm/m/n/10 ar-gu-ment, \T1/zi4/m/n/10 R_GCTORTURE_
WAIT \T1/ptm/m/n/10 to \T1/zi4/m/n/10 wait\T1/ptm/m/n/10 , and
[229] [230]
Underfull \hbox (badness 1092) in paragraph at lines 16055--16060
[][]\T1/zi4/m/n/10 library.dynam[][][]\T1/ptm/m/n/10 , or can be found af-ter t
he DLL has been loaded us-ing
[231] [232] [233]
Underfull \hbox (badness 6741) in paragraph at lines 16305--16309
\T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing \
T1/zi4/m/n/10 CRoutine\T1/ptm/m/n/10 , \T1/zi4/m/n/10 CallRoutine\T1/ptm/m/n/10
 ,
[234] [235] [236] [237] [238] [239] [240] [241] [242]
Underfull \vbox (badness 10000) has occurred while \output is active [243]
[244] [245] [246] [247] [248] [249] [250] [251] [252]
Underfull \hbox (badness 1478) in paragraph at lines 17594--17597
[]\T1/ptm/m/n/10 A char-ac-ter vec-tor, or an ob-ject to be con-verted to a cha
r-ac-ter vec-tor
[253] [254] [255]
Underfull \hbox (badness 10000) in paragraph at lines 17849--17851
[]\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 http : / / www
 . unicode . org / reports / tr35 /
[256] [257] [258] [259] [260] [261] [262] [263] [264]
Underfull \hbox (badness 1442) in paragraph at lines 18447--18449
[]\T1/ptm/m/n/10 the choice of de-fault graph-ics de-vice launched when needed 
and by [][]\T1/zi4/m/n/10 dev.new[][][]\T1/ptm/m/n/10 : see
[265]
Underfull \hbox (badness 2452) in paragraph at lines 18539--18555
[][][]\T1/zi4/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.c
omplex[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.double[][][]\T1/ptm/m/n/10 ,
 [][]\T1/zi4/m/n/10 as.integer[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.logi
cal[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.raw[][][]\T1/ptm/m/n/10 , [][]\
T1/zi4/m/n/10 as.vector[][][]\T1/ptm/m/n/10 ,
[266] [267] [268] [269] [270] [271]
Underfull \hbox (badness 1248) in paragraph at lines 18958--18961
[]\T1/zi4/m/n/10 is.atomic \T1/ptm/m/n/10 is true for the [][]atomic[][][] type
s (\T1/zi4/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "integer"\T1/ptm/m/n
/10 , \T1/zi4/m/n/10 "numeric"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "complex"\T1/ptm/
m/n/10 ,
[272] [273] [274] [275]
Underfull \hbox (badness 4739) in paragraph at lines 19216--19218
[]\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere
d, see
[276] [277] [278] [279] [280] [281] [282]
Underfull \hbox (badness 1596) in paragraph at lines 19646--19651
\T1/ptm/m/n/10 trix or, if \T1/zi4/m/n/10 simplify = "array"\T1/ptm/m/n/10 , an
 ar-ray if ap-pro-pri-ate, by ap-ply-ing \T1/zi4/m/n/10 simplify2array()\T1/ptm
/m/n/10 .
[283] [284] [285] [286] [287] [288] [289] [290] [291]
Underfull \hbox (badness 2469) in paragraph at lines 20250--20255
[]\T1/ptm/m/n/10 In late 2017 a \T1/zi4/m/n/10 libcurl \T1/ptm/m/n/10 in-stal-l
a-tion was seen di-vided into two li-braries, \T1/zi4/m/n/10 libcurl \T1/ptm/m/
n/10 and
[292]
Underfull \hbox (badness 10000) in paragraph at lines 20264--20271
[][][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][]
 \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs /
[293] [294] [295]
Underfull \hbox (badness 1014) in paragraph at lines 20507--20512
[]\T1/ptm/m/n/10 Normally \T1/zi4/m/n/10 library \T1/ptm/m/n/10 re-turns (in-vi
s-i-bly) the list of at-tached pack-ages, but \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/1
0 or \T1/zi4/m/n/10 FALSE \T1/ptm/m/n/10 if
[296] [297] [298] [299] [300] [301] [302] [303] [304] [305] [306]
Underfull \hbox (badness 1264) in paragraph at lines 21309--21314
[]\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways 
be sup-ported:
[307]
Underfull \hbox (badness 4441) in paragraph at lines 21338--21341
[]\T1/ptm/m/n/10 Note that set-ting cat-e-gory \T1/zi4/m/n/10 "LC_ALL" \T1/ptm/
m/n/10 sets only cat-e-gories \T1/zi4/m/n/10 "LC_COLLATE"\T1/ptm/m/n/10 , \T1/z
i4/m/n/10 "LC_CTYPE"\T1/ptm/m/n/10 ,
[308] [309] [310] [311] [312] [313] [314] [315] [316] [317]
Underfull \hbox (badness 6047) in paragraph at lines 22085--22087
[]\T1/ptm/m/n/10 The al-go-rithm used by \T1/zi4/m/n/10 make.unique \T1/ptm/m/n
/10 has the prop-erty that \T1/zi4/m/n/10 make.unique(c(A,B)) ==
[318] [319] [320] [321] [322] [323] [324] [325] [326] [327] [328] [329]
[330] [331] [332] [333]
Underfull \hbox (badness 1077) in paragraph at lines 23126--23132
\T1/zi4/m/n/10 / / en . wikipedia . org / wiki / Bzip2$[][]\T1/ptm/m/n/10 , [][
]$\T1/zi4/m/n/10 http : / / tukaani . org / xz/$[][] \T1/ptm/m/n/10 and [][]$\T
1/zi4/m/n/10 https : / / en . wikipedia .
[334] [335] [336] [337] [338] [339] [340] [341]
Underfull \hbox (badness 2790) in paragraph at lines 23631--23634
[]\T1/zi4/m/n/10 packageStartupMessage \T1/ptm/m/n/10 is a vari-ant whose mes-s
ages can be sup-pressed sep-a-rately by

Underfull \hbox (badness 1571) in paragraph at lines 23631--23634
\T1/zi4/m/n/10 suppressPackageStartupMessages\T1/ptm/m/n/10 . (They are still m
es-sages, so can be sup-pressed by
[342] [343] [344] [345]
Underfull \hbox (badness 1194) in paragraph at lines 23913--23916
[]\T1/ptm/m/n/10 The de-fault method for \T1/zi4/m/n/10 anyNA \T1/ptm/m/n/10 ha
n-dles atomic vec-tors with-out a class and \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 .
 It calls
[346] [347]
Underfull \hbox (badness 2368) in paragraph at lines 24119--24125
[]\T1/ptm/m/n/10 For an [][]\T1/zi4/m/n/10 environment[][][] env\T1/ptm/m/n/10 
, \T1/zi4/m/n/10 names(env) \T1/ptm/m/n/10 gives the names of the cor-re-spond-
ing list, i.e.,

Underfull \hbox (badness 4981) in paragraph at lines 24119--24125
\T1/zi4/m/n/10 names(as.list(env,all.names = TRUE)) \T1/ptm/m/n/10 which are al
so given by [][]\T1/zi4/m/n/10 ls[][][](env,all.names =
[348] [349] [350] [351] [352] [353]
Underfull \hbox (badness 10000) in paragraph at lines 24504--24507
[]\T1/ptm/m/n/10 optional [][]\T1/zi4/m/n/10 logical[][][] \T1/ptm/m/n/10 even-
tu-ally to be passed to \T1/zi4/m/n/10 print()\T1/ptm/m/n/10 , used by
[354] [355] [356] [357] [358] [359] [360] [361] [362]
Underfull \hbox (badness 10000) in paragraph at lines 25113--25115
[]\T1/zi4/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m
ore ef-fi-cient than \T1/zi4/m/n/10 pkg %in%
[363] [364] [365] [366] [367] [368] [369] [370] [371] [372] [373] [374]
Underfull \hbox (badness 1038) in paragraph at lines 25953--25961
[]\T1/ptm/m/n/10 the pack-ages that are at-tached by de-fault when \T1/phv/m/n/
10 R \T1/ptm/m/n/10 starts up. Ini-tially

Underfull \hbox (badness 1735) in paragraph at lines 25953--25961
\T1/ptm/m/n/10 set from value of the en-vi-ron-ment vari-able \T1/zi4/m/n/10 R_
DEFAULT_PACKAGES\T1/ptm/m/n/10 , or if that is un-

Underfull \hbox (badness 1292) in paragraph at lines 25953--25961
\T1/ptm/m/n/10 set to \T1/zi4/m/n/10 c("datasets","utils","grDevices","graphics
","stats","methods")\T1/ptm/m/n/10 . (Set

Underfull \hbox (badness 1881) in paragraph at lines 25962--25965
[]\T1/ptm/m/n/10 integer value con-trol-ling the print-ing of lan-guage con-str
ucts which are

Underfull \hbox (badness 6220) in paragraph at lines 25981--25983
[]\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see

[375]
Underfull \hbox (badness 2142) in paragraph at lines 26122--26126
[]\T1/ptm/m/n/10 the de-fault pa-per for-mat used by [][]\T1/zi4/m/n/10 postscr
ipt[][][]\T1/ptm/m/n/10 ; set by en-vi-ron-ment vari-able
[376]
Underfull \hbox (badness 1968) in paragraph at lines 26172--26177
[]\T1/ptm/m/n/10 the com-mand used by [][]\T1/zi4/m/n/10 postscript[][][] \T1/p
tm/m/n/10 for print-ing; set by en-vi-ron-ment vari-able
[377] [378] [379]
Underfull \hbox (badness 10000) in paragraph at lines 26460--26466
[]\T1/ptm/m/n/10 The URL of a Bio-con-duc-tor mir-ror for use by [][]\T1/zi4/m/
n/10 setRepositories[][][]\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 26460--26466
\T1/ptm/m/n/10 e.g. the de-fault `\T1/zi4/m/n/10 "https://bioconductor.org"\T1/
ptm/m/n/10 ' or the Eu-ro-pean mir-ror

Underfull \hbox (badness 10000) in paragraph at lines 26460--26466
\T1/ptm/m/n/10 `\T1/zi4/m/n/10 "https://bioconductor.statistik.tu-dortmund.de"\
T1/ptm/m/n/10 '. Can be set by

Underfull \hbox (badness 10000) in paragraph at lines 26473--26476
[]\T1/ptm/m/n/10 default Cc: ad-dress used by [][]\T1/zi4/m/n/10 create.post[][
][] \T1/ptm/m/n/10 (and hence[][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/n/10
 and

Underfull \hbox (badness 2689) in paragraph at lines 26499--26501
[]\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na
l HTTP server, see
[380]
Underfull \hbox (badness 10000) in paragraph at lines 26534--26539
[]\T1/ptm/m/n/10 Used by [][]\T1/zi4/m/n/10 install.packages[][][] \T1/ptm/m/n/
10 (and in-di-rectly

Underfull \hbox (badness 2529) in paragraph at lines 26540--26551
\T1/ptm/m/n/10 in-di-rectly [][]\T1/zi4/m/n/10 update.packages[][][]\T1/ptm/m/n
/10 ) on plat-forms which sup-port bi-nary pack-ages. Pos-si-

Underfull \hbox (badness 2512) in paragraph at lines 26540--26551
\T1/ptm/m/n/10 ble val-ues are \T1/zi4/m/n/10 "never"\T1/ptm/m/n/10 , \T1/zi4/m
/n/10 "interactive" \T1/ptm/m/n/10 (which means ask in in-ter-ac-tive use and

Underfull \hbox (badness 7203) in paragraph at lines 26552--26555
[]\T1/ptm/m/n/10 default email-ing method used by [][]\T1/zi4/m/n/10 create.pos
t[][][] \T1/ptm/m/n/10 and hence [][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/
n/10 and

Underfull \hbox (badness 10000) in paragraph at lines 26576--26581
[]\T1/zi4/m/n/10 "source" \T1/ptm/m/n/10 (the de-fault ex-cept un-der a CRAN ma
-cOS build),

Underfull \hbox (badness 2057) in paragraph at lines 26576--26581
\T1/zi4/m/n/10 "mac.binary.el-capitan" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "both"
 \T1/ptm/m/n/10 (the de-fault for CRAN ma-cOS builds).
[381] [382] [383] [384] [385] [386] [387]
Underfull \hbox (badness 10000) in paragraph at lines 27094--27097
[]\T1/zi4/m/n/10 str2expression(s) \T1/ptm/m/n/10 and \T1/zi4/m/n/10 str2lang(s
) \T1/ptm/m/n/10 re-turn spe-cial ver-sions of
[388]
Underfull \hbox (badness 7925) in paragraph at lines 27173--27177
[]\T1/ptm/m/n/10 for a [][]\T1/zi4/m/n/10 character[][][] \T1/ptm/m/n/10 vec-to
r \T1/zi4/m/n/10 s\T1/ptm/m/n/10 , \T1/zi4/m/n/10 str2expression(s) \T1/ptm/m/n
/10 cor-re-sponds to

Underfull \hbox (badness 1622) in paragraph at lines 27173--27177
[][]\T1/zi4/m/n/10 parse[][][](text = s,keep.source=FALSE)\T1/ptm/m/n/10 , whic
h is al-ways of type ([][]\T1/zi4/m/n/10 typeof[][][]\T1/ptm/m/n/10 ) and [][]\
T1/zi4/m/n/10 class[][][]

Underfull \hbox (badness 6125) in paragraph at lines 27178--27187
[]\T1/ptm/m/n/10 for a [][]\T1/zi4/m/n/10 character[][][] \T1/ptm/m/n/10 string
 \T1/zi4/m/n/10 s\T1/ptm/m/n/10 , \T1/zi4/m/n/10 str2lang(s) \T1/ptm/m/n/10 cor
-re-sponds to [][]\T1/zi4/m/n/10 parse[][][](text =
[389] [390] [391] [392] [393] [394] [395] [396] [397] [398] [399]
Underfull \hbox (badness 2726) in paragraph at lines 27899--27902
[]\T1/ptm/m/n/10 character string (or \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 ) in-di
-cat-ing [][]\T1/zi4/m/n/10 NA[][][] \T1/ptm/m/n/10 val-ues in printed out-put,
 see
[400] [401] [402] [403] [404] [405] [406] [407] [408] [409] [410] [411]
[412] [413] [414] [415] [416] [417] [418] [419] [420] [421] [422] [423]
[424]
Underfull \hbox (badness 1533) in paragraph at lines 29593--29596
[]\T1/ptm/m/n/10 As with all com-piled code, mis-specifying these func-tions ca
n crash \T1/phv/m/n/10 R\T1/ptm/m/n/10 . Do in-clude the
[425] [426]
Underfull \hbox (badness 1163) in paragraph at lines 29756--29767
[]\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no \T1/zi4/m/n/10 NA\
T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in
[427] [428] [429] [430] [431] [432] [433] [434] [435] [436] [437] [438]
[439] [440] [441] [442] [443] [444] [445] [446] [447] [448]
Underfull \hbox (badness 10000) in paragraph at lines 31299--31303
[]\T1/zi4/m/n/10 regexpr \T1/ptm/m/n/10 and \T1/zi4/m/n/10 gregexpr \T1/ptm/m/n
/10 sup-port `named cap-ture'. If groups are named, e.g.,

Underfull \hbox (badness 1221) in paragraph at lines 31299--31303
\T1/zi4/m/n/10 "(?<first>[A-Z][a-z]+)" \T1/ptm/m/n/10 then the po-si-tions of t
he matches are also re-turned by name.
[449]
Underfull \hbox (badness 6188) in paragraph at lines 31321--31323
[]\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 http : / / p
ubs . opengroup . org / onlinepubs / 9699919799 /
[450] [451] [452] [453] [454] [455] [456] [457]
Underfull \hbox (badness 1655) in paragraph at lines 31877--31879
[]\T1/ptm/m/n/10 a vec-tor (atomic, not a list) for \T1/zi4/m/n/10 rle()\T1/ptm
/m/n/10 ; an ob-ject of class \T1/zi4/m/n/10 "rle" \T1/ptm/m/n/10 for
[458] [459] [460] [461] [462] [463] [464] [465] [466] [467] [468] [469]
[470] [471] [472] [473]
Underfull \hbox (badness 2261) in paragraph at lines 32999--33004
[]\T1/ptm/m/n/10 If \T1/zi4/m/n/10 strip.white \T1/ptm/m/n/10 is of length 1, i
t ap-plies to all fields; oth-er-wise, if
[474]
Underfull \hbox (badness 10000) in paragraph at lines 33026--33032
[]\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac-
ters

Underfull \hbox (badness 1484) in paragraph at lines 33026--33032
\T1/ptm/m/n/10 `\T1/zi4/m/n/10 \a,\b,\f,\n,\r,\t,\v\T1/ptm/m/n/10 ' and oc-tal 
and hex-adec-i-mal rep-re-sen-ta-tions like
[475] [476] [477] [478] [479] [480] [481] [482] [483] [484] [485] [486]
[487] [488]
Underfull \hbox (badness 10000) in paragraph at lines 34026--34028
[]\T1/ptm/m/n/10 Encoded `\T1/zi4/m/n/10 file://\T1/ptm/m/n/10 ' URLs should be
 in the Win-dows stan-dard form,
[489] [490] [491] [492] [493] [494] [495] [496] [497] [498] [499] [500]
[501] [502] [503] [504] [505] [506] [507] [508] [509] [510] [511] [512]
[513] [514] [515] [516] [517] [518] [519]
Underfull \hbox (badness 1072) in paragraph at lines 36270--36274
[]\T1/ptm/m/n/10 On front-ends which sup-port it, the com-mands his-tory is rea
d from the file spec-i-fied by

Underfull \hbox (badness 10000) in paragraph at lines 36275--36281
[]\T1/ptm/m/n/10 The command-line op-tion `\T1/zi4/m/n/10 --vanilla\T1/ptm/m/n/
10 ' im-plies `\T1/zi4/m/n/10 --no-site-file\T1/ptm/m/n/10 ', `\T1/zi4/m/n/10 -
-no-init-file\T1/ptm/m/n/10 ',

Underfull \hbox (badness 1681) in paragraph at lines 36275--36281
\T1/ptm/m/n/10 `\T1/zi4/m/n/10 --no-environ\T1/ptm/m/n/10 ' and (ex-cept for \T
1/zi4/m/n/10 R CMD\T1/ptm/m/n/10 ) `\T1/zi4/m/n/10 --no-restore\T1/ptm/m/n/10 '
 Un-der Win-dows, it also im-plies
[520]
Underfull \hbox (badness 10000) in paragraph at lines 36305--36311
[]\T1/ptm/m/n/10 On sys-tems with sub-architectures (mainly Win-dows), the file
s `\T1/zi4/m/n/10 Renviron.site\T1/ptm/m/n/10 '

Underfull \hbox (badness 10000) in paragraph at lines 36305--36311
\T1/ptm/m/n/10 and `\T1/zi4/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' are looked for
 first in architecture-specific di-rec-to-ries,

Underfull \hbox (badness 1320) in paragraph at lines 36305--36311
\T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/n/10 /etc/i386/R
environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/zi4/m/n/10 .Renviron.i386\T1/ptm/m/
n/10 ' will be used in
[521] [522] [523] [524] [525]
Underfull \hbox (badness 1142) in paragraph at lines 36668--36674
[]\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the \T1/zi4/m/n/10 form
at \T1/ptm/m/n/10 meth-ods is \T1/zi4/m/n/10 "%Y-%m-%d
[526] [527] [528] [529] [530] [531] [532] [533] [534] [535] [536] [537]
[538] [539] [540] [541] [542] [543] [544]
Underfull \hbox (badness 1565) in paragraph at lines 37941--37943
[]\T1/ptm/m/n/10 integer code used in \T1/zi4/m/n/10 quantile(*,type=quantile.t
ype) \T1/ptm/m/n/10 for the de-fault
[545] [546] [547] [548] [549] [550] [551] [552] [553] [554]
Underfull \hbox (badness 1616) in paragraph at lines 38643--38648
\T1/zi4/m/n/10 system("id") \T1/ptm/m/n/10 is much more portable on Unix-alikes
, pro-vided only the POSIX op-tions
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[]\T1/ptm/m/n/10 logical. If \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , func-tions kee
p their source in-clud-ing com-ments, see
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[]\T1/ptm/m/n/10 On 64-bit plat-forms \T1/zi4/m/n/10 bin \T1/ptm/m/n/10 can hav
e $\OT1/cmr/m/n/10 2[]$ \T1/ptm/m/n/10 or more el-e-ments (i.e., \T1/zi4/m/n/10
 length(bin) >
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[][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [
][]$https : / / developer . r-[]project . org /
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[][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r
emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 taskCallbackManager[
][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer .
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[][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][
] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / data . iana . org / time-[
]zones /
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[]\T1/zi4/m/n/10 try \T1/ptm/m/n/10 eval-u-ates an ex-pres-sion and traps any e
r-rors that oc-cur dur-ing the eval-u-a-tion. If

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\T1/ptm/m/n/10 an er-ror oc-curs then the er-ror mes-sage is printed to the [][
]\T1/zi4/m/n/10 stderr[][][] \T1/ptm/m/n/10 con-nec-tion un-less
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[]\T1/ptm/m/n/10 When a func-tion call-ing \T1/zi4/m/n/10 UseMethod("fun") \T1/
ptm/m/n/10 is ap-plied to an ob-ject with class at-tribute
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[]\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di-
ately, even if
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[]\T1/ptm/m/n/10 See the de-scrip-tion of [][]\T1/zi4/m/n/10 options[][][]("war
n") \T1/ptm/m/n/10 for the cir-cum-stances un-der which there is a
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\T1/ptm/m/n/10 If [][]\T1/zi4/m/n/10 names[][][](.dimnames) \T1/ptm/m/n/10 is n
ot empty, these are used as col-umn names.

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[]\T1/ptm/m/n/10 If \T1/zi4/m/n/10 arr.ind == TRUE \T1/ptm/m/n/10 and \T1/zi4/m
/n/10 x \T1/ptm/m/n/10 is an [][]\T1/zi4/m/n/10 array[][][] \T1/ptm/m/n/10 (has
 a [][]\T1/zi4/m/n/10 dim[][][] \T1/ptm/m/n/10 at-tribute), the re-sult is
[626] [627] [628] [629] [630] [631] [632] [633] [634]
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[]\T1/zi4/m/n/10 .packages() \T1/ptm/m/n/10 re-turns the names of the cur-rentl
y at-tached pack-ages \T1/ptm/m/it/10 in-vis-i-bly \T1/ptm/m/n/10 whereas
[635]
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[]\T1/zi4/m/n/10 .standard_regexps \T1/ptm/m/n/10 re-turns a list of `stan-dard
' reg-exps, in-clud-ing el-e-ments named
[636]) (compiler-pkg.tex
Chapter 2.
[637] [638] [639] [640]) (datasets-pkg.tex
Chapter 3.
[641] [642] [643] [644] [645] [646]
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[]\T1/ptm/m/n/10 MacDonell, W.R. (1902). On crim-i-nal an-thro-pom-e-try and th
e iden-ti-fi-ca-tion of crim-i-nals.
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[700]
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[701] [702] [703] [704] [705] [706] [707] [708] [709] [710] [711] [712]
[713] [714] [715]) (grDevices-pkg.tex [716]
Chapter 4.
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[]\T1/ptm/m/n/10 numeric vec-tor of length 3, \T1/zi4/m/n/10 c(mi,ma,n.)\T1/ptm
/m/n/10 , with iden-ti-cal mean-ing to

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[]\T1/ptm/m/n/10 Apart from that, [][]\T1/zi4/m/n/10 axisTicks[][][]() \T1/ptm/
m/n/10 just calls the C func-tion \T1/zi4/m/n/10 CreateAtVector() \T1/ptm/m/n/1
0 in

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\T1/ptm/m/n/10 `\T1/zi4/m/n/10 <Rsrc>/src/main/plot.c\T1/ptm/m/n/10 ' which is 
also called by the base \T1/ptm/b/n/10 graph-ics \T1/ptm/m/n/10 pack-age func-t
ion
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[733]
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[]\T1/ptm/m/n/10 There is cur-rently no doc-u-men-ta-tion about the al-go-rithm
. The source code is in
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[]\T1/zi4/m/n/10 densCols \T1/ptm/m/n/10 com-putes and re-turns the set of col-
ors that will be used in plot-ting, call-ing
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\T1/ptm/m/n/10 by [][]\T1/zi4/m/n/10 rasterImage[][][] \T1/ptm/m/n/10 and [][]\
T1/zi4/m/n/10 grid.raster[][][]\T1/ptm/m/n/10 ? Pos-si-ble val-ues \T1/zi4/m/n/
10 "no"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "yes" \T1/ptm/m/n/10 and
[740] [741] [742] [743] [744] [745]
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\T1/zi4/m/n/10 "png48"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pngmono"\T1/ptm/m/n/10 ,
 \T1/zi4/m/n/10 "pnggray"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pngalpha"\T1/ptm/m/n/
10 , \T1/zi4/m/n/10 "bmp16"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "bmp16m" "bmp256"\T1
/ptm/m/n/10 , \T1/zi4/m/n/10 "bmp32b"\T1/ptm/m/n/10 ,
[746]
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[]\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the 
set-ting of
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[]\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript
 doc-u-men-ta-tion) are
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[]\T1/zi4/m/n/10 nclass.FD \T1/ptm/m/n/10 uses the Freedman-Diaconis choice bas
ed on the inter-quartile range
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[]\T1/ptm/m/n/10 For use with \T1/zi4/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv
e a C in-te-ger for-mat such as
[773] [774] [775] [776] [777] [778] [779] [780] [781] [782]
Underfull \hbox (badness 10000) in paragraph at lines 4514--4519
[][][]$\T1/zi4/m/n/10 https : / / www . adobe . com / content / dam / acom / en
 / devnet / actionscript / articles / PLRM . pdf$[][]

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\T1/ptm/m/n/10 or PDF [][]$\T1/zi4/m/n/10 https : / / www . adobe . com / devne
t / acrobat / pdfs / pdf _ reference _ 1-[]7 . pdf$[][] \T1/ptm/m/n/10 and in
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[]\T1/ptm/m/n/10 The TIFF spec-i-fi-ca-tion, in-clud-ing ex-ten-sions, at [][]$
\T1/zi4/m/n/10 https : / / partners . adobe . com / public /
[787] [788]
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[]\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently 
al-lowed val-ues
[789]
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\T1/ptm/m/n/10 it is one of \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4
/m/n/10 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/
zi4/m/n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm
/m/n/10 ,

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[]\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East 
Asian lan-guages -- see
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[]\T1/ptm/m/n/10 Color mod-els pro-vided for back-wards com-pat-i-bil-ity are \
T1/zi4/m/n/10 "rgb" \T1/ptm/m/n/10 (which is RGB+gray) and

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[]\T1/ptm/m/n/10 Support for Com-puter Mod-ern fonts is based on a con-tri-bu-t
ion by Brian D'Urso
[792] [793] [794]
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[]\T1/ptm/m/n/10 Mappings for a num-ber of stan-dard Adobe fonts (and URW equiv
-a-lents) are also pro-

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\T1/ptm/m/n/10 vided: \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4/m/n/1
0 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/zi4/m/
n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/1
0 ,

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\T1/zi4/m/n/10 "NewCenturySchoolbook"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Palatino"
 \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "Times"\T1/ptm/m/n/10 ; \T1/zi4/m/n/10 "URWG
othic"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "URWBookman"\T1/ptm/m/n/10 ,
[795]
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[]\T1/zi4/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/zi4
/m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu /

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\T1/zi4/m/n/10 chinese-[]fonts-[]truetype/$[][]\T1/ptm/m/n/10 . Ken Lunde's CJK
V re-sources are at [][]$\T1/zi4/m/n/10 ftp : / / ftp . oreilly .
[796] [797]
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[]\T1/ptm/m/n/10 arguments \T1/zi4/m/n/10 onefile\T1/ptm/m/n/10 , \T1/zi4/m/n/1
0 family\T1/ptm/m/n/10 , \T1/zi4/m/n/10 title\T1/ptm/m/n/10 , \T1/zi4/m/n/10 fo
nts\T1/ptm/m/n/10 , \T1/zi4/m/n/10 encoding\T1/ptm/m/n/10 , \T1/zi4/m/n/10 bg\T
1/ptm/m/n/10 , \T1/zi4/m/n/10 fg\T1/ptm/m/n/10 , \T1/zi4/m/n/10 width\T1/ptm/m/
n/10 ,
[798] [799] [800] [801] [802] [803] [804] [805]
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[]\T1/zi4/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red
/green/blue) into HSV space
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[]\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used
. One of
[818]
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[]\T1/zi4/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK 
lan-guages and
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[]\T1/ptm/m/n/10 the font fam-ily to be used. This must be one of \T1/zi4/m/n/1
0 "AvantGarde"\T1/ptm/m/n/10 ,
[824] [825]
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[]\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., \T1/zi4/m/n/10 n
umber[i] \T1/ptm/m/n/10 is the mul-ti-plic-ity of
[826] [827] [828]) (graphics-pkg.tex
Chapter 5.
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[][][]\T1/zi4/m/n/10 boxplot.default[][][] \T1/ptm/m/n/10 which al-ready works 
nowa-days with data.frames; [][]\T1/zi4/m/n/10 boxplot.formula[][][]\T1/ptm/m/n
/10 ,
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\T1/ptm/m/n/10 be in as-cend-ing or-der. (The rest of this de-scrip-tion does n
ot ap-ply to
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[]\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing if log-a-rith-mic axes are 
to be used, see
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[]\T1/ptm/b/it/10 R.O.\T1/ptm/m/n/10 ; size of de-fault char-ac-ter \T1/zi4/m/n
/10 (width,height) \T1/ptm/m/n/10 in user co-or-di-nate units.

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\T1/zi4/m/n/10 par("cxy") \T1/ptm/m/n/10 is \T1/zi4/m/n/10 par("cin")/par("pin"
) \T1/ptm/m/n/10 scaled to user co-or-di-nates. Note that
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[904 <C:/projects/BUILD/R-source-win64/library/graphics/help/figures/mai.pdf>]
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[905 <C:/projects/BUILD/R-source-win64/library/graphics/help/figures/oma.pdf>]
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[]\T1/ptm/m/n/10 The five stan-dard dash-dot line types (\T1/zi4/m/n/10 lty = 2
:6\T1/ptm/m/n/10 ) cor-re-spond to
[907] [908] [909] [910] [911] [912] [913] [914] [915] [916] [917] [918]
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[][] 
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[]\T1/ptm/m/n/10 For each \T1/zi4/m/n/10 i\T1/ptm/m/n/10 , a line seg-ment is d
rawn be-tween the point \T1/zi4/m/n/10 (x0[i],y0[i]) \T1/ptm/m/n/10 and the poi
nt
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[]\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color

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[]\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color
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s}) has been already used, duplicate ignored
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                   \relax 
l.8915 \HeaderA{units}{Graphical Units}{units}
                                               [963] [964] [965] [966])
(grid-pkg.tex
Chapter 6.
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[]\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 preDrawDetails \T1/ptm/m/n/10 and \T1
/zi4/m/n/10 postDrawDetails \T1/ptm/m/n/10 are also called in the cal-cu-la-tio
n of
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[][][]\T1/ptm/m/n/10 Grid[][][], [][]\T1/zi4/m/n/10 pushViewport[][][]\T1/ptm/m
/n/10 , [][]\T1/zi4/m/n/10 popViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10
 downViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 seekViewport[][][]\T1/pt
m/m/n/10 , [][]\T1/zi4/m/n/10 upViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/
10 unit[][][]\T1/ptm/m/n/10 ,
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[1036]
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[]\T1/ptm/m/n/10 Both func-tions cre-ate a seg-ments grob (a graph-i-cal ob-jec
t de-scrib-ing seg-ments), but only
[1037] [1038] [1039] [1040]
Underfull \hbox (badness 7256) in paragraph at lines 4731--4733
[]\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject
s are co-erced by
[1041] [1042] [1043] [1044] [1045] [1046] [1047] [1048] [1049] [1050] [1051]
[1052] [1053] [1054] [1055] [1056] [1057] [1058] [1059] [1060] [1061] [1062]
[1063] [1064] [1065] [1066] [1067] [1068]
Underfull \hbox (badness 1824) in paragraph at lines 6535--6538
[]\T1/ptm/m/n/10 This can be use-ful for re-turn-ing to your start-ing point by
 do-ing some-thing like \T1/zi4/m/n/10 depth
[1069] [1070] [1071] [1072]) (methods-pkg.tex
Chapter 7.
[1073] [1074] [1075] [1076] [1077] [1078] [1079] [1080]
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[1083] [1084] [1085] [1086] [1087] [1088] [1089] [1090]
Underfull \hbox (badness 2237) in paragraph at lines 1385--1387
[]\T1/ptm/m/n/10 The class \T1/zi4/m/n/10 "className" \T1/ptm/m/n/10 ex-tends \
T1/zi4/m/n/10 "character" \T1/ptm/m/n/10 and has a slot \T1/zi4/m/n/10 "package
"\T1/ptm/m/n/10 , also of class
[1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098]
Underfull \hbox (badness 2181) in paragraph at lines 1932--1939
[]\T1/ptm/m/n/10 Two vir-tual classes are sup-plied to test for ref-er-ence ob-
jects: \T1/zi4/m/n/10 is(x,"refClass") \T1/ptm/m/n/10 tests

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[]\T1/ptm/m/n/10 The ar-gu-ment to \T1/zi4/m/n/10 insertSource \T1/ptm/m/n/10 c
an be an ob-ject of class

Underfull \hbox (badness 1038) in paragraph at lines 1981--1986
\T1/ptm/m/n/10 file name is passed to \T1/zi4/m/n/10 insertSource \T1/ptm/m/n/1
0 it calls \T1/zi4/m/n/10 evalSource \T1/ptm/m/n/10 to ob-tain the
[1099] [1100] [1101]
Underfull \hbox (badness 2213) in paragraph at lines 2214--2219
[]\T1/ptm/m/n/10 To re-strict the search to classes in a par-tic-u-lar pack-age
, use \T1/zi4/m/n/10 where =
[1102] [1103] [1104] [1105] [1106]
Underfull \hbox (badness 10000) in paragraph at lines 2574--2577
[]\T1/ptm/m/n/10 As you might ex-pect [][]\T1/zi4/m/n/10 setGeneric[][][] \T1/p
tm/m/n/10 and [][]\T1/zi4/m/n/10 setGroupGeneric[][][] \T1/ptm/m/n/10 cre-ate o
b-jects of class
[1107] [1108]
Underfull \hbox (badness 1132) in paragraph at lines 2714--2718
[]\T1/ptm/m/n/10 In \T1/zi4/m/n/10 getGenerics\T1/ptm/m/n/10 , if \T1/zi4/m/n/1
0 TRUE\T1/ptm/m/n/10 , the \T1/zi4/m/n/10 package \T1/ptm/m/n/10 slot of the re
-turned re-sult is in

Underfull \hbox (badness 1033) in paragraph at lines 2746--2751
\T1/ptm/m/n/10 In ad-di-tion, \T1/zi4/m/n/10 removeGeneric \T1/ptm/m/n/10 re-mo
ves the func-tion it-self; \T1/zi4/m/n/10 removeMethods \T1/ptm/m/n/10 re-store
s the
[1109] [1110] [1111] [1112] [1113] [1114] [1115]
Underfull \hbox (badness 1102) in paragraph at lines 3303--3305
[]\T1/zi4/m/n/10 getPackageName \T1/ptm/m/n/10 re-turns the character-string na
me of the pack-age (with-out the ex-tra-ne-ous
[1116] [1117] [1118] [1119] [1120]
Underfull \hbox (badness 10000) in paragraph at lines 3634--3639
[]\T1/ptm/m/n/10 The \T1/zi4/m/n/10 initialize \T1/ptm/m/n/10 method for these 
classes takes spe-cial ar-gu-ments

Underfull \hbox (badness 10000) in paragraph at lines 3642--3651
[]\T1/ptm/m/n/10 The
[1121] [1122]
Underfull \hbox (badness 10000) in paragraph at lines 3762--3763
[] \T1/zi4/m/n/10 Pos <-setClass("Pos",slots = c(latitude = "numeric",longitude
 = "numeric",altitude
[1123] [1124] [1125] [1126] [1127] [1128] [1129] [1130] [1131]
Underfull \hbox (badness 1769) in paragraph at lines 4472--4478
[]\T1/ptm/m/n/10 class [][]\T1/zi4/m/n/10 MethodsList[][][] \T1/ptm/m/n/10 for 
the ob-jects defin-ing sets of meth-ods as-so-ci-ated with a par-tic-u-lar

Underfull \hbox (badness 1939) in paragraph at lines 4472--4478
\T1/zi4/m/n/10 MethodDefinition\T1/ptm/m/n/10 , or an ex-ten-sion. Class [][]\T
1/zi4/m/n/10 MethodWithNext[][][] \T1/ptm/m/n/10 for an ex-ten-sion used by
[1132] [1133] [1134] [1135] [1136] [1137] [1138] [1139] [1140]
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[1143] [1144]
Underfull \hbox (badness 4036) in paragraph at lines 5437--5440
[]\T1/ptm/m/n/10 Object of class \T1/zi4/m/n/10 "PossibleMethod" \T1/ptm/m/n/10
 the method to use in re-sponse to a
[1145]
Underfull \hbox (badness 3803) in paragraph at lines 5512--5514
[]\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p
assed to
[1146] [1147] [1148]
Underfull \hbox (badness 1087) in paragraph at lines 5744--5749
[]\T1/ptm/m/n/10 In ad-di-tion, the cur-rently avail-able gener-ics with meth-o
ds for this class are found (us-ing
[1149] [1150] [1151] [1152] [1153] [1154] [1155] [1156]
Underfull \hbox (badness 1675) in paragraph at lines 6451--6457
\T1/ptm/m/n/10 can be con-verted ex-plic-itly as \T1/zi4/m/n/10 externalRefMeth
od(f)\T1/ptm/m/n/10 , which re-turns an ob-ject of class
[1157] [1158] [1159] [1160]
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[1162] [1163]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.S4}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.6973 \aliasA{S4}{S3Part}{S4}
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nation with the same identifier (name{Rfn.Complex}) has been already used, dupl
icate ignored
<to be read again> 
                   \relax 
l.7229 \aliasA{Complex}{S4groupGeneric}{Complex}
                                                pdfTeX warning (ext4): destinat
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 ignored
<to be read again> 
                   \relax 
l.7231 \aliasA{Logic}{S4groupGeneric}{Logic}
                                            pdfTeX warning (ext4): destination 
with the same identifier (name{Rfn.Math}) has been already used, duplicate igno
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<to be read again> 
                   \relax 
l.7232 \aliasA{Math}{S4groupGeneric}{Math}
                                          pdfTeX warning (ext4): destination wi
th the same identifier (name{Rfn.Ops}) has been already used, duplicate ignored

<to be read again> 
                   \relax 
l.7234 \aliasA{Ops}{S4groupGeneric}{Ops}
                                        pdfTeX warning (ext4): destination with
 the same identifier (name{Rfn.Summary}) has been already used, duplicate ignor
ed
<to be read again> 
                   \relax 
l.7235 \aliasA{Summary}{S4groupGeneric}{Summary}
                                                 [1167]
Underfull \hbox (badness 2050) in paragraph at lines 7296--7300
[]\T1/ptm/m/n/10 The mem-bers of the group de-fined by a par-tic-u-lar generic 
can be ob-tained by call-ing
[1168] [1169]
Underfull \hbox (badness 1286) in paragraph at lines 7484--7486
[]\T1/ptm/m/n/10 for \T1/zi4/m/n/10 .selectSuperClasses() \T1/ptm/m/n/10 only, 
a [][]\T1/zi4/m/n/10 list[][][] \T1/ptm/m/n/10 of class ex-ten-sions, typ-i-cal
ly
[1170] [1171] [1172] [1173] [1174] [1175] [1176] [1177] [1178] [1179] [1180]
[1181] [1182] [1183] [1184] [1185] [1186] [1187] [1188] [1189] [1190] [1191]
[1192] [1193] [1194] [1195] [1196] [1197] [1198] [1199] [1200] [1201] [1202]
Underfull \hbox (badness 1137) in paragraph at lines 10011--10019
[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/zi4/m/n/10 ne
w("signature",functionDef,...)\T1/ptm/m/n/10 . The
[1203] [1204] [1205] [1206] [1207] [1208] [1209]
Underfull \hbox (badness 1852) in paragraph at lines 10564--10568
[]\T1/ptm/m/n/10 Each of the classes ex-tends the cor-re-spond-ing un-traced cl
ass, from the data part; e.g.,
[1210] [1211] [1212]) (parallel-pkg.tex
Chapter 8.

Underfull \hbox (badness 5490) in paragraph at lines 14--16
[]\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `\T1/zi4
/m/n/10 "L\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 Ecuyer-CMRG"\T1/ptm/m/n/10 ' [][]RNG[
][][]: see
[1213] [1214] [1215] [1216] [1217] [1218] [1219] [1220]
Underfull \hbox (badness 3386) in paragraph at lines 595--598
[]\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by \T1/zi4/m/n/10 .R
andom.seed \T1/ptm/m/n/10 when the
[1221] [1222] [1223]) (splines-pkg.tex [1224]
Chapter 9.

Underfull \hbox (badness 10000) in paragraph at lines 22--24
[]\T1/ptm/m/n/10 Douglas M. Bates \T1/zi4/m/n/10 <bates@stat.wisc.edu> \T1/ptm/
m/n/10 and William N. Ven-ables
[1225] [1226] [1227] [1228] [1229] [1230] [1231] [1232] [1233] [1234] [1235]
[1236] [1237] [1238]) (stats-pkg.tex
Chapter 10.
[1239] [1240] [1241] [1242] [1243] [1244] [1245] [1246] [1247] [1248] [1249]
[1250] [1251]
Underfull \hbox (badness 1412) in paragraph at lines 875--877
[]\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from \T1/zi4/m/n/10 lm 
\T1/ptm/m/n/10 or \T1/zi4/m/n/10 aov\T1/ptm/m/n/10 , or a for-mula for
[1252] [1253] [1254] [1255] [1256] [1257] [1258]
Underfull \hbox (badness 2503) in paragraph at lines 1356--1359
[]\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of 
\T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 ,
[1259] [1260]
Underfull \hbox (badness 10000) in paragraph at lines 1536--1540
[]\T1/ptm/m/n/10 An ob-ject of class \T1/zi4/m/n/10 c("aov","lm") \T1/ptm/m/n/1
0 or for mul-ti-ple re-sponses of class
[1261] [1262] [1263] [1264] [1265] [1266] [1267] [1268] [1269] [1270] [1271]
[1272] [1273] [1274] [1275] [1276] [1277] [1278] [1279] [1280] [1281] [1282]
[1283] [1284] [1285] [1286] [1287] [1288]
Underfull \hbox (badness 2503) in paragraph at lines 3437--3440
[]\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of 
\T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 ,
[1289] [1290] [1291] [1292] [1293] [1294] [1295] [1296] [1297] [1298] [1299]
[1300] [1301] [1302]
Underfull \hbox (badness 1127) in paragraph at lines 4351--4354
[]\T1/ptm/m/n/10 standardized resid-u-als, \T1/zi4/m/n/10 (observed -expected) 
/ sqrt(V)\T1/ptm/m/n/10 , where \T1/zi4/m/n/10 V \T1/ptm/m/n/10 is the
[1303] [1304] [1305] [1306] [1307]
Underfull \hbox (badness 3989) in paragraph at lines 4681--4688
[]\T1/ptm/m/n/10 a nu-meric vec-tor of length 2, equal to say $\OT1/cmr/m/n/10 
(\OML/cmm/m/it/10 g[]; g[]\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 , where $\OML/cmm/m/
it/10 g[] \OT1/cmr/m/n/10 =
[1308] [1309] [1310] [1311] [1312] [1313] [1314] [1315] [1316]
Underfull \hbox (badness 2556) in paragraph at lines 5317--5320
[]\T1/ptm/m/n/10 character; par-tially matched to \T1/zi4/m/n/10 "circular"\T1/
ptm/m/n/10 , \T1/zi4/m/n/10 "open"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "filter"\T1/p
tm/m/n/10 . For

Underfull \hbox (badness 2932) in paragraph at lines 5334--5336
[]\T1/ptm/m/n/10 Note that the usual def-i-ni-tion of con-vo-lu-tion of two se-
quences \T1/zi4/m/n/10 x \T1/ptm/m/n/10 and \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is 
given by
[1317] [1318] [1319] [1320] [1321] [1322]
Underfull \hbox (badness 2503) in paragraph at lines 5726--5730
[]\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of 
\T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 ,
[1323] [1324] [1325] [1326] [1327] [1328] [1329] [1330] [1331] [1332] [1333]
[1334] [1335]
Underfull \hbox (badness 7081) in paragraph at lines 6520--6523
[]\T1/ptm/m/n/10 Objects of class \T1/zi4/m/n/10 "hclust" \T1/ptm/m/n/10 can be
 con-verted to class \T1/zi4/m/n/10 "dendrogram" \T1/ptm/m/n/10 us-ing method

Underfull \hbox (badness 10000) in paragraph at lines 6524--6526
[]\T1/zi4/m/n/10 rev.dendrogram \T1/ptm/m/n/10 sim-ply re-turns the den-dro-gra
m \T1/zi4/m/n/10 x \T1/ptm/m/n/10 with re-versed nodes, see also
[1336] [1337] [1338] [1339] [1340] [1341] [1342] [1343] [1344] [1345] [1346]
[1347]
Underfull \hbox (badness 10000) in paragraph at lines 7369--7372
[]\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][]\T
1/zi4/m/n/10 dist[][][]()\T1/ptm/m/n/10 , the
[1348] [1349] [1350] [1351] [1352] [1353] [1354] [1355] [1356] [1357] [1358]
[1359] [1360] [1361] [1362] [1363] [1364] [1365] [1366] [1367] [1368]
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[1370] [1371] [1372]
Underfull \hbox (badness 2626) in paragraph at lines 9048--9051
[]\T1/ptm/m/n/10 Either \T1/zi4/m/n/10 "convolution" \T1/ptm/m/n/10 or \T1/zi4/
m/n/10 "recursive" \T1/ptm/m/n/10 (and can be ab-bre-vi-ated). If
[1373] [1374]
Underfull \hbox (badness 2503) in paragraph at lines 9155--9159
[]\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of 
\T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 ,
[1375] [1376] [1377] [1378] [1379] [1380] [1381] [1382] [1383] [1384] [1385]
[1386] [1387] [1388] [1389] [1390] [1391] [1392] [1393]
Underfull \hbox (badness 4518) in paragraph at lines 10465--10470
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1394] [1395] [1396] [1397] [1398]
Underfull \hbox (badness 2142) in paragraph at lines 10825--10828
[]\T1/ptm/m/n/10 positive con-ver-gence tol-er-ance $\OML/cmm/m/it/10 $\T1/ptm
/m/n/10 ; the it-er-a-tions con-verge when $\OMS/cmsy/m/n/10 j\OML/cmm/m/it/10 
dev \OMS/cmsy/m/n/10 �

Underfull \hbox (badness 1253) in paragraph at lines 10844--10847
[]\T1/ptm/m/n/10 When \T1/zi4/m/n/10 trace \T1/ptm/m/n/10 is true, calls to [][
]\T1/zi4/m/n/10 cat[][][] \T1/ptm/m/n/10 pro-duce the out-put for each IWLS it-
er-a-tion. Hence,
[1399]
Underfull \hbox (badness 1708) in paragraph at lines 10906--10910
[]\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter-
na-tives are:
[1400] [1401] [1402] [1403] [1404]
Underfull \hbox (badness 1694) in paragraph at lines 11302--11305
[]\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these 
de-fault to
[1405] [1406] [1407] [1408] [1409] [1410]
Underfull \hbox (badness 10000) in paragraph at lines 11629--11632
[]\T1/ptm/m/n/10 If one of $\OML/cmm/m/it/10 m; n; k$\T1/ptm/m/n/10 , ex-ceeds 
[][]\T1/zi4/m/n/10 .Machine[][][]$integer.max\T1/ptm/m/n/10 , cur-rently the eq
uiv-a-lent of

Underfull \hbox (badness 1281) in paragraph at lines 11629--11632
\T1/zi4/m/n/10 qhyper(runif(nn),m,n,k) \T1/ptm/m/n/10 is used, when a bi-no-mia
l ap-prox-i-ma-tion may be con-sid-er-ably
[1411] [1412]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.hat}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.11783 \aliasA{hat}{influence.measures}{hat}
                                              [1413] [1414]
Underfull \hbox (badness 1484) in paragraph at lines 11918--11920
[]\T1/ptm/m/n/10 The func-tion \T1/zi4/m/n/10 hat() \T1/ptm/m/n/10 ex-ists main
ly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing
[1415] [1416] [1417] [1418] [1419] [1420] [1421] [1422] [1423]
Underfull \hbox (badness 10000) in paragraph at lines 12511--12513
[]\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][]\T1/zi4/m/n/10 solve.defa
ult[][][] \T1/ptm/m/n/10 when \T1/zi4/m/n/10 SSinit =
[1424] [1425] [1426] [1427] [1428]
Underfull \hbox (badness 2894) in paragraph at lines 12847--12851
[]\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f
ault method
[1429] [1430] [1431] [1432] [1433] [1434] [1435] [1436] [1437] [1438] [1439]
[1440]
Underfull \hbox (badness 4518) in paragraph at lines 13597--13602
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1441] [1442] [1443] [1444] [1445] [1446] [1447] [1448] [1449]
Underfull \hbox (badness 4518) in paragraph at lines 14249--14254
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1450] [1451]
Underfull \hbox (badness 8151) in paragraph at lines 14387--14391
[]\T1/ptm/m/n/10 Only for the (de-fault) case \T1/zi4/m/n/10 (surface = "interp
olate",statistics =

Underfull \hbox (badness 1199) in paragraph at lines 14394--14396
[]\T1/ptm/m/n/10 the num-ber of it-er-a-tions used in ro-bust fit-ting, i.e. on
ly if \T1/zi4/m/n/10 family \T1/ptm/m/n/10 is
[1452] [1453] [1454] [1455] [1456] [1457] [1458] [1459] [1460] [1461] [1462]
[1463] [1464] [1465] [1466] [1467] [1468]
Underfull \hbox (badness 2503) in paragraph at lines 15465--15469
[]\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of 
\T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 ,
[1469] [1470] [1471] [1472] [1473] [1474] [1475]
Underfull \hbox (badness 4621) in paragraph at lines 15977--15983
[]\T1/zi4/m/n/10 model.offset \T1/ptm/m/n/10 and \T1/zi4/m/n/10 model.response 
\T1/ptm/m/n/10 are equiv-a-lent to \T1/zi4/m/n/10 model.extract(,"offset") \T1/
ptm/m/n/10 and
[1476] [1477] [1478] [1479] [1480] [1481] [1482] [1483] [1484] [1485] [1486]
[1487] [1488] [1489] [1490] [1491] [1492] [1493] [1494] [1495] [1496] [1497]
[1498] [1499] [1500] [1501] [1502]
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[1504] [1505] [1506] [1507] [1508] [1509] [1510] [1511] [1512] [1513] [1514]
[1515]
Underfull \hbox (badness 1377) in paragraph at lines 18576--18581
[]\T1/ptm/m/n/10 A vec-tor of scal-ing val-ues for the pa-ram-e-ters. Op-ti-miz
a-tion is per-formed on

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[]\T1/ptm/m/n/10 A vec-tor of step sizes for the finite-difference ap-prox-i-ma
-tion to the gra-di-ent, on

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[]\T1/ptm/m/n/10 Relative con-ver-gence tol-er-ance. The al-go-rithm stops if i
t is un-able to re-duce

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\T1/ptm/m/n/10 the value by a fac-tor of \T1/zi4/m/n/10 reltol * (abs(val) + re
ltol) \T1/ptm/m/n/10 at a step. De-faults to
[1516]
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[]\T1/ptm/m/n/10 The fre-quency of re-ports for the \T1/zi4/m/n/10 "BFGS"\T1/pt
m/m/n/10 , \T1/zi4/m/n/10 "L-BFGS-B" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "SANN" \
T1/ptm/m/n/10 meth-ods if
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 []\T1/zi4/m/n/9 ## 1-D minimization: "Brent" or optimize() being preferred.. b
ut NM may be ok and "unavoidable",[] 

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 []\T1/zi4/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list(
warn.1d.NelderMead = FALSE)))[] 
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[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
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[]\T1/ptm/m/n/10 In the Cook's dis-tance vs leverage/(1-leverage) plot, con-tou
rs of stan-dard-ized resid-u-als
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[]\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting
 of the con-fi-dence
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[]\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of 
\T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 ,
[1544]
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[]\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Exact Poisson test" \T1
/ptm/m/n/10 or \T1/zi4/m/n/10 "Comparison of Poisson
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[]\T1/ptm/m/n/10 For time-series pre-dic-tion, [][]\T1/zi4/m/n/10 predict.ar[][
][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 predict.Arima[][][]\T1/ptm/m/n/10 , [][]
\T1/zi4/m/n/10 predict.arima0[][][]\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
[1582] [1583] [1584] [1585] [1586] [1587] [1588] [1589] [1590]
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 []  \T1/zi4/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty
p, ...), quantile(x, prob, type=1)))[] 
[1591] [1592] [1593]
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[]\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by

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\T1/zi4/m/n/10 cutree(hclust.obj,k = k)\T1/ptm/m/n/10 , can be spec-i-fied for 
ef-fi-ciency if al-ready
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[]\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult \T1/zi4/m/n/10 y = run
med(x,k) \T1/ptm/m/n/10 sim-ply has \T1/zi4/m/n/10 y[j] =
[1603]
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[][][]\T1/zi4/m/n/10 smoothEnds[][][] \T1/ptm/m/n/10 which im-ple-ments Tukey's
 end point rule and is called by de-fault from
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[1611]
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[]\T1/ptm/m/n/10 Each of the fol-low-ing are \T1/zi4/m/n/10 "selfStart" \T1/ptm
/m/n/10 mod-els (with ex-am-ples) [][]\T1/zi4/m/n/10 SSasymp[][][]\T1/ptm/m/n/1
0 , [][]\T1/zi4/m/n/10 SSasympOff[][][]\T1/ptm/m/n/10 ,
[1612] [1613] [1614]
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[]\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods. 
Passed to

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\T1/ptm/m/n/10 where \T1/zi4/m/n/10 NN <-[][]nobs[][][](object,use.fallback = u
se.fallback) \T1/ptm/m/n/10 and \T1/zi4/m/n/10 PP
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[1637]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1638] [1639] [1640] [1641]
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 []       \T1/zi4/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5]
 == frac(log(2), e^{phi[2]})}),[] 

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[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1642] [1643] [1644] [1645]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1646]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1647]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1648] [1649]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1650]
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[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 x\T1/p
tm/m/n/10 . It is the value of the ex-pres-sion
[1651] [1652] [1653] [1654] [1655] [1656] [1657] [1658]
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[]\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex-trac-tion
, which
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Underfull \hbox (badness 5431) in paragraph at lines 28514--28516
[]\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/z
i4/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if
[1669] [1670] [1671]
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[]\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/z
i4/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if
[1672] [1673] [1674] [1675] [1676]
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[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
[1677] [1678] [1679] [1680] [1681]
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[]\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial
 resid-u-als, when
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[1693] [1694] [1695] [1696] [1697] [1698]
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[]\T1/ptm/m/n/10 Setting \T1/zi4/m/n/10 extendInt \T1/ptm/m/n/10 to a non-\T1/z
i4/m/n/10 "no" \T1/ptm/m/n/10 string, means search-ing for the cor-rect \T1/zi4
/m/n/10 interval =
[1699] [1700] [1701] [1702] [1703] [1704]
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[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
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[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
[1713] [1714] [1715] [1716] [1717] [1718] [1719] [1720] [1721]) (stats4-pkg.tex
[1722]
Chapter 11.
[1723] [1724] [1725] [1726] [1727] [1728]pdfTeX warning (ext4): destination wit
h the same identifier (name{Rfn.show.Rdash.methods}) has been already used, dup
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l.407 ...Package \pkg{stats4}}{show.Rdash.methods}
                                                   [1729] [1730] [1731])
(tcltk-pkg.tex [1732]
Chapter 12.
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[]\T1/zi4/m/n/10 tcl \T1/ptm/m/n/10 pro-vides a generic in-ter-face to call-ing
 any Tk or Tcl com-mand by sim-ply run-ning
[1741] [1742] [1743] [1744] [1745]
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[1747] [1748] [1749] [1750] [1751] [1752]) (tools-pkg.tex
Chapter 13.
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[1754]
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[]\T1/zi4/m/n/10 assertWarning() \T1/ptm/m/n/10 as-serts that a warn-ing will b
e sig-nalled, but \T1/ptm/m/it/10 not \T1/ptm/m/n/10 an er-ror, whereas
[1755] [1756]
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[]\T1/ptm/m/n/10 At a min-i-mum, the en-vi-ron-ment should con-tain rou-tines t
o ren-der each of the 12 types

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\T1/ptm/m/n/10 of bib-li-o-graphic en-try sup-ported by [][]\T1/zi4/m/n/10 bibe
ntry[][][] \T1/ptm/m/n/10 as well as sev-eral other rou-tines de-

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\T1/zi4/m/n/10 formatIncollection\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatInProcee
dings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatManual\T1/ptm/m/n/10 , \T1/zi4/m/n/1
0 formatMastersthesis\T1/ptm/m/n/10 ,

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\T1/zi4/m/n/10 formatMisc\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatPhdthesis\T1/ptm
/m/n/10 , \T1/zi4/m/n/10 formatProceedings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 forma
tTechreport \T1/ptm/m/n/10 and
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[]\T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gine 
to use. Over-rides any
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\T1/ptm/m/n/10 giv-ing the repos-i-to-ries to use for lo-cat-ing re-verse de-pe
n-den-cies (de-
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[]\T1/ptm/m/n/10 a log-i-cal in-di-cat-ing whether to also sum-ma-rize the re-v
erse de-pen-den-cies

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[]\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a 
pre-vi-ous

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[]\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us-ing


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\T1/zi4/m/n/10 summarize_check_packages_in_dir_results \T1/ptm/m/n/10 and \T1/z
i4/m/n/10 summarize_check_packages_in_dir_timings\T1/ptm/m/n/10 ,
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[]\T1/zi4/m/n/10 CRAN_memtest_notes() \T1/ptm/m/n/10 is now dep-re-cated, with 
its func-tion-al-ity in-te-grated into that of
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a
 sub-set of
[1778]
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor of \T1/phv/m/n/10 R \T1/ptm/m/n/10 li-br
ary trees, or \T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 for all known trees (see
[1779] [1780] [1781]pdfTeX warning (ext4): destination with the same identifier
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l.1899 \aliasA{GSC}{find\_gs\_cmd}{GSC}
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 []\T1/zi4/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl
ogo.svg}{options: width=100}",[] 
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a
 sub-set of
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[]\T1/zi4/m/sl/10 NULL \T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec-t
or of links, as re-turned by
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[]\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run
,
[1811] [1812]
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[]\T1/ptm/m/n/10 Where sup-ported (\T1/zi4/m/sl/10 texi2dvi \T1/ptm/m/n/10 5.0 
and later; \T1/zi4/m/sl/10 texify.exe \T1/ptm/m/n/10 from MiK-TeX), op-tion
[1813]
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[]\T1/ptm/m/n/10 a ma-trix spec-i-fy-ing all pack-ages in-stalled on the lo-cal
 sys-tem, as from
[1814] [1815] [1816] [1817] [1818]
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[]\T1/ptm/m/n/10 Users should ex-pect sig-nif-i-cantly smaller speedups over \T
1/zi4/m/sl/10 write_PACKAGES \T1/ptm/m/n/10 in the \T1/zi4/m/sl/10 type ==
[1819]
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[]\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/zi4/m/sl/10 p
o/\T1/ptm/m/sl/10 pkgname\T1/zi4/m/sl/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists.
 The

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\T1/ptm/m/n/10 `\T1/zi4/m/sl/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in 
the pack-age are ex-am-ined to cre-ate a file
[1820] [1821] [1822]
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[]\T1/ptm/m/n/10 The de-fault cor-re-sponds to the fields needed by [][]\T1/zi4
/m/sl/10 available.packages[][][]\T1/ptm/m/n/10 :
[1823]
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[]\T1/ptm/m/n/10 For a re-mote repos-i-tory there is a trade-off be-tween down-
load speed and time spent by
[1824] [1825] [1826]) (utils-pkg.tex
Chapter 14.

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[]\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T
1/zi4/m/sl/10 insertions\T1/ptm/m/n/10 ',
[1827] [1828] [1829] [1830] [1831]
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\T1/zi4/m/sl/10 c("vertical","horizontal","cascade","minimize","restore") \T1/p
tm/m/n/10 with
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[]\T1/ptm/m/n/10 Functions \T1/zi4/m/sl/10 aspell_package_Rd_files\T1/ptm/m/n/1
0 , \T1/zi4/m/sl/10 aspell_package_vignettes\T1/ptm/m/n/10 ,

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\T1/zi4/m/sl/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 aspel
l_package_C_files \T1/ptm/m/n/10 per-form spell check-ing on the
[1837] [1838]
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[]\T1/ptm/m/n/10 Argument \T1/zi4/m/sl/10 filters \T1/ptm/m/n/10 can be used to
 se-lect which of the pack-ages on the repos-i-to-

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\T1/ptm/m/n/10 ries are re-ported. It is called with its de-fault value (\T1/zi
4/m/sl/10 NULL\T1/ptm/m/n/10 ) by func-tions such as
[1839]
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[]\T1/ptm/m/n/10 Where pro-vided by the repos-i-tory, fields \T1/zi4/m/sl/10 "O
S_type"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "License"\T1/ptm/m/n/10 , \T1/zi4/m/sl/
10 "License_is_FOSS"\T1/ptm/m/n/10 ,
[1840] [1841] [1842]
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[]\T1/ptm/m/n/10 (\T1/ptm/m/it/10 deprecated\T1/ptm/m/n/10 , use \T1/zi4/m/sl/1
0 bibtex = T|F \T1/ptm/m/n/10 in-stead!) a num-ber, say $\OML/cmm/m/it/10 m$\T1
/ptm/m/n/10 , in-di-cat-

Underfull \hbox (badness 2961) in paragraph at lines 1089--1097
\T1/ptm/m/n/10 ing that the bib-tex code should be given in ad-di-tion to the f
or-mat-

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\T1/ptm/m/n/10 ted tex \T1/ptm/m/it/10 when \T1/ptm/m/n/10 there are not more t
han $\OML/cmm/m/it/10 m$ \T1/ptm/m/n/10 en-tries. The de-fault is

Underfull \hbox (badness 3735) in paragraph at lines 1089--1097
\T1/ptm/m/n/10 taken as [][]\T1/zi4/m/sl/10 getOption[][][]("citation.bibtex.ma
x",1) \T1/ptm/m/n/10 which is \T1/zi4/m/sl/10 1 \T1/ptm/m/n/10 typ-i-cally.

Underfull \hbox (badness 1817) in paragraph at lines 1089--1097
\T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f
ault by

Underfull \hbox (badness 10000) in paragraph at lines 1101--1103
[]\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing
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Underfull \hbox (badness 1371) in paragraph at lines 1606--1608
[]\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T
1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to
[1850] [1851] [1852] [1853] [1854] [1855] [1856] [1857] [1858]
Underfull \hbox (badness 2057) in paragraph at lines 2215--2217
[]\T1/ptm/m/n/10 None for \T1/zi4/m/sl/10 chooseCRANmirror()\T1/ptm/m/n/10 , th
is func-tion is in-voked for its side ef-fect of up-dat-ing
[1859] [1860] [1861] [1862] [1863]pdfTeX warning (ext4): destination with the s
ame identifier (name{Rfn.clipboard}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.2566 ... the Clipboard in MS Windows}{clipboard}
                                                   [1864] [1865]
Underfull \hbox (badness 1748) in paragraph at lines 2733--2736
[]\T1/ptm/m/n/10 A [][]\T1/zi4/m/sl/10 list[][][] \T1/ptm/m/n/10 or [][]\T1/zi4
/m/sl/10 array[][][]\T1/ptm/m/n/10 , see the \T1/zi4/m/sl/10 simplify \T1/ptm/m
/n/10 ar-gu-ment above. In the lat-ter case, the iden-tity
[1866] [1867] [1868] [1869] [1870] [1871]
Underfull \hbox (badness 5388) in paragraph at lines 3142--3146
[]\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .tab\T1/ptm/m/n/10 ', `\T1/zi4/
m/sl/10 .txt\T1/ptm/m/n/10 ' or `\T1/zi4/m/sl/10 .TXT\T1/ptm/m/n/10 ' are read 
us-ing [][]\T1/zi4/m/sl/10 read.table[][][](...,header =

Underfull \hbox (badness 2285) in paragraph at lines 3147--3150
[]\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .csv\T1/ptm/m/n/10 ' or `\T1/zi
4/m/sl/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/zi4/m/sl/10 read.table[]
[][](...,header = TRUE,sep =
[1872] [1873] [1874] [1875] [1876] [1877] [1878] [1879] [1880] [1881] [1882]
Underfull \hbox (badness 1430) in paragraph at lines 3915--3923
[]\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by
 the \T1/zi4/m/sl/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the
[1883]
Underfull \hbox (badness 1231) in paragraph at lines 3992--4004
[]\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers 
via en-vi-ron-ment vari-able
[1884] [1885]
Underfull \hbox (badness 10000) in paragraph at lines 4152--4154
[]\T1/ptm/m/n/10 additional ar-gu-ments to be passed to [][]\T1/zi4/m/sl/10 dow
nload.file[][][] \T1/ptm/m/n/10 and
[1886] [1887] [1888] [1889] [1890] [1891] [1892] [1893] [1894] [1895] [1896]pdf
TeX warning (ext4): destination with the same identifier (name{Rfn.format}) has
 been already used, duplicate ignored
<to be read again> 
                   \relax 
l.4850 ...mat Unordered and Ordered Lists}{format}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.format.1}) has been already used, dupl
icate ignored
<to be read again> 
                   \relax 
l.4850 ...mat Unordered and Ordered Lists}{format}
                                                   [1897] [1898] [1899]
[1900] [1901] [1902] [1903] [1904]
Underfull \hbox (badness 1622) in paragraph at lines 5369--5373
[]\T1/ptm/m/n/10 This func-tion will search for Win-dows han-dles, for pass-ing
 to ex-ter-nal GUIs or to the
[1905] [1906] [1907] [1908] [1909] [1910] [1911] [1912] [1913]
Underfull \hbox (badness 1371) in paragraph at lines 6005--6007
[]\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T
1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to
[1914]
Underfull \hbox (badness 1502) in paragraph at lines 6094--6099
[]\T1/ptm/m/n/10 a char-ac-ter string to be matched in the help page `key-words
'. `Key-

Underfull \hbox (badness 2103) in paragraph at lines 6094--6099
\T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are 
listed in file
[1915] [1916] [1917]
Underfull \hbox (badness 10000) in paragraph at lines 6267--6276
[]\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de
x,
[1918]
Underfull \hbox (badness 2150) in paragraph at lines 6331--6334
[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion 
to search. See
[1919]
Underfull \hbox (badness 3118) in paragraph at lines 6462--6464
[]\T1/ptm/m/n/10 For de-tails of the lock-ing which is done, see the sec-tion `
Lock-ing' in the help for
[1920] [1921] [1922]
Underfull \hbox (badness 1325) in paragraph at lines 6626--6630
[]\T1/ptm/m/n/10 a ma-trix as re-turned by [][]\T1/zi4/m/sl/10 available.packag
es[][][] \T1/ptm/m/n/10 list-ing pack-ages avail-able

Underfull \hbox (badness 4726) in paragraph at lines 6638--6644
\T1/ptm/m/n/10 used if \T1/zi4/m/sl/10 repos = NULL\T1/ptm/m/n/10 . Can also be
 a char-ac-ter vec-tor, a sub-set of

Underfull \hbox (badness 10000) in paragraph at lines 6710--6713
[]\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to
 be

Underfull \hbox (badness 10000) in paragraph at lines 6710--6713
\T1/ptm/m/n/10 passed to \T1/zi4/m/sl/10 R CMD INSTALL \T1/ptm/m/n/10 for a sou
rce pack-age in-stall. E.g.,
[1923]
Underfull \hbox (badness 3219) in paragraph at lines 6786--6793
[]\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is \T1/zi4/m/sl/
10 "both" \T1/ptm/m/n/10 which means `use bi-nary if avail-

Underfull \hbox (badness 5175) in paragraph at lines 6786--6793
\T1/ptm/m/n/10 able and cur-rent, oth-er-wise try source'. The ac-tion if there
 are source pack-ages

Underfull \hbox (badness 1342) in paragraph at lines 6786--6793
\T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com
-piled is con-trolled by

Underfull \hbox (badness 1596) in paragraph at lines 6786--6793
[][]\T1/zi4/m/sl/10 getOption[][][]("install.packages.compile.from.source")\T1/
ptm/m/n/10 . \T1/zi4/m/sl/10 type = "both" \T1/ptm/m/n/10 will be silently
[1924]
Underfull \hbox (badness 2932) in paragraph at lines 6794--6797
[]\T1/ptm/m/n/10 Using pack-ages with \T1/zi4/m/sl/10 type = "source" \T1/ptm/m
/n/10 al-ways works pro-vided the pack-age con-tains no
[1925]
Underfull \hbox (badness 10000) in paragraph at lines 6930--6935
[][][]\T1/zi4/m/sl/10 update.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10
 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 download.packages
[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 installed.packages[][][]\T1/ptm/m/n/
10 ,
[1926] [1927] [1928] [1929] [1930] [1931] [1932] [1933] [1934] [1935] [1936]
[1937] [1938] [1939] [1940] [1941] [1942] [1943] [1944] [1945] [1946] [1947]
[1948]
Underfull \hbox (badness 10000) in paragraph at lines 8431--8433
[]\T1/ptm/m/n/10 for \T1/zi4/m/sl/10 asDateBuilt()\T1/ptm/m/n/10 , a [][]\T1/zi
4/m/sl/10 character[][][] \T1/ptm/m/n/10 string as from
[1949]
Underfull \hbox (badness 2310) in paragraph at lines 8453--8458
[]\T1/ptm/m/n/10 If a `\T1/zi4/m/sl/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the
 given pack-age is found and can suc-cess-fully be read,
[1950] [1951] [1952] [1953] [1954] [1955] [1956]
Underfull \hbox (badness 1248) in paragraph at lines 8977--8981
[]\T1/zi4/m/sl/10 R CMD build \T1/ptm/m/n/10 builds \T1/phv/m/n/10 R \T1/ptm/m/
n/10 source tar-balls. The name(s) of the pack-ages are taken from the
[1957]
Underfull \hbox (badness 1789) in paragraph at lines 9055--9057
[]\T1/ptm/m/n/10 See `Writ-ing R Ex-ten-sions' and the `R for Win-dows FAQ' for
 more dis-cus-sion of the
[1958] [1959] [1960] [1961] [1962] [1963] [1964] [1965] [1966]
Underfull \vbox (badness 5533) has occurred while \output is active [1967]
[1968] [1969]
Underfull \hbox (badness 1097) in paragraph at lines 9892--9895
[]\T1/ptm/m/n/10 The name \T1/zi4/m/sl/10 "clipboard" \T1/ptm/m/n/10 may also b
e used on Win-dows, in which case
[1970] [1971]
Underfull \hbox (badness 3000) in paragraph at lines 10028--10033
[][][]\T1/zi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 type.conve
rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for 
read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i
dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/zi4/m/sl/10 read.t
able[][][]\T1/ptm/m/n/10 ;
[1972] [1973] [1974] [1975] [1976] [1977] [1978] [1979]
Underfull \hbox (badness 2134) in paragraph at lines 10611--10616
[][][]\T1/zi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 type.conve
rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for 
read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i
dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/zi4/m/sl/10 write.
table[][][]\T1/ptm/m/n/10 ;
[1980]
Underfull \hbox (badness 10000) in paragraph at lines 10667--10672
[]\T1/ptm/m/n/10 The `hive' con-tain-ing the key. The ab-bre-vi-a-tions are for


Underfull \hbox (badness 10000) in paragraph at lines 10667--10672
\T1/zi4/m/sl/10 HKEY_LOCAL_MACHINE\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 HKEY_CLASSES
_ROOT\T1/ptm/m/n/10 . \T1/zi4/m/sl/10 HKEY_CURRENT_USER\T1/ptm/m/n/10 ,
[1981] [1982] [1983] [1984] [1985] [1986] [1987]
Underfull \hbox (badness 2469) in paragraph at lines 11155--11159
[]\T1/ptm/m/n/10 Wikipedia con-trib-u-tors (2006). Ro-man nu-mer-als. Wikipedia
, The Free En-cy-clo-pe-dia.

Underfull \hbox (badness 3428) in paragraph at lines 11155--11159
[][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / w / index . php ? title
 = Roman _ numerals & oldid = 78252134$[][]\T1/ptm/m/n/10 . Ac-
[1988] [1989] [1990] [1991] [1992]
Underfull \hbox (badness 4060) in paragraph at lines 11486--11489
[]\T1/ptm/m/n/10 If `\T1/zi4/m/sl/10 --default-packages\T1/ptm/m/n/10 ' is not 
used, then \T1/zi4/m/sl/10 Rscript \T1/ptm/m/n/10 checks the en-vi-ron-ment var
i-able

Overfull \hbox (18.77168pt too wide) in paragraph at lines 11514--11514
 []\T1/zi4/m/n/9 Rscript --default-packages=methods,datasets,utils,grDevices,gr
aphics,stats -e \TS1/zi4/m/n/9 '\T1/zi4/m/n/9 sessionInfo()\TS1/zi4/m/n/9 '[] 
[1993] [1994] [1995] [1996]
Underfull \hbox (badness 2150) in paragraph at lines 11753--11755
[][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/
ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 https : / / www . gnu . org / software / emac
s / manual /
[1997] [1998] [1999]
Underfull \hbox (badness 10000) in paragraph at lines 11972--11976
[]\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/sl/10 stylepath \T1/ptm/m/n/10 is n
ow taken from the en-vi-ron-ment vari-able
[2000]
Underfull \hbox (badness 10000) in paragraph at lines 12003--12009
[]\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y
ou can add a
[2001] [2002]
Underfull \hbox (badness 1009) in paragraph at lines 12197--12209
[]\T1/ptm/m/n/10 Before each code chunk is eval-u-ated, zero or more hook func-
tions can be ex-e-cuted. If
[2003]
Underfull \hbox (badness 4779) in paragraph at lines 12234--12236
[]\T1/ptm/m/n/10 The file `\T1/zi4/m/sl/10 Rconsole\T1/ptm/m/n/10 ' con-fig-ure
s the R GUI (\T1/zi4/m/sl/10 Rgui\T1/ptm/m/n/10 ) con-sole un-der MS Win-dows a
nd

Underfull \hbox (badness 1077) in paragraph at lines 12264--12271
\T1/ptm/m/n/10 (strip-ping any trail-ing slash), oth-er-wise to the Win-dows `p
er-sonal' di-rec-tory, oth-er-wise to
[2004] [2005] [2006] [2007] [2008] [2009]
Underfull \hbox (badness 3780) in paragraph at lines 12665--12669
[]\T1/ptm/m/n/10 A Bio-con-duc-tor mir-ror can be se-lected by set-ting [][]\T1
/zi4/m/sl/10 options[][][]("BioC_mirror")\T1/ptm/m/n/10 , e.g. via

Underfull \hbox (badness 2635) in paragraph at lines 12681--12684
[]\T1/ptm/m/n/10 Repository `\T1/zi4/m/sl/10 CRAN\T1/ptm/m/n/10 ' is treated sp
e-cially: the value is taken from the cur-rent set-ting of
[2010] [2011] [2012]
Underfull \hbox (badness 2302) in paragraph at lines 12885--12887
[]\T1/ptm/m/n/10 Convert file paths to the short form. This is an in-ter-face t
o the Win-dows API call
[2013] [2014] [2015] [2016] [2017]
Underfull \hbox (badness 10000) in paragraph at lines 13181--13186
[]\T1/ptm/m/n/10 logical; if \T1/zi4/m/sl/10 TRUE \T1/ptm/m/n/10 (de-fault), []
[]\T1/zi4/m/sl/10 deparse[][][](control = <S>) \T1/ptm/m/n/10 will not have

Underfull \hbox (badness 5970) in paragraph at lines 13190--13193
[]\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t
ive
[2018]
Underfull \vbox (badness 10000) has occurred while \output is active [2019]
[2020] [2021] [2022] [2023]
Underfull \hbox (badness 2932) in paragraph at lines 13610--13617
[]\T1/ptm/m/n/10 If \T1/zi4/m/sl/10 syntax = NULL \T1/ptm/m/n/10 (the de-fault)
 then the avail-able syn-tax ob-jects are con-sulted in turn,

Underfull \hbox (badness 1688) in paragraph at lines 13610--13617
\T1/ptm/m/n/10 and se-lected if their \T1/zi4/m/sl/10 extension \T1/ptm/m/n/10 
com-po-nent matches (as a reg-exp) the file name. Ob-
[2024] [2025] [2026] [2027]
Underfull \hbox (badness 6510) in paragraph at lines 13919--13923
[]\T1/ptm/m/n/10 When ar-gu-ment \T1/zi4/m/sl/10 tar \T1/ptm/m/n/10 is set to t
he com-mand \T1/zi4/m/sl/10 tar \T1/ptm/m/n/10 on ma-cOS, en-vi-ron-ment vari-a
ble

Underfull \hbox (badness 10000) in paragraph at lines 13926--13929
[][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ 
format)$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 http : / / pubs . opengroup .
 org /

Underfull \hbox (badness 2245) in paragraph at lines 13926--13929
\T1/zi4/m/sl/10 onlinepubs / 9699919799 / utilities / pax . html # tag _ 20 _ 9
2 _ 13 _ 06$[][] \T1/ptm/m/n/10 for the way the POSIX
[2028] [2029] [2030] [2031] [2032] [2033] [2034] [2035] [2036]
Underfull \hbox (badness 10000) in paragraph at lines 14590--14595
[]\T1/ptm/m/n/10 Arguments such as \T1/zi4/m/sl/10 destdir \T1/ptm/m/n/10 and \
T1/zi4/m/sl/10 dependencies \T1/ptm/m/n/10 to be passed to

Underfull \hbox (badness 3861) in paragraph at lines 14590--14595
[][]\T1/zi4/m/sl/10 install.packages[][][] \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 i
gnore_repo_cache\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 max_repo_cache_age \T1/ptm/m/n
/10 and
[2037]
Underfull \hbox (badness 1052) in paragraph at lines 14596--14598
[]\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and
 in-stall. See

Underfull \hbox (badness 10000) in paragraph at lines 14655--14658
[][][]\T1/zi4/m/sl/10 install.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/1
0 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 download.package
s[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 installed.packages[][][]\T1/ptm/m/n
/10 ,
[2038] [2039] [2040] [2041] [2042] [2043] [2044] [2045] [2046] [2047] [2048]
[2049]
Underfull \hbox (badness 10000) in paragraph at lines 15428--15430
[]\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec-
tion e.g. \T1/zi4/m/sl/10 file =
[2050] [2051] [2052]) [2053] [2054] (KernSmooth-pkg.tex
Chapter 15.
[2055] [2056] [2057] [2058] [2059] [2060] [2061] [2062] [2063] [2064])
(MASS-pkg.tex
Chapter 16.
[2065] [2066] [2067] [2068] [2069] [2070] [2071] [2072] [2073] [2074] [2075]
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Underfull \hbox (badness 7944) in paragraph at lines 2694--2697
[]\T1/ptm/m/n/10 further ar-gu-ments for \T1/zi4/m/sl/10 plot \T1/ptm/m/n/10 an
d graph-i-cal pa-ram-e-ters. Note that
[2102] [2103] [2104]
Underfull \hbox (badness 10000) in paragraph at lines 2864--2869
\T1/zi4/m/sl/10 "geometric"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "log-normal"\T1/ptm
/m/n/10 , \T1/zi4/m/sl/10 "lognormal"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "logistic
"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "negative
[2105] [2106]
Underfull \hbox (badness 4686) in paragraph at lines 3032--3034
[]\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i-
na-tor ex-ceeds
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Underfull \hbox (badness 1117) in paragraph at lines 4791--4794
[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
rm \T1/zi4/m/sl/10 response ~
[2132]
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[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
rm \T1/zi4/m/sl/10 response ~
[2133] [2134] [2135] [2136] [2137] [2138] [2139] [2140] [2141] [2142] [2143]
[2144] [2145] [2146] [2147] [2148] [2149]pdfTeX warning (ext4): destination wit
h the same identifier (name{Rfn.npk}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.6111 ...sical N, P, K Factorial Experiment}{npk}
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l.6111 ...sical N, P, K Factorial Experiment}{npk}
                                                   [2150] [2151] [2152]
[2153] [2154]
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[2156] [2157] [2158] [2159] [2160] [2161] [2162]
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[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
rm \T1/zi4/m/sl/10 response ~
[2163]
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[]\T1/ptm/m/n/10 The log-log and com-ple-men-tary log-log links are the in-crea
s-ing func-tions $\OML/cmm/m/it/10 F[]\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 p\OT1/c
mr/m/n/10 ) =
[2164] [2165] [2166]
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\T1/ptm/m/n/10 only the first \T1/zi4/m/sl/10 dimen \T1/ptm/m/n/10 dis-crim-i-n
ant com-po-nents are used (ex-cept for
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[]\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i-
na-tor ex-ceeds
[2176] [2177] [2178] [2179] [2180] [2181] [2182] [2183] [2184] [2185] [2186]
[2187] [2188] [2189] [2190] [2191] [2192] [2193] [2194] [2195] [2196] [2197]
[2198] [2199] [2200] [2201] [2202] [2203] [2204] [2205] [2206] [2207] [2208]
[2209] [2210] [2211] [2212]) (Matrix-pkg.tex
Chapter 17.

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[]\T1/ptm/m/n/10 Note that the cur-rent im-ple-men-ta-tion de-tails are sub-jec
t to change, and if you

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\T1/ptm/m/n/10 con-sider work-ing with these classes, please con-tact the pack-
age main-tain-ers
[2213]
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[]\T1/ptm/m/n/10 This is cur-rently ex-per-i-men-tal and not yet used for our o
wn code. Please con-tact us
[2214] [2215] [2216] [2217]
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[]\T1/ptm/m/n/10 logical; if true the re-sult will be sym-met-ric (in-her-it-in
g from class
[2218] [2219]
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[]\T1/ptm/m/n/10 The value of \T1/zi4/m/sl/10 bdiag() \T1/ptm/m/n/10 in-heris f
rom class [][]\T1/zi4/m/sl/10 CsparseMatrix[][][]\T1/ptm/m/n/10 , whereas \T1/z
i4/m/sl/10 .bdiag() \T1/ptm/m/n/10 re-turns a
[2220] [2221] [2222] [2223] [2224]
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[]\T1/zi4/m/sl/10 signature(from = "CHMfactor",to = "sparseMatrix") \T1/ptm/m/n
/10 (or equiv-a-lently, \T1/zi4/m/sl/10 to =
[2225] [2226]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.chol}) has been already used, duplicate ignored
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                   \relax 
l.1134 ...- 'Matrix' S4 Generic and Methods}{chol}
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                   \relax 
l.1134 ...- 'Matrix' S4 Generic and Methods}{chol}
                                                  
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\T1/ptm/m/n/10 sider [][]\T1/zi4/m/sl/10 Cholesky[][][]() \T1/ptm/m/n/10 in suc
h sit-u-a-tions, since \T1/zi4/m/sl/10 chol(x,pivot=TRUE) \T1/ptm/m/n/10 uses t
he same al-go-rithm
[2227pdfTeX warning (ext4): destination with the same identifier (name{Rfn.chol
,dsCMatrix.Rdash.method}) has been already used, duplicate ignored

\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.1209 \item[chol]
                   \code{signature(x = "dgeMatrix")}: works viapdfTeX warning (
ext4): destination with the same identifier (name{Rfn.chol,lsCMatrix.Rdash.meth
od}) has been already used, duplicate ignored

\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.1209 \item[chol]
                   \code{signature(x = "dgeMatrix")}: works viapdfTeX warning (
ext4): destination with the same identifier (name{Rfn.chol,nsCMatrix.Rdash.meth
od}) has been already used, duplicate ignored

\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
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l.1209 \item[chol]
                   \code{signature(x = "dgeMatrix")}: works via] [2228]
[2229]
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[]\T1/ptm/m/n/10 This is a generic func-tion with spe-cial meth-ods for dif-fer
-ent types of ma-tri-ces. Use
[2230] [2231]
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[]\T1/ptm/m/n/10 Class \T1/zi4/m/sl/10 "MatrixFactorization" \T1/ptm/m/n/10 and
 \T1/zi4/m/sl/10 "dtrMatrix"\T1/ptm/m/n/10 , di-rectly. Class \T1/zi4/m/sl/10 "
dgeMatrix"\T1/ptm/m/n/10 , by class

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[]\T1/ptm/m/n/10 Both these fac-tor-iza-tions can \T1/ptm/m/it/10 di-rectly \T1
/ptm/m/n/10 be treated as (tri-an-gu-lar) ma-tri-ces, as they ex-tend
[2232]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.col
Sums}) has been already used, duplicate ignored
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                   \relax 
l.1623 ... Row and Column Sums and Means}{colSums}
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                   \relax 
l.1623 ... Row and Column Sums and Means}{colSums}
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                   \relax 
l.1624 \aliasA{colMeans}{colSums}{colMeans}
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l.1656 \aliasA{rowSums}{colSums}{rowSums}
                                          [2233] [2234] [2235]
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[]\T1/ptm/m/n/10 a num-ber $\OML/cmm/m/it/10 > \OT1/cmr/m/n/10 0$\T1/ptm/m/n/10
 , the es-ti-mated (1-norm) con-di-tion num-ber $[]$; when
[2236] [2237] [2238] [2239] [2240]
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[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/zi4/m/sl/10 n
ew("dgCMatrix",...)\T1/ptm/m/n/10 , more typ-i-cally via
[2241] [2242] [2243] [2244]
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[]\T1/ptm/m/n/10 However this means that a ma-trix typ-i-cally can tbe stored i
n more than one pos-si-ble
[2245] [2246]
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[]\T1/zi4/m/sl/10 Diagonal() \T1/ptm/m/n/10 re-turns an ob-ject of class [][]\T
1/zi4/m/sl/10 ddiMatrix[][][] \T1/ptm/m/n/10 or [][]\T1/zi4/m/sl/10 ldiMatrix[]
[][] \T1/ptm/m/n/10 (with ``su-per-class''
[2247]
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[]\T1/zi4/m/sl/10 signature(x = "diagonalMatrix")\T1/ptm/m/n/10 : all these gro
up meth-ods re-turn a
[2248] [2249] [2250]
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[]\T1/zi4/m/sl/10 signature(x = "dMatrix",digits = "numeric")\T1/ptm/m/n/10 : t
his group con-tains [][]\T1/zi4/m/sl/10 round[][][]() \T1/ptm/m/n/10 and

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[][][]\T1/zi4/m/sl/10 drop0[][][](x,tol=1e-10) \T1/ptm/m/n/10 is some-times pre
fer-able to (and more ef-fi-cient than)
[2251] [2252]
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[]\T1/ptm/m/n/10 a Ma-trix like \T1/zi4/m/sl/10 x \T1/ptm/m/n/10 but with no ex
-plicit ze-ros, i.e., \T1/zi4/m/sl/10 !any(x@x == 0)\T1/ptm/m/n/10 , al-ways in
-her-it-ing from
[2253] [2254] [2255] [2256] [2257]
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[]\T1/zi4/m/sl/10 signature(x = "dspMatrix",type = "character")\T1/ptm/m/n/10 ,
 or \T1/zi4/m/sl/10 x = "dsyMatrix" \T1/ptm/m/n/10 or \T1/zi4/m/sl/10 type =

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[]\T1/zi4/m/sl/10 signature(x = "dspMatrix",type = "character")\T1/ptm/m/n/10 ,
 or \T1/zi4/m/sl/10 x = "dsyMatrix" \T1/ptm/m/n/10 or \T1/zi4/m/sl/10 type =
[2258] [2259]
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[]\T1/ptm/m/n/10 Class \T1/zi4/m/sl/10 "dgCMatrix"\T1/ptm/m/n/10 , di-rectly. C
lass \T1/zi4/m/sl/10 "triangularMatrix"\T1/ptm/m/n/10 , di-rectly. Class \T1/zi
4/m/sl/10 "dMatrix"\T1/ptm/m/n/10 ,
[2260] [2261]
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[]\T1/zi4/m/sl/10 signature(x = "dtpMatrix",logarithm = "logical")\T1/ptm/m/n/1
0 : the [][]\T1/zi4/m/sl/10 determinant[][][](x)
[2262] [2263] [2264] [2265] [2266] [2267]
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 [] \T1/zi4/m/n/9 readHB(gzcon(url("http://www.cise.ufl.edu/research/sparse/RB/
Boeing/msc00726.tar.gz"))))[] 

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 [] \T1/zi4/m/n/9 readMM(gzcon(url("ftp://math.nist.gov/pub/MatrixMarket2/Harwe
ll-Boeing/counterx/jgl009.mtx.gz"))))[] 
[2268] [2269]
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[]\T1/ptm/m/n/10 a string spec-i-fy-ing how the \T1/zi4/m/sl/10 zero.print \T1/
ptm/m/n/10 codes should be aligned, see
[2270] [2271] [2272] [2273] [2274]
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[]\T1/ptm/m/n/10 color for the bor-der of each rect-an-gle. \T1/zi4/m/sl/10 NA 
\T1/ptm/m/n/10 means no bor-der is drawn.

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\T1/ptm/m/n/10 When \T1/zi4/m/sl/10 NULL \T1/ptm/m/n/10 as by de-fault, \T1/zi4
/m/sl/10 border.col <-if(lwd < .01) NA else NULL \T1/ptm/m/n/10 is

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[]\T1/ptm/m/n/10 All meth-ods cur-rently end up call-ing the method for the [][
]\T1/zi4/m/sl/10 dgTMatrix[][][] \T1/ptm/m/n/10 class. Use
[2275]
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 []\T1/zi4/m/n/9 image(USCounties, c(1,100), c(1,100), useAbs=FALSE, lwd=3, bor
der.col = adjustcolor("skyblue", 1/2))[] 
[2276]
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[]\T1/ptm/m/n/10 While ``row-indexing'' (of more than one row \T1/ptm/m/it/10 o
r \T1/ptm/m/n/10 us-ing \T1/zi4/m/sl/10 drop=FALSE\T1/ptm/m/n/10 ) stays within
 the

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[]\T1/zi4/m/sl/10 signature(x = "matrix",y = "indMatrix") \T1/ptm/m/n/10 and ot
her sig-na-tures (use
[2277]
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[]\T1/zi4/m/sl/10 signature(from = "numeric",to = "indMatrix")\T1/ptm/m/n/10 : 
a user con-ve-nience, to al-low

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[]\T1/zi4/m/sl/10 signature(from = "indMatrix",to = "matrix")\T1/ptm/m/n/10 : c
o-er-cion to a tra-di-tional
[2278] [2279] [2280] [2281] [2282]
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[]\T1/zi4/m/sl/10 isTriangular(M) \T1/ptm/m/n/10 re-turns a [][]\T1/zi4/m/sl/10
 logical[][][] \T1/ptm/m/n/10 in-di-cat-ing if \T1/zi4/m/sl/10 M \T1/ptm/m/n/10
 is a tri-an-gu-lar ma-trix. Anal-o-gously,
[2283] [2284] [2285] [2286]
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[]\T1/zi4/m/sl/10 signature(x = "ndenseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally
 equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2287]
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[]\T1/ptm/m/n/10 Class \T1/zi4/m/sl/10 "ldenseMatrix"\T1/ptm/m/n/10 , di-rectly
. Class \T1/zi4/m/sl/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/zi4/m/sl/10 "lde
nseMatrix"\T1/ptm/m/n/10 . Class
[2288]
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[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/zi4/m/sl/10 t[][][]() \T1/ptm/m/n/10
 and co-er-cion meth-ods (for [][]\T1/zi4/m/sl/10 as[][][](.)\T1/ptm/m/n/10 ); 
use, e.g.,
[2289]
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[]\T1/zi4/m/sl/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-call
y equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2290]
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[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/zi4/m/sl/10 t[][][]() \T1/ptm/m/n/10
 and co-er-cion meth-ods (for [][]\T1/zi4/m/sl/10 as[][][](.)\T1/ptm/m/n/10 ; u
se, e.g.,
[2291]
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[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/zi4/m/sl/10 t[][][]() \T1/ptm/m/n/10
 and co-er-cion meth-ods (for [][]\T1/zi4/m/sl/10 as[][][](.)\T1/ptm/m/n/10 ; u
se, e.g.,
[2292]
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[]\T1/zi4/m/sl/10 lu() \T1/ptm/m/n/10 is a generic func-tion with spe-cial meth
-ods for dif-fer-ent types of ma-tri-ces. Use
[2293] [2294] [2295]
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[]\T1/ptm/m/n/10 Note that when the re-sult-ing ma-trix is di-ag-o-nal (``math-
e-mat-i-cally''),
[2296]
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[]\T1/ptm/m/n/10 Most of the time, the func-tion works via a tra-di-tional (\T1
/ptm/m/it/10 full\T1/ptm/m/n/10 ) [][]\T1/zi4/m/sl/10 matrix[][][]\T1/ptm/m/n/1
0 . How-ever,
[2297]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.det
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                   \relax 
l.6868 \aliasA{det}{Matrix-class}{det}
                                      
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[]\T1/zi4/m/sl/10 signature(x = "Matrix")\T1/ptm/m/n/10 : sim-ply de-fined as \
T1/zi4/m/sl/10 prod(dim(x)) \T1/ptm/m/n/10 (and hence of mode

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[]\T1/zi4/m/sl/10 signature(object = "Matrix")\T1/ptm/m/n/10 : draws an [][]\T1
/zi4/m/sl/10 image[][][] \T1/ptm/m/n/10 of the ma-trix en-tries, us-ing

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[2298]pdfTeX warning (ext4): destination with the same identifier (name{Rfn..Rp
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                   \relax 
l.7044 ...*\%}{matrix-products}{.Rpcent.*.Rpcent.}
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l.7152 ...A{crossprod}{matrix-products}{crossprod}
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                   \relax 
l.7252 ...tcrossprod}{matrix-products}{tcrossprod}
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l.7356 
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rossprod.Rdash.methods}) has been already used, duplicate ignored

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l.7356 
       ] [2300]
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[]\T1/zi4/m/sl/10 signature(x = "dtrMatrix",y = "matrix") \T1/ptm/m/n/10 and ot
her sig-na-tures (use

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\T1/zi4/m/sl/10 showMethods("%*%",class="dtrMatrix")\T1/ptm/m/n/10 ): ma-trix m
ul-ti-pli-ca-tion. Mul-ti-pli-ca-tion of

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[]\T1/zi4/m/sl/10 signature(x = "CsparseMatrix",y = "missing") \T1/ptm/m/n/10 r
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[]\T1/zi4/m/sl/10 signature(x = "TsparseMatrix",y = "missing") \T1/ptm/m/n/10 r
e-turns \T1/zi4/m/sl/10 t(x) %*% x \T1/ptm/m/n/10 as an

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[]\T1/zi4/m/sl/10 signature(x = "dtrMatrix",y = "matrix") \T1/ptm/m/n/10 and ot
her sig-na-tures, see
[2301] [2302]
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[]\T1/ptm/m/n/10 classes in-her-it-ing from \T1/zi4/m/sl/10 "MatrixFactorizatio
n"\T1/ptm/m/n/10 , such as [][]\T1/zi4/m/sl/10 LU[][][]\T1/ptm/m/n/10 , [][]\T1
/zi4/m/sl/10 Cholesky[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 CHMfactor[][][]
\T1/ptm/m/n/10 , and
[2303]
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[]\T1/zi4/m/sl/10 signature(x = "ndenseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally
 equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2304]
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[]\T1/ptm/m/n/10 logical in-di-cat-ing if \T1/zi4/m/sl/10 X <-(X + t(X))/2 \T1/
ptm/m/n/10 should be done, af-ter \T1/zi4/m/sl/10 X
[2305] [2306]
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[]\T1/ptm/m/n/10 Class \T1/zi4/m/sl/10 "ndenseMatrix"\T1/ptm/m/n/10 , di-rectly
. Class \T1/zi4/m/sl/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/zi4/m/sl/10 "nde
nseMatrix"\T1/ptm/m/n/10 . Class

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[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/zi4/m/sl/10 t[][][]() \T1/ptm/m/n/10
 and co-er-cion meth-ods (for [][]\T1/zi4/m/sl/10 as[][][](.)\T1/ptm/m/n/10 ); 
use, e.g.,
[2308] [2309]
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[]\T1/ptm/m/n/10 fast sim-ple meth-ods
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m}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.8154 \HeaderA{norm}{Matrix Norms}{norm}
                                         pdfTeX warning (ext4): destination wit
h the same identifier (name{Rfn.norm.1}) has been already used, duplicate ignor
ed
<to be read again> 
                   \relax 
l.8154 \HeaderA{norm}{Matrix Norms}{norm}
                                          [2311] [2312]
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[]\T1/zi4/m/sl/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-call
y equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2313]
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[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/zi4/m/sl/10 t[][][]() \T1/ptm/m/n/10
 and co-er-cion meth-ods (for [][]\T1/zi4/m/sl/10 as[][][](.)\T1/ptm/m/n/10 ; u
se, e.g.,
[2314]
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[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/zi4/m/sl/10 t[][][]() \T1/ptm/m/n/10
 and co-er-cion meth-ods (for [][]\T1/zi4/m/sl/10 as[][][](.)\T1/ptm/m/n/10 ; u
se, e.g.,
[2315]
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[]\T1/zi4/m/sl/10 signature(x = "matrix",y = "pMatrix") \T1/ptm/m/n/10 and othe
r sig-na-tures (use

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[]\T1/zi4/m/sl/10 signature(from = "numeric",to = "pMatrix")\T1/ptm/m/n/10 : a 
user con-ve-nience, to al-low
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ntifier (name{Rfn.qr}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.8956 \aliasA{qr}{qr-methods}{qr}
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xt4): destination with the same identifier (name{Rfn.rcond}) has been already u
sed, duplicate ignored
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                   \relax 
l.9252 ... the Reciprocal Condition Number}{rcond}
                                                   [2325] [2326] [2327]
[2328]
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[]\T1/ptm/m/n/10 The al-go-rithm first sam-ples ``en-coded'' $\OT1/cmr/m/n/10 (
\OML/cmm/m/it/10 i; j\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 s with-out re-place-ment,
 via one di-men-sional

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\T1/ptm/m/n/10 in-dices, if not \T1/zi4/m/sl/10 symmetric [][]sample.int[][][](
nrow*ncol,nnz)\T1/ptm/m/n/10 , then---if \T1/zi4/m/sl/10 rand.x \T1/ptm/m/n/10 
is not \T1/zi4/m/sl/10 NULL\T1/ptm/m/n/10 ---

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\T1/ptm/m/n/10 gets \T1/zi4/m/sl/10 x <-rand.x(nnz) \T1/ptm/m/n/10 and calls []
[]\T1/zi4/m/sl/10 sparseMatrix[][][](i=i,j=j,x=x,..)\T1/ptm/m/n/10 . When \T1/z
i4/m/sl/10 rand.x=NULL\T1/ptm/m/n/10 ,
[2329] [2330] [2331] [2332]pdfTeX warning (ext4): destination with the same ide
ntifier (name{Rfn.solve}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.9829 \aliasA{solve}{solve-methods}{solve}
                                            [2333]
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[]\T1/ptm/m/n/10 with ex-tra ar-gu-ment list \T1/zi4/m/sl/10 ( sparse =
[2334]
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[]\T1/ptm/m/n/10 , and sim-i-lar \T1/zi4/m/sl/10 b\T1/ptm/m/n/10 , in-clud-ing 
\T1/zi4/m/sl/10 "missing"\T1/ptm/m/n/10 , and

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[]\T1/ptm/m/n/10 Construct a sparse model or ``de-sign'' ma-trix, form a for-mu
la and data frame
[2335]
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[]\T1/ptm/m/n/10 character string or \T1/zi4/m/sl/10 NULL \T1/ptm/m/n/10 or (co
-er-ca-ble to)

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[]\T1/ptm/m/n/10 should fac-tors have un-used lev-els dropped? The de-fault for

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[]\T1/zi4/m/sl/10 signature(from = "factor",to = "sparseMatrix")\T1/ptm/m/n/10 
: Co-er-cion of a fac-tor to

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\T1/zi4/m/sl/10 "sparseMatrix" \T1/ptm/m/n/10 pro-duces the ma-trix of in-di-ca
-tor \T1/ptm/b/n/10 rows \T1/ptm/m/n/10 stored as an ob-ject of class
[2344]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.qr.
Q}) has been already used, duplicate ignored
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                   \relax 
l.10824 \aliasA{qr.Q}{sparseQR-class}{qr.Q}
                                            [2345] [2346]
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[]\T1/ptm/m/n/10 vector of the non zero en-tries; may be miss-ing in which case
 a
[2347] [2348]
Underfull \hbox (badness 10000) in paragraph at lines 11216--11219
[]\T1/zi4/m/sl/10 signature(x = "sparseVector") \T1/ptm/m/n/10 re-peat \T1/zi4/
m/sl/10 x\T1/ptm/m/n/10 , with the same ar-gu-ment list
[2349]
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[2351] [2352]
Underfull \hbox (badness 10000) in paragraph at lines 11485--11490
[]\T1/ptm/m/n/10 The va-lid-ity checks do not re-quire a sym-met-ric \T1/zi4/m/
sl/10 Dimnames \T1/ptm/m/n/10 slot, so it can be
[2353]
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[]\T1/ptm/m/n/10 These are generic func-tions with sev-eral meth-ods for dif-fe
r-ent ma-trix classes, use e.g.,
[2354] [2355]
Underfull \hbox (badness 1831) in paragraph at lines 11740--11746
[]\T1/ptm/m/n/10 For con-ve-nience, meth-ods for some op-er-a-tions such as \T1
/zi4/m/sl/10 %*% \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 crossprod \T1/ptm/m/n/10 ar
e de-fined
[2356]
Underfull \hbox (badness 1902) in paragraph at lines 11775--11779
[]\T1/ptm/m/n/10 Note that \T1/zi4/m/sl/10 new(.)\T1/ptm/m/n/10 , [][]\T1/zi4/m
/sl/10 spMatrix[][][] \T1/ptm/m/n/10 or [][]\T1/zi4/m/sl/10 sparseMatrix[][][] 
\T1/ptm/m/n/10 con-struc-tors for \T1/zi4/m/sl/10 "dgTMatrix" \T1/ptm/m/n/10 (a
nd other
[2357] [2358] [2359] [2360] [2361] [2362]
Underfull \hbox (badness 6910) in paragraph at lines 12288--12290
[]\T1/ptm/m/n/10 is cur-rently a sim-ple fall-back
[2363] [2364] [2365]) (boot-pkg.tex [2366]
Chapter 18.
[2367] [2368] [2369] [2370] [2371] [2372] [2373] [2374] [2375] [2376]
Underfull \hbox (badness 1297) in paragraph at lines 797--807
[]\T1/ptm/m/n/10 Where random-number gen-er-a-tion is done in the worker pro-ce
sses, the de-fault be-haviour
[2377]
Underfull \hbox (badness 1881) in paragraph at lines 824--826
[]\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi
-cient boot-strap sim-u-la-tion.
[2378]
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[2380]
Underfull \hbox (badness 10000) in paragraph at lines 1066--1070
[]\T1/ptm/m/n/10 A vec-tor of char-ac-ter strings rep-re-sent-ing the type of i
n-ter-

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\T1/ptm/m/n/10 vals re-quired. The value should be any sub-set of the val-ues

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\T1/zi4/m/sl/10 c("norm","basic","stud","perc","bca") \T1/ptm/m/n/10 or sim-ply
 \T1/zi4/m/sl/10 "all" \T1/ptm/m/n/10 which will
[2381]
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[]\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est. The de-fa
ult value is
[2382] [2383] [2384] [2385]
Underfull \hbox (badness 1571) in paragraph at lines 1443--1445
[]\T1/ptm/m/n/10 Rawlings, J.O. (1988) \T1/ptm/m/it/10 Ap-plied Re-gres-sion An
al-y-sis\T1/ptm/m/n/10 . Wadsworth and Brooks/Cole Statis-
[2386] [2387] [2388] [2389] [2390] [2391]
Underfull \hbox (badness 1005) in paragraph at lines 1797--1804
[]\T1/ptm/m/n/10 The sim-u-la-tion type. Pos-si-ble types are \T1/zi4/m/sl/10 "
ordinary" \T1/ptm/m/n/10 (case re-sam-pling),
[2392] [2393]
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Underfull \hbox (badness 7379) in paragraph at lines 2081--2083
[]\T1/ptm/m/n/10 The length of time (in months) that the res-i-dent spent at Ch
an-ning House.
[2395] [2396] [2397] [2398]
Underfull \hbox (badness 1565) in paragraph at lines 2335--2340
[]\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est on the ori
g-i-nal data set
[2399]
Underfull \hbox (badness 1881) in paragraph at lines 2429--2431
[]\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi
-cient boot-strap sim-u-la-tion.
[2400] [2401]
Underfull \hbox (badness 2970) in paragraph at lines 2533--2537
[]\T1/ptm/m/n/10 The un-bi-ased es-ti-ma-tor uses a mul-ti-plier of \T1/zi4/m/s
l/10 n/((n-1)*(n-2)) \T1/ptm/m/n/10 where \T1/zi4/m/sl/10 n \T1/ptm/m/n/10 is t
he sam-ple

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\T1/ptm/m/n/10 size, if \T1/zi4/m/sl/10 unbiased \T1/ptm/m/n/10 is \T1/zi4/m/sl
/10 FALSE \T1/ptm/m/n/10 then a mul-ti-plier of \T1/zi4/m/sl/10 1/n \T1/ptm/m/n
/10 is used. This is mul-ti-plied by
[2402] [2403] [2404] [2405] [2406] [2407] [2408] [2409] [2410] [2411] [2412]
[2413] [2414] [2415] [2416] [2417] [2418] [2419] [2420] [2421] [2422] [2423]
[2424]
Underfull \hbox (badness 10000) in paragraph at lines 4187--4189
[]\T1/ptm/m/n/10 The quan-tiles at which the plots are re-quired. The de-fault 
is
[2425] [2426] [2427] [2428] [2429] [2430] [2431] [2432] [2433] [2434] [2435]
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[]\T1/ptm/m/n/10 The in-dex of the statis-tic of in-ter-est within the out-put 
of a call to
[2436] [2437] [2438] [2439]
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[]\T1/ptm/m/n/10 An in-te-ger giv-ing the num-ber of classes to be used in the 
boot-strap

Underfull \hbox (badness 1668) in paragraph at lines 5235--5238
\T1/ptm/m/n/10 his-togram. The de-fault is the in-te-ger be-tween 10 and 100 cl
os-est to
[2440] [2441] [2442] [2443] [2444] [2445] [2446] [2447] [2448] [2449] [2450]
Underfull \hbox (badness 4954) in paragraph at lines 6018--6021
[]\T1/ptm/m/n/10 The re-turned value is an ob-ject of class \T1/zi4/m/sl/10 "sa
ddle.distn"\T1/ptm/m/n/10 . See the help file for
[2451] [2452] [2453] [2454] [2455] [2456] [2457] [2458] [2459]
Underfull \hbox (badness 1596) in paragraph at lines 6739--6743
[]\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sec-ond ar-gu-m
ent ex-pected by
[2460] [2461] [2462] [2463] [2464] [2465] [2466] [2467] [2468] [2469])
(class-pkg.tex [2470]
Chapter 19.
[2471] [2472] [2473] [2474] [2475] [2476] [2477] [2478] [2479] [2480] [2481]
[2482] [2483] [2484] [2485] [2486]) (cluster-pkg.tex
Chapter 20.
[2487] [2488] [2489] [2490] [2491]
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[2493] [2494] [2495] [2496]
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[]\T1/ptm/m/n/10 Setting this to \T1/zi4/m/sl/10 FALSE \T1/ptm/m/n/10 saves mem
-ory (and hence time), but dis-ables
[2497]
Underfull \hbox (badness 1412) in paragraph at lines 771--776
[]\T1/ptm/m/n/10 Kaufman and Rousseeuw (see [][]\T1/zi4/m/sl/10 agnes[][][]\T1/
ptm/m/n/10 ), orig-i-nally. Met-ric \T1/zi4/m/sl/10 "jaccard"\T1/ptm/m/n/10 : K
amil Ko-zlowski
[2498] [2499]
Underfull \hbox (badness 10000) in paragraph at lines 864--866
[]\T1/ptm/m/n/10 list with sil-hou-ette width in-for-ma-tion for the best sam-p
le, see
[2500] [2501]
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[]\T1/ptm/m/n/10 simply cor-re-sponds to the global max-i-mum, i.e., is

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[]\T1/ptm/m/n/10 This, the de-fault, has been pro-posed by Mar-tin Maech-ler in
 2012,
[2502] [2503] [2504]
Underfull \hbox (badness 6110) in paragraph at lines 1190--1194
[]\T1/ptm/m/n/10 when \T1/zi4/m/sl/10 x \T1/ptm/m/n/10 does not have a \T1/zi4/
m/sl/10 diss \T1/ptm/m/n/10 nor a \T1/zi4/m/sl/10 data \T1/ptm/m/n/10 com-po-ne
nt, e.g., for
[2505] [2506] [2507]
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[2508] [2509]
Underfull \hbox (badness 2503) in paragraph at lines 1571--1574
[]\T1/ptm/m/n/10 an ob-ject of class \T1/zi4/m/sl/10 "hclust" \T1/ptm/m/n/10 or
 \T1/zi4/m/sl/10 "twins"\T1/ptm/m/n/10 , i.e., typ-i-cally the re-sult of
[2510] [2511] [2512] [2513] [2514] [2515] [2516] [2517]
Underfull \hbox (badness 10000) in paragraph at lines 2162--2165


Underfull \hbox (badness 10000) in paragraph at lines 2176--2182
[][][]\T1/zi4/m/sl/10 predict.ellipsoid[][][] \T1/ptm/m/n/10 which is also the 
[][]\T1/zi4/m/sl/10 predict[][][] \T1/ptm/m/n/10 method for \T1/zi4/m/sl/10 ell
ipsoid \T1/ptm/m/n/10 ob-jects.
[2518] [2519] [2520] [2521]
Underfull \hbox (badness 6675) in paragraph at lines 2411--2413
[]\T1/ptm/m/n/10 list with sil-hou-ette in-for-ma-tion of the near-est crisp cl
us-ter-ing, see
[2522] [2523] [2524] [2525] [2526] [2527] [2528]
Underfull \hbox (badness 2980) in paragraph at lines 2902--2906
[][][]\T1/zi4/m/sl/10 agnes[][][] \T1/ptm/m/n/10 for back-ground and ref-er-enc
es; [][]\T1/zi4/m/sl/10 pam.object[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 cl
ara[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 daisy[][][]\T1/ptm/m/n/10 , [][]\
T1/zi4/m/sl/10 partition.object[][][]\T1/ptm/m/n/10 ,
[2529] [2530] [2531] [2532] [2533]
Underfull \hbox (badness 1142) in paragraph at lines 3243--3246
[]\T1/ptm/m/n/10 graphical pa-ram-e-ters (see [][]\T1/zi4/m/sl/10 par[][][]\T1/
ptm/m/n/10 ) may also be sup-plied and are passed to
[2534] [2535]
Underfull \hbox (badness 1142) in paragraph at lines 3362--3365
[]\T1/ptm/m/n/10 graphical pa-ram-e-ters (see [][]\T1/zi4/m/sl/10 par[][][]\T1/
ptm/m/n/10 ) may also be sup-plied and are passed to
[2536] [2537] [2538] [2539]
Underfull \hbox (badness 2582) in paragraph at lines 3585--3590
[][][]\T1/zi4/m/sl/10 partition.object[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/1
0 clusplot.partition[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 clusplot.default
[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 pam[][][]\T1/ptm/m/n/10 , [][]\T1/zi
4/m/sl/10 pam.object[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 clara[][][]\T1/p
tm/m/n/10 ,
[2540]
Underfull \hbox (badness 3209) in paragraph at lines 3647--3652
[]\T1/ptm/m/n/10 Note that cur-rently the method func-tion sim-ply calls \T1/zi
4/m/sl/10 plot([][]as.hclust[][][](x),...)\T1/ptm/m/n/10 , which

Underfull \hbox (badness 8019) in paragraph at lines 3647--3652
\T1/ptm/m/n/10 dis-patches to [][]\T1/zi4/m/sl/10 plot.hclust[][][](..)\T1/ptm/
m/n/10 . If more flex-i-ble plots are needed, con-sider \T1/zi4/m/sl/10 xx
[2541] [2542] [2543] [2544]
Underfull \hbox (badness 10000) in paragraph at lines 3939--3941
[]\T1/ptm/m/n/10 a \T1/zi4/m/sl/10 dissimilarity \T1/ptm/m/n/10 ob-ject or a \T
1/zi4/m/sl/10 summary.dissimilarity \T1/ptm/m/n/10 one for
[2545] [2546] [2547] [2548]
Underfull \hbox (badness 2626) in paragraph at lines 4163--4168
[]\T1/ptm/m/n/10 arguments passed [][]\T1/zi4/m/sl/10 barplot[][][]()\T1/ptm/m/
n/10 ; note that the de-fault used to be \T1/zi4/m/sl/10 col =
[2549]
Underfull \hbox (badness 1383) in paragraph at lines 4241--4246
[]\T1/ptm/m/n/10 While \T1/zi4/m/sl/10 silhouette() \T1/ptm/m/n/10 is \T1/ptm/m
/it/10 in-trin-sic \T1/ptm/m/n/10 to the [][]\T1/zi4/m/sl/10 partition[][][] \T
1/ptm/m/n/10 clus-ter-ings, and hence has a (triv-ial)
[2550] [2551] [2552] [2553] [2554] [2555] [2556]
Underfull \hbox (badness 10000) in paragraph at lines 4684--4686
[]\T1/ptm/m/n/10 Sample data set ac-com-pa-ny-ing the ref-er-ence be-low (file 
`\T1/zi4/m/sl/10 xclara.dat\T1/ptm/m/n/10 ' in side
[2557] [2558]) (codetools-pkg.tex
Chapter 21.
[2559] [2560] [2561] [2562] [2563]) (foreign-pkg.tex [2564]
Chapter 22.
[2565] [2566] [2567] [2568] [2569] [2570] [2571] [2572]
Underfull \hbox (badness 10000) in paragraph at lines 506--515
[]\T1/ptm/m/n/10 character: what to do with du-pli-cated value la-bels for dif-
fer-

Underfull \hbox (badness 10000) in paragraph at lines 506--515
\T1/ptm/m/n/10 ent lev-els. For \T1/zi4/m/sl/10 "append" \T1/ptm/m/n/10 (the de
-fault), the first orig-i-nal value

Underfull \hbox (badness 10000) in paragraph at lines 506--515
\T1/ptm/m/n/10 la-bel is kept while fur-ther du-pli-cated la-bels are re-named 
to
[2573]
Overfull \hbox (6.73795pt too wide) in paragraph at lines 625--625
 []\T1/zi4/m/n/9 ### Expect lots of warnings as value labels (corresponding to 
R factor labels) are uncomplete,[] 
[2574] [2575] [2576]
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[2577] [2578] [2579] [2580] [2581] [2582] [2583]
Underfull \hbox (badness 10000) in paragraph at lines 1267--1273
[]\T1/ptm/m/n/10 The work for this func-tion is done by \T1/zi4/m/sl/10 foreign
:::writeForeignStata\T1/ptm/m/n/10 ,
[2584] [2585]) (lattice-pkg.tex [2586]
Chapter 23.
[2587] [2588] [2589] [2590] [2591] [2592] [2593] [2594] [2595] [2596] [2597]
[2598] [2599] [2600] [2601] [2602]
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\T1/ptm/m/n/10 no-ta-tion for the x and y axes re-spec-tively. See doc-u-men-ta
-tion for
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[][][]\T1/zi4/m/sl/10 Lattice[][][] \T1/ptm/m/n/10 for an overview of the pack-
age, as well as [][]\T1/zi4/m/sl/10 barchart.table[][][]\T1/ptm/m/n/10 , [][]\T
1/zi4/m/sl/10 print.trellis[][][]\T1/ptm/m/n/10 ,

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[][]\T1/zi4/m/sl/10 panel.stripplot[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 p
anel.superpose[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 panel.loess[][][]\T1/p
tm/m/n/10 , [][]\T1/zi4/m/sl/10 panel.average[][][]\T1/ptm/m/n/10 , [][]\T1/zi4
/m/sl/10 strip.default[][][]\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 additional ar-gu-ments passed to [][]\T1/zi4/m/sl/10 xyplot[][
][]\T1/ptm/m/n/10 , which may pass them on to

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[]\T1/ptm/m/n/10 graphical ar-gu-ments, which are pro-cessed and even-tu-ally p
assed to
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[]\T1/ptm/m/n/10 When \T1/zi4/m/sl/10 breaks \T1/ptm/m/n/10 is un-spec-i-fied, 
the value of
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[]\T1/ptm/m/n/10 A color ramp spec-i-fi-ca-tion, as in the \T1/zi4/m/sl/10 col.
regions \T1/ptm/m/n/10 ar-gu-ment in
[2623]
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[]\T1/ptm/m/n/10 Other use-ful ar-gu-ments are men-tioned in the help page for 
the de-fault panel func-tion
[2624] [2625] [2626] [2627] [2628] [2629] [2630]pdfTeX warning (ext4): destinat
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[]\T1/ptm/m/n/10 A pos-si-ble use of this ar-gu-ment is to change the de-fault 
set-tings

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\T1/ptm/m/n/10 by spec-i-fy-ing \T1/zi4/m/sl/10 lattice.options(default.theme =
 "col.whitebg")\T1/ptm/m/n/10 .

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\T1/ptm/m/n/10 For back-compatibility, this is ini-tially (when lat-tice is loa
ded) set to
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[]\T1/ptm/m/n/10 A char-ac-ter string giv-ing the name of a com-po-nent. If un-
spec-i-fied in

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[]\T1/ptm/m/n/10 A log-i-cal flag, in-di-cat-ing whether a warn-ing should be i
s-sued when
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[]\T1/ptm/m/n/10 A color spec-i-fi-ca-tion. \T1/zi4/m/sl/10 col \T1/ptm/m/n/10 
is used for com-po-nents \T1/zi4/m/sl/10 "plot.symbol"\T1/ptm/m/n/10 ,

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[]\T1/ptm/m/n/10 fill color, ap-pli-ca-ble for com-po-nents \T1/zi4/m/sl/10 plo
t.symbol\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 plot.polygon\T1/ptm/m/n/10 ,

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[]\T1/ptm/m/n/10 border color, ap-pli-ca-ble for com-po-nents \T1/zi4/m/sl/10 p
lot.polygon \T1/ptm/m/n/10 and
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[]\T1/zi4/m/sl/10 plot.shingle \T1/ptm/m/n/10 dis-plays the ranges of shin-gles
 via rect-an-gles. \T1/zi4/m/sl/10 print.shingle \T1/ptm/m/n/10 and
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[]\T1/ptm/m/n/10 logical, spec-i-fy-ing whether the la-bels etc should be hor-i
-zon-tal.

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\T1/zi4/m/sl/10 horizontal=FALSE \T1/ptm/m/n/10 is use-ful for strips on the le
ft of pan-els us-ing
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[]\T1/ptm/m/n/10 logical, whether the view-port be-ing as-signed fo-cus should 
be high-

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[]\T1/ptm/m/n/10 For \T1/zi4/m/sl/10 panel.identify.qqmath\T1/ptm/m/n/10 , ex-t
ra pa-ram-e-ters are passed on to

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\T1/zi4/m/sl/10 panel.identify\T1/ptm/m/n/10 . For \T1/zi4/m/sl/10 panel.identi
fy\T1/ptm/m/n/10 , ex-tra ar-gu-ments are treated as

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\T1/ptm/m/n/10 graph-i-cal pa-ram-e-ters and are used for la-belling. For \T1/z
i4/m/sl/10 trellis.focus

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\T1/ptm/m/n/10 and \T1/zi4/m/sl/10 trellis.switchFocus\T1/ptm/m/n/10 , these ar
e used (in com-bi-na-tion with

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[][]\T1/zi4/m/sl/10 lattice.options[][][]\T1/ptm/m/n/10 ) for high-light-ing th
e cho-sen view-port if so re-quested.
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[]\T1/ptm/m/n/10 Graphical pa-ram-e-ters for the bars. By de-fault, the trel-li
s pa-ram-e-

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\T1/ptm/m/n/10 ter \T1/zi4/m/sl/10 plot.polygon \T1/ptm/m/n/10 is used if there
 is no group-ing vari-able, oth-er-wise
[2668] [2669]
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[]\T1/ptm/m/n/10 Creates Box and Whisker plot of \T1/zi4/m/sl/10 x \T1/ptm/m/n/
10 for ev-ery level of \T1/zi4/m/sl/10 y \T1/ptm/m/n/10 (or the other way round
 if
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\T1/ptm/m/n/10 to know what ar-gu-ments this func-tion is passed when called. U
se
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[]\T1/ptm/m/n/10 Further ar-gu-ments, of-ten graph-i-cal pa-ram-e-ters, even-tu
-ally passed on to
[2685] [2686]
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[]\T1/ptm/m/n/10 default colours are ob-tained from \T1/zi4/m/sl/10 plot.symbol
 \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 plot.line \T1/ptm/m/n/10 us-ing
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[]\T1/ptm/m/n/10 A log-i-cal flag de-ter-min-ing whether the de-fault graph-i-c
al pa-ram-e-ters for
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[]\T1/ptm/m/n/10 Extra ar-gu-ments. Passed down to \T1/zi4/m/sl/10 panel.superp
ose \T1/ptm/m/n/10 from
[2701]
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[]\T1/ptm/m/n/10 Deepayan Sarkar \T1/zi4/m/sl/10 <Deepayan.Sarkar@R-project.org
> \T1/ptm/m/n/10 (\T1/zi4/m/sl/10 panel.superpose.2 \T1/ptm/m/n/10 orig-i-nally
 con-
[2702] [2703]
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[]\T1/ptm/m/n/10 details of his-togram cal-cu-la-tions. \T1/zi4/m/sl/10 type \T
1/ptm/m/n/10 has a dif-fer-ent mean-ing in
[2704]
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[]\T1/ptm/m/n/10 numeric vec-tor of length two, rep-re-sent-ing prob-a-bil-i-ti
es. If used with
[2705] [2706]
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[]\T1/ptm/m/n/10 which packet (counted ac-cord-ing to the packet or-der, de-scr
ibed in

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[]\T1/ptm/m/n/10 list, sim-i-lar to those pro-duced by \T1/zi4/m/sl/10 xscale.c
omponents.default \T1/ptm/m/n/10 and
[2707] [2708] [2709] [2710]
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[]\T1/ptm/m/n/10 returns a list with sev-eral com-po-nents, in-clud-ing \T1/zi4
/m/sl/10 left,right,left.name,right.name,condition
[2711] [2712] [2713] [2714] [2715] [2716] [2717]
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[]\T1/ptm/m/n/10 Factor with lev-els \T1/zi4/m/sl/10 "Svansota"\T1/ptm/m/n/10 ,
 \T1/zi4/m/sl/10 "No. 462"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "Manchuria"\T1/ptm/m
/n/10 , \T1/zi4/m/sl/10 "No. 475"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "Velvet"\T1/p
tm/m/n/10 ,

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[]\T1/ptm/m/n/10 Factor with 6 lev-els: \T1/zi4/m/sl/10 "Grand Rapids"\T1/ptm/m
/n/10 , \T1/zi4/m/sl/10 "Duluth"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "University Fa
rm"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "Morris"\T1/ptm/m/n/10 ,
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l.9853 \aliasA{melanoma}{H\_melanoma}{melanoma}
                                                [2721] [2722] [2723]
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[]\T1/ptm/m/n/10 Rural Health Re-form Pol-icy Re-search Cen-ter. _Ex-plor-ing R
u-ral and Ur-ban Mor-tal-

Underfull \hbox (badness 1509) in paragraph at lines 10077--10080
\T1/ptm/m/n/10 ity Dif-fer-ences_, Au-gust 2015 Bethesda, MD. [][]$\T1/zi4/m/sl
/10 https : / / ruralhealth . und . edu / projects /
[2724] [2725]) (mgcv-pkg.tex [2726]
Chapter 24.
[2727] [2728] [2729]
Underfull \hbox (badness 1142) in paragraph at lines 171--175
\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from

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\T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known 
scale.
[2730] [2731] [2732] [2733]
Underfull \hbox (badness 10000) in paragraph at lines 365--372
[][][]\T1/zi4/m/sl/10 mgcv.parallel[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 m
gcv-package[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 gamObject[][][]\T1/ptm/m/
n/10 , [][]\T1/zi4/m/sl/10 gam.models[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10
 smooth.terms[][][]\T1/ptm/m/n/10 ,

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[][]\T1/zi4/m/sl/10 linear.functional.terms[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m
/sl/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 te[][][] [][]predict.gam[][]
[]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 plot.gam[][][]\T1/ptm/m/n/10 , [][]\T1/z
i4/m/sl/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 gam.side[][][]
\T1/ptm/m/n/10 ,
[2734] [2735] [2736] [2737] [2738] [2739] [2740]
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[]\T1/ptm/m/n/10 Choosing the ba-sis di-men-sion, and check-ing the choice, whe
n us-ing pe-nal-ized re-gres-sion
[2741]
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[]\T1/ptm/m/n/10 Wood, S.N. (2017) Gen-er-al-ized Ad-di-tive Mod-els: An In-tro
-duc-tion with R (2nd edi-tion).
[2742]
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\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
[2766]
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\T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known 
scale.
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[]\T1/ptm/m/n/10 Random ef-fects can be added to \T1/zi4/m/sl/10 gam \T1/ptm/m/
n/10 mod-els us-ing \T1/zi4/m/sl/10 s(...,bs="re") \T1/ptm/m/n/10 terms (see
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[]\T1/ptm/m/n/10 list of the square root penal-ties: last en-try is root of fix
ed penalty, if
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[2804]
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\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
[2805]
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[]\T1/zi4/m/sl/10 gamm \T1/ptm/m/n/10 per-forms poorly with bi-nary data, since
 it uses PQL. It is bet-ter to use \T1/zi4/m/sl/10 gam \T1/ptm/m/n/10 with
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[]\T1/ptm/m/n/10 one sided for-mula con-tain-ing vari-ables needed for pre-dic-
tion, used by
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[]\T1/ptm/m/n/10 A pre-fit gam ob-ject, as pro-duced by \T1/zi4/m/sl/10 gam(...
,fit=FALSE) \T1/ptm/m/n/10 or
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\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
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[2832] [2833] [2834]
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[]\T1/ptm/m/n/10 If \T1/zi4/m/sl/10 rho \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 thet
a \T1/ptm/m/n/10 were sup-plied then deriva-tives are w.r.t. these. In this cas
e, and if
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Underfull \hbox (badness 1242) in paragraph at lines 7272--7273
[]\T1/ptm/m/n/10 Development of mgcv ver-sion 1.8 was part funded by EP-SRC gra
nts EP/K005251/1 and
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Underfull \hbox (badness 6001) in paragraph at lines 7912--7914
[]\T1/ptm/m/n/10 Simon N. Wood \T1/zi4/m/sl/10 <simon.wood@r-project.org> \T1/p
tm/m/n/10 mod-i-fied from Ven-ables and Rip-ley's
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[]\T1/ptm/m/n/10 The fol-low-ing func-tions are pro-vided: \T1/zi4/m/sl/10 Dim.
pdIndot\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 coef.pdIdnot\T1/ptm/m/n/10 , \T1/zi4/m/
sl/10 corMatrix.pdIdnot\T1/ptm/m/n/10 ,

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\T1/zi4/m/sl/10 logDet.pdIdnot\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 pdConstruct.pdId
not\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 pdFactor.pdIdnot\T1/ptm/m/n/10 , \T1/zi4/m/
sl/10 pdMatrix.pdIdnot\T1/ptm/m/n/10 ,
[2874]
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[]\T1/ptm/m/n/10 These func-tions (\T1/zi4/m/sl/10 pdTens\T1/ptm/m/n/10 , \T1/z
i4/m/sl/10 pdConstruct.pdTens\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 pdFactor.pdTens\T
1/ptm/m/n/10 , \T1/zi4/m/sl/10 pdMatrix.pdTens\T1/ptm/m/n/10 ,
[2875] [2876] [2877] [2878] [2879] [2880] [2881] [2882] [2883] [2884] [2885]
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[]\T1/ptm/m/n/10 To fa-cil-i-tate plot-ting with [][]\T1/zi4/m/sl/10 termplot[]
[][]\T1/ptm/m/n/10 , if \T1/zi4/m/sl/10 object \T1/ptm/m/n/10 pos-sesses an at-
tribute \T1/zi4/m/sl/10 "para.only" \T1/ptm/m/n/10 and
[2886] [2887] [2888]
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[]\T1/ptm/m/n/10 To fa-cil-i-tate plot-ting with [][]\T1/zi4/m/sl/10 termplot[]
[][]\T1/ptm/m/n/10 , if \T1/zi4/m/sl/10 object \T1/ptm/m/n/10 pos-sesses an at-
tribute \T1/zi4/m/sl/10 "para.only" \T1/ptm/m/n/10 and
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[2892]
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[]\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a
tes at which

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\T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are 
as for

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[]\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f
i-ca-tion ob-jects of class
[2893]
Underfull \hbox (badness 1205) in paragraph at lines 9870--9872
[]\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a
tes at which

Underfull \hbox (badness 2689) in paragraph at lines 9870--9872
\T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are 
as for
[2894] [2895] [2896]
Underfull \hbox (badness 1253) in paragraph at lines 10069--10071
[]\T1/ptm/m/n/10 Note that the op-ti-mized smooth-ing pa-ram-e-ter se-lec-tion 
cri-te-rion re-ported is one of GCV,
[2897] [2898] [2899] [2900]
Underfull \hbox (badness 4792) in paragraph at lines 10255--10258
[]\T1/ptm/m/n/10 Alternatively, but less straight-for-wardly, the \T1/zi4/m/sl/
10 paraPen \T1/ptm/m/n/10 ar-gu-ment to [][]\T1/zi4/m/sl/10 gam[][][] \T1/ptm/m
/n/10 can be used:

Underfull \hbox (badness 10000) in paragraph at lines 10255--10258
\T1/ptm/m/n/10 see [][]\T1/zi4/m/sl/10 gam.models[][][]\T1/ptm/m/n/10 . If smoo
th-ing pa-ram-e-ter es-ti-ma-tion is by ML or REML (e.g.
[2901]
Underfull \hbox (badness 10000) in paragraph at lines 10350--10353
[]\T1/ptm/m/n/10 the type of resid-u-als wanted. Usu-ally one of \T1/zi4/m/sl/1
0 "deviance"\T1/ptm/m/n/10 ,
[2902] [2903] [2904] [2905] [2906] [2907] [2908] [2909] [2910] [2911] [2912]
Underfull \hbox (badness 3861) in paragraph at lines 10978--10981
[]\T1/ptm/m/n/10 INTERNAL rou-tine to ap-ply ini-tial Sl re-parameterization to
 model ma-trix X, or, if
[2913] [2914]
Underfull \hbox (badness 1320) in paragraph at lines 11084--11089
\T1/ptm/m/n/10 and \T1/zi4/m/sl/10 b.orig = D*b.repara \T1/ptm/m/n/10 (where \T
1/zi4/m/sl/10 b.orig \T1/ptm/m/n/10 is the orig-i-nal pa-ram-e-ter vec-tor). If
 ma-
[2915] [2916]
Underfull \hbox (badness 1975) in paragraph at lines 11190--11195
[]\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f
i-ca-tion ob-jects of class
[2917]
Underfull \hbox (badness 1762) in paragraph at lines 11279--11291
\T1/ptm/m/n/10 plate re-gres-sion splines: see [][]\T1/zi4/m/sl/10 tprs[][][]\T
1/ptm/m/n/10 ); \T1/zi4/m/sl/10 ts.smooth.spec \T1/ptm/m/n/10 (thin plate re-gr
es-sion splines with
[2918] [2919] [2920]
Underfull \vbox (badness 10000) has occurred while \output is active [2921]
Underfull \hbox (badness 7667) in paragraph at lines 11491--11497
[][][]\T1/zi4/m/sl/10 gam[][][] \T1/ptm/m/n/10 can use adap-tive smooths of one
 or two vari-ables, spec-i-fied via terms like

Underfull \hbox (badness 10000) in paragraph at lines 11532--11533
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2922] [2923] [2924] [2925] [2926] [2927]
Underfull \hbox (badness 10000) in paragraph at lines 11808--11810
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2928] [2929]
Underfull \hbox (badness 10000) in paragraph at lines 11936--11937
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2930] [2931]
Underfull \hbox (badness 1436) in paragraph at lines 12074--12081
\T1/ptm/m/n/10 nest-ing of the smooth within the fac-tor. Note how-ever that: i
) \T1/zi4/m/sl/10 gamm \T1/ptm/m/n/10 only al-lows one
[2932] [2933]
Underfull \hbox (badness 10000) in paragraph at lines 12168--12169
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2934] [2935] [2936] [2937] [2938] [2939] [2940] [2941] [2942] [2943]
Underfull \hbox (badness 10000) in paragraph at lines 12754--12760
[]\T1/ptm/m/n/10 A smooth spec-i-fi-ca-tion ob-ject as pro-duced by a

Underfull \hbox (badness 1292) in paragraph at lines 12754--12760
\T1/zi4/m/sl/10 s(...,bs="so",xt=list(bnd=bnd,...)) \T1/ptm/m/n/10 term in a \T
1/zi4/m/sl/10 gam \T1/ptm/m/n/10 for-mula. Note
[2944] [2945] [2946]
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Underfull \vbox (badness 10000) has occurred while \output is active [2948]
[2949]
Underfull \hbox (badness 10000) in paragraph at lines 13097--13098
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2950] [2951] [2952] [2953]
Underfull \hbox (badness 3895) in paragraph at lines 13358--13361
[][][]\T1/zi4/m/sl/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths of any
 num-ber of vari-ables, spec-i-fied via terms like
[2954]
Underfull \hbox (badness 10000) in paragraph at lines 13403--13405
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2955] [2956] [2957] [2958]
Underfull \hbox (badness 1371) in paragraph at lines 13620--13626
[]\T1/zi4/m/sl/10 bs="ad" \T1/ptm/m/n/10 Uni-vari-ate and bi-vari-ate adap-tive
 smooths are avail-able (see

Underfull \hbox (badness 10000) in paragraph at lines 13660--13664
[][][]\T1/zi4/m/sl/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 te[][][]\T1/p
tm/m/n/10 , [][]\T1/zi4/m/sl/10 t2[][][] [][]tprs[][][]\T1/ptm/m/n/10 ,[][]\T1/
zi4/m/sl/10 Duchon.spline[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 cubic.regre
ssion.spline[][][]\T1/ptm/m/n/10 ,[][]\T1/zi4/m/sl/10 p.spline[][][]\T1/ptm/m/n
/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 13660--13664
[][]\T1/zi4/m/sl/10 mrf[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 soap[][][]\T1
/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 Spherical.Spline[][][]\T1/ptm/m/n/10 , [][]\T
1/zi4/m/sl/10 adaptive.smooth[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 user.de
fined.smooth[][][]\T1/ptm/m/n/10 ,

Overfull \hbox (46.8009pt too wide) in paragraph at lines 13660--13664
[][]\T1/zi4/m/sl/10 smooth.construct.re.smooth.spec[][][]\T1/ptm/m/n/10 , [][]\
T1/zi4/m/sl/10 smooth.construct.gp.smooth.spec[][][]\T1/ptm/m/n/10 ,[][]\T1/zi4
/m/sl/10 factor.smooth.interaction[][][] 
[2959] [2960] [2961] [2962]
Underfull \hbox (badness 2326) in paragraph at lines 13865--13872
[]\T1/ptm/m/n/10 These wrap-per func-tions ex-ist to al-low smooths spec-i-fied
 us-ing [][]\T1/zi4/m/sl/10 smooth.construct[][][] \T1/ptm/m/n/10 and
[2963]
Underfull \hbox (badness 2158) in paragraph at lines 13950--13950
[]\T1/ptm/m/it/10 Extract smooth-ing pa-ram-e-ter es-ti-ma-tor co-vari-ance ma-
trix from
[2964] [2965] [2966] [2967] [2968] [2969] [2970] [2971] [2972] [2973] [2974]
Underfull \vbox (badness 10000) has occurred while \output is active [2975]
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[2987] [2988] [2989] [2990]
Underfull \hbox (badness 1796) in paragraph at lines 15594--15597
[]\T1/ptm/m/n/10 other op-tions to pass on to [][]\T1/zi4/m/sl/10 persp[][][]\T
1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 image[][][] \T1/ptm/m/n/10 or [][]\T1/zi4/m/
sl/10 contour[][][]\T1/ptm/m/n/10 . In par-tic-u-lar
[2991] [2992] [2993] [2994] [2995] [2996]) (nlme-pkg.tex
Chapter 25.
[2997] [2998] [2999] [3000] [3001] [3002] [3003] [3004] [3005] [3006] [3007]
[3008] [3009] [3010] [3011] [3012] [3013] [3014] [3015] [3016] [3017] [3018]
[3019] [3020] [3021] [3022] [3023] [3024] [3025] [3026]
Underfull \hbox (badness 2875) in paragraph at lines 1994--2000
[]\T1/ptm/m/n/10 an op-tional log-i-cal value or one-sided for-mula, in-di-cat-
ing a co-vari-ate

Underfull \hbox (badness 1466) in paragraph at lines 1994--2000
\T1/ptm/m/n/10 that is in-ner to the \T1/zi4/m/sl/10 displayLevel \T1/ptm/m/n/1
0 group-ing fac-tor. If equal to \T1/zi4/m/sl/10 TRUE\T1/ptm/m/n/10 ,
[3027] [3028] [3029] [3030]
Underfull \hbox (badness 10000) in paragraph at lines 2256--2262
[][][]\T1/zi4/m/sl/10 ACF.lme[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 corARMA
[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 corClasses[][][]\T1/ptm/m/n/10 , [][
]\T1/zi4/m/sl/10 Dim.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 Initi
alize.corStruct[][][]\T1/ptm/m/n/10 ,
[3031] [3032] [3033] [3034] [3035] [3036] [3037] [3038] [3039] [3040] [3041]
[3042] [3043] [3044] [3045] [3046] [3047] [3048] [3049] [3050] [3051] [3052]
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Underfull \hbox (badness 1067) in paragraph at lines 4414--4419
\T1/ptm/m/n/10 ma-trix), \T1/zi4/m/sl/10 fitted \T1/ptm/m/n/10 (fit-ted val-ues
), and \T1/zi4/m/sl/10 residuals \T1/ptm/m/n/10 (resid-u-als). De-faults to
[3064] [3065] [3066] [3067] [3068] [3069] [3070] [3071] [3072] [3073] [3074]
[3075]
Underfull \hbox (badness 10000) in paragraph at lines 5160--5164
[][][]\T1/zi4/m/sl/10 getCovariate.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/
m/sl/10 getCovariate.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 getCo
variate.varFunc[][][]\T1/ptm/m/n/10 ,
[3076] [3077] [3078] [3079] [3080] [3081] [3082]
Underfull \hbox (badness 10000) in paragraph at lines 5592--5595
[][][]\T1/zi4/m/sl/10 getGroupsFormula[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/1
0 getGroups.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 getGroups.gls[
][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 getGroups.lmList[][][]\T1/ptm/m/n/10 
,
[3083] [3084] [3085] [3086] [3087] [3088] [3089]
Underfull \hbox (badness 10000) in paragraph at lines 5973--5978
[][][]\T1/zi4/m/sl/10 getGroupsFormula.gls[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/
sl/10 getGroupsFormula.lmList[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 getGrou
psFormula.lme[][][]\T1/ptm/m/n/10 ,
[3090] [3091] [3092] [3093]
Underfull \hbox (badness 1490) in paragraph at lines 6243--6254
[][][]\T1/zi4/m/sl/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 glsC
ontrol[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 glsObject[][][]\T1/ptm/m/n/10 
, [][]\T1/zi4/m/sl/10 glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 plot.
gls[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 predict.gls[][][]\T1/ptm/m/n/10 ,
 [][]\T1/zi4/m/sl/10 qqnorm.gls[][][]\T1/ptm/m/n/10 ,
[3094]
Underfull \hbox (badness 10000) in paragraph at lines 6307--6309
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
[3095] [3096] [3097] [3098] [3099] [3100]
Underfull \hbox (badness 10000) in paragraph at lines 6721--6723
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
[3101] [3102] [3103] [3104]
Underfull \hbox (badness 10000) in paragraph at lines 6994--7001
[][][]\T1/zi4/m/sl/10 formula[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 gapply[
][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 gsummary[][][]\T1/ptm/m/n/10 , [][]\T
1/zi4/m/sl/10 lme[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 plot.nffGroupedData
[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 plot.nfnGroupedData[][][]\T1/ptm/m/n
/10 ,
[3105] [3106] [3107] [3108]
Underfull \hbox (badness 10000) in paragraph at lines 7254--7259
[][][]\T1/zi4/m/sl/10 Initialize.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/
sl/10 Initialize.lmeStruct[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 Initialize
.glsStruct[][][]\T1/ptm/m/n/10 ,
[3109] [3110] [3111] [3112] [3113] [3114] [3115] [3116] [3117] [3118] [3119]
[3120] [3121] [3122] [3123] [3124] [3125] [3126] [3127]
Underfull \hbox (badness 10000) in paragraph at lines 8521--8523
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
[3128]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.sig
ma}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.8572 \aliasA{sigma}{lmeObject}{sigma}
                                        [3129] [3130] [3131] [3132]
Underfull \hbox (badness 10000) in paragraph at lines 8802--8809
[][][]\T1/zi4/m/sl/10 lm[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 lme.lmList[]
[][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 plot.lmList[][][]\T1/ptm/m/n/10 , [][]
\T1/zi4/m/sl/10 pooledSD[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 predict.lmLi
st[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 residuals.lmList[][][]\T1/ptm/m/n/
10 ,
[3133] [3134] [3135] [3136] [3137] [3138] [3139] [3140]
Underfull \hbox (badness 10000) in paragraph at lines 9324--9331
[][][]\T1/zi4/m/sl/10 lme[][][]\T1/ptm/m/n/10 ,[][]\T1/zi4/m/sl/10 gls[][][]\T1
/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 logLik.corStruct[][][]\T1/ptm/m/n/10 , [][]\T
1/zi4/m/sl/10 logLik.glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 logLik
.lmeStruct[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 logLik.lmList[][][]\T1/ptm
/m/n/10 ,
[3141] [3142] [3143] [3144] [3145]pdfTeX warning (ext4): destination with the s
ame identifier (name{Rfn.Matrix}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.9686 ...rA{Matrix}{Assign Matrix Values}{Matrix}
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ation with the same identifier (name{Rfn.Matrix.1}) has been already used, dupl
icate ignored
<to be read again> 
                   \relax 
l.9686 ...rA{Matrix}{Assign Matrix Values}{Matrix}
                                                   [3146] [3147] [3148]
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Underfull \hbox (badness 1596) in paragraph at lines 10459--10485
[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a two-sided for-mula o
f the form
[3158] [3159]
Underfull \hbox (badness 1490) in paragraph at lines 10597--10603
[][][]\T1/zi4/m/sl/10 nlmeControl[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 nlm
e.nlsList[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 nlmeObject[][][]\T1/ptm/m/n
/10 , [][]\T1/zi4/m/sl/10 nlsList[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 nlm
eStruct[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 pdClasses[][][]\T1/ptm/m/n/10
 , [][]\T1/zi4/m/sl/10 reStruct[][][]\T1/ptm/m/n/10 ,
[3160] [3161] [3162] [3163]
Underfull \hbox (badness 10000) in paragraph at lines 10838--10840
[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
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[3175] [3176] [3177] [3178] [3179] [3180] [3181] [3182] [3183] [3184] [3185]
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Underfull \hbox (badness 1286) in paragraph at lines 13734--13741
[]\T1/ptm/m/n/10 an op-tional log-i-cal func-tion or func-tion. If \T1/zi4/m/sl
/10 TRUE \T1/ptm/m/n/10 and ei-ther \T1/zi4/m/sl/10 inner \T1/ptm/m/n/10 or
[3206] [3207] [3208] [3209] [3210] [3211] [3212] [3213]
Underfull \hbox (badness 1215) in paragraph at lines 14280--14282
[]\T1/ptm/m/n/10 an op-tional nu-meric vec-tor with the lim-its for the y-axis.
 De-faults to
[3214] [3215] [3216] [3217] [3218] [3219] [3220] [3221] [3222] [3223] [3224]
[3225] [3226]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.random.effects}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.15177 ...Extract Random Effects}{random.effects}
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ation with the same identifier (name{Rfn.random.effects.1}) has been already us
ed, duplicate ignored
<to be read again> 
                   \relax 
l.15177 ...Extract Random Effects}{random.effects}
                                                   [3227] [3228] [3229]
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Underfull \hbox (badness 1067) in paragraph at lines 15888--15893
\T1/ptm/m/n/10 ma-trix), \T1/zi4/m/sl/10 fitted \T1/ptm/m/n/10 (fit-ted val-ues
), and \T1/zi4/m/sl/10 residuals \T1/ptm/m/n/10 (resid-u-als). De-faults to
[3238] [3239] [3240] [3241]
Underfull \hbox (badness 1448) in paragraph at lines 16131--16140
\T1/ptm/m/n/10 Op-tions in-clude \T1/zi4/m/sl/10 "response" \T1/ptm/m/n/10 for 
the "raw" resid-u-als (ob-served - fit-ted),
[3242] [3243] [3244] [3245] [3246] [3247] [3248] [3249] [3250] [3251]
Underfull \hbox (badness 1728) in paragraph at lines 16836--16839
[]\T1/ptm/m/n/10 an op-tional log-i-cal value used to con-trol the amount of ou
t-put in the
[3252] [3253] [3254] [3255] [3256]
Underfull \hbox (badness 8056) in paragraph at lines 17171--17180
\T1/zi4/m/sl/10 Symmetry" \T1/ptm/m/n/10 for \T1/zi4/m/sl/10 pdCompSymm\T1/ptm/
m/n/10 , \T1/zi4/m/sl/10 "Diagonal" \T1/ptm/m/n/10 for \T1/zi4/m/sl/10 pdDiag\T
1/ptm/m/n/10 , \T1/zi4/m/sl/10 "Multiple of

Underfull \hbox (badness 10000) in paragraph at lines 17171--17180
\T1/zi4/m/sl/10 an Identity" \T1/ptm/m/n/10 for \T1/zi4/m/sl/10 pdIdent\T1/ptm/
m/n/10 , \T1/zi4/m/sl/10 "General Positive-Definite,Natural

Underfull \hbox (badness 5756) in paragraph at lines 17171--17180
\T1/zi4/m/sl/10 Parametrization" \T1/ptm/m/n/10 for \T1/zi4/m/sl/10 pdNatural\T
1/ptm/m/n/10 , \T1/zi4/m/sl/10 "General Positive-Definite" \T1/ptm/m/n/10 for
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\T1/ptm/m/n/10 for \T1/zi4/m/sl/10 varComb\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "Con
stant plus power of covariate" \T1/ptm/m/n/10 for \T1/zi4/m/sl/10 varConstPower
\T1/ptm/m/n/10 ,
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[][][]\T1/zi4/m/sl/10 Variogram.corExp[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/1
0 Variogram.corGaus[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 Variogram.corLin[
][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 Variogram.corRatio[][][]\T1/ptm/m/n/1
0 ,

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[][]\T1/zi4/m/sl/10 Variogram.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl
/10 Variogram.corSpher[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 Variogram.defa
ult[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 Variogram.gls[][][]\T1/ptm/m/n/10
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[][][]\T1/zi4/m/sl/10 corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 Vari
ogram[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 Variogram.default[][][]\T1/ptm/
m/n/10 , [][]\T1/zi4/m/sl/10 Variogram.corExp[][][]\T1/ptm/m/n/10 , [][]\T1/zi4
/m/sl/10 Variogram.corGaus[][][]\T1/ptm/m/n/10 ,
[3274] [3275] [3276] [3277] [3278] [3279] [3280] [3281] [3282] [3283] [3284]
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[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
rm \T1/zi4/m/sl/10 response ~
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l.326 ... Myelogenous Leukemia survival data}{aml}
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[]\T1/ptm/m/n/10 F.J. Anscombe (1949). Trans-for-ma-tions of Pois-son, bi-no-mi
al and negative-binomial data.
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l.1178 ...erapy for Stage B/C colon cancer}{colon}
                                                  
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"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "deviance"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "d
fbeta"\T1/ptm/m/n/10 ,
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[][][]\T1/zi4/m/sl/10 survfit.formula[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10
 survfit.coxph[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 survfit.object[][][]\T
1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 print.survfit[][][]\T1/ptm/m/n/10 , [][]\T1/
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"plain"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "log" \T1/ptm/m/n/10 (the de-fault), \T
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[]\T1/ptm/m/n/10 survival times, for time de-pen-dent pre-dic-tion. It gives th
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[]\T1/zi4/m/it/10 %*%,diagonalMatrix,diagonalMatrix-method 

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[]\T1/zi4/m/it/10 %*%,diagonalMatrix,sparseMatrix-method 

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[]\T1/zi4/m/it/10 %*%,lsparseMatrix,lsparseMatrix-method 
[3528]
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[]\T1/zi4/m/it/10 %*%,nsparseMatrix,nsparseMatrix-method 

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[]\T1/zi4/m/it/10 %*%,sparseMatrix,diagonalMatrix-method 

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[]\T1/zi4/m/it/10 %&%,CsparseMatrix,diagonalMatrix-method 

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[]\T1/zi4/m/it/10 %&%,diagonalMatrix,CsparseMatrix-method 
[3529]
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[]\T1/zi4/m/it/10 %&%,diagonalMatrix,diagonalMatrix-method 

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[]\T1/zi4/m/it/10 %&%,diagonalMatrix,sparseMatrix-method 

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[]\T1/zi4/m/it/10 %&%,nCsparseMatrix,nCsparseMatrix-method 

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[]\T1/zi4/m/it/10 %&%,nCsparseMatrix,nsparseMatrix-method 

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[]\T1/zi4/m/it/10 %&%,nsparseMatrix,nCsparseMatrix-method 

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[]\T1/zi4/m/it/10 %&%,nsparseMatrix,nsparseMatrix-method 

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[]\T1/zi4/m/it/10 %&%,sparseMatrix,diagonalMatrix-method 
[3530]
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[3531]
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[]\T1/zi4/m/it/10 all.equal,sparseMatrix,sparseMatrix-method 

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[]\T1/zi4/m/it/10 all.equal,sparseMatrix,sparseVector-method 

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[]\T1/zi4/m/it/10 all.equal,sparseVector,sparseMatrix-method 

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[]\T1/zi4/m/it/10 all.equal,sparseVector,sparseVector-method 
[3532]
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[]\T1/zi4/m/it/10 Arith,CsparseMatrix,CsparseMatrix-method 

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[]\T1/zi4/m/it/10 Arith,ddenseMatrix,ddenseMatrix-method 

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[]\T1/zi4/m/it/10 Arith,ddenseMatrix,sparseVector-method 

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[]\T1/zi4/m/it/10 Arith,dsparseVector,dsparseVector-method 
[3533]
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[]\T1/zi4/m/it/10 Arith,sparseVector,ddenseMatrix-method 

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[]\T1/zi4/m/it/10 Arith,sparseVector,sparseVector-method 

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[]\T1/zi4/m/it/10 Arith,triangularMatrix,diagonalMatrix-method 
[3534] [3535] [3536]
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[3537] [3538] [3539]
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[]\T1/zi4/m/it/10 cbind2,denseMatrix,sparseMatrix-method 

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[]\T1/zi4/m/it/10 cbind2,diagonalMatrix,sparseMatrix-method 

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[]\T1/zi4/m/it/10 cbind2,sparseMatrix,denseMatrix-method 

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[]\T1/zi4/m/it/10 cbind2,sparseMatrix,diagonalMatrix-method 
[3540]
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[]\T1/zi4/m/it/10 cbind2,sparseMatrix,sparseMatrix-method 
[3541] [3542] [3543]
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[]\T1/zi4/m/it/10 coerce,atomicVector,dsparseVector-method 

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[]\T1/zi4/m/it/10 coerce,atomicVector,sparseVector-method 

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[]\T1/zi4/m/it/10 coerce,CHMfactor,triangularMatrix-method 

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[]\T1/zi4/m/it/10 coerce,CsparseMatrix,denseMatrix-method 

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[]\T1/zi4/m/it/10 coerce,CsparseMatrix,lsparseMatrix-method 

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[]\T1/zi4/m/it/10 coerce,CsparseMatrix,matrix.coo-method 

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[]\T1/zi4/m/it/10 coerce,CsparseMatrix,matrix.csc-method 

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[]\T1/zi4/m/it/10 coerce,CsparseMatrix,matrix.csr-method 

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[]\T1/zi4/m/it/10 coerce,CsparseMatrix,sparseVector-method 

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[3544]
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[]\T1/zi4/m/it/10 coerce,ddiMatrix,symmetricMatrix-method 

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[]\T1/zi4/m/it/10 coerce,ddiMatrix,triangularMatrix-method 

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[]\T1/zi4/m/it/10 coerce,denseMatrix,CsparseMatrix-method 

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[]\T1/zi4/m/it/10 coerce,denseMatrix,generalMatrix-method 

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[]\T1/zi4/m/it/10 coerce,denseMatrix,RsparseMatrix-method 

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[]\T1/zi4/m/it/10 coerce,denseMatrix,symmetricMatrix-method 

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[]\T1/zi4/m/it/10 coerce,dgeMatrix,triangularMatrix-method 

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[]\T1/zi4/m/it/10 coerce,dgTMatrix,symmetricMatrix-method 

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[]\T1/zi4/m/it/10 coerce,dgTMatrix,triangularMatrix-method 

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[]\T1/zi4/m/it/10 coerce,diagonalMatrix,denseMatrix-method 

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[3545]
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[3546]
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[3547]
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[3548] [3549]
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[3550]
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[]\T1/zi4/m/it/10 coerce,ngTMatrix,symmetricMatrix-method 

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[]\T1/zi4/m/it/10 coerce,ngTMatrix,triangularMatrix-method 

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[]\T1/zi4/m/it/10 coerce,nsparseVector,isparseVector-method 

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[3551]
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[3552]
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[]\T1/zi4/m/it/10 coerce,xsparseVector,dsparseVector-method 

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[3553]
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[]\T1/zi4/m/it/10 Compare,CsparseMatrix,CsparseMatrix-method 

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[3554] [3555] [3556]
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Chapter 1.
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[]\T1/ptm/m/n/10 a small pos-i-tive floating-point num-ber \T1/zi4/m/n/10 x \T1
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[]\T1/ptm/m/n/10 character string, the pre-ferred set-ting for [][]\T1/zi4/m/n/
10 options[][][]("pkgType")\T1/ptm/m/n/10 . Val-ues
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[]\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T
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[]\T1/ptm/m/n/10 If the calls to \T1/zi4/m/n/10 FUN \T1/ptm/m/n/10 re-turn vec-
tors of dif-fer-ent lengths, \T1/zi4/m/n/10 apply \T1/ptm/m/n/10 re-turns a lis
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 []\T1/zi4/m/n/9 ## http://www.mathworks.de/de/help/matlab/matlab_prog/represen
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[]\T1/ptm/m/n/10 The val-ues of the splits can also be ob-tained (less ef-fi-ci
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[][][]\T1/zi4/m/n/10 apply[][][] \T1/ptm/m/n/10 al-ways sim-pli-fies com-mon le
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 []   \T1/zi4/m/n/10 c.factor <- function(..., recursive=TRUE) unlist(list(...)
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor, or an ob-ject that can be co-erced to c
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[]\T1/ptm/m/n/10 character string, par-tially matched to \T1/zi4/m/n/10 c("defa
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[]\T1/ptm/m/n/10 A note on `\T1/zi4/m/n/10 file://\T1/ptm/m/n/10 ' URLs. The mo
st gen-eral form (from RFC1738) is
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[]\T1/ptm/m/n/10 As from \T1/phv/m/n/10 R \T1/ptm/m/n/10 3.0.0 the en-cod-ing \
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\T1/ptm/m/n/10 writ-ing it should be writ-ten ex-plic-itly, e.g. by \T1/zi4/m/n
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[]\T1/ptm/m/n/10 A length-one log-i-cal vec-tor that is not \T1/zi4/m/n/10 NA\T
1/ptm/m/n/10 . Con-di-tions of length greater

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\T1/ptm/m/n/10 than one are cur-rently ac-cepted with a warn-ing, but only the 
first el-e-
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Underfull \hbox (badness 2096) in paragraph at lines 7583--7587
\T1/zi4/m/n/10 status _ codes$[][] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https
 : / / en . wikipedia . org / wiki / List _ of _ FTP _ server _ return _ codes$
[][]\T1/ptm/m/n/10 .
[111] [112]
Underfull \hbox (badness 2351) in paragraph at lines 7701--7704
[][][]\T1/zi4/m/n/10 split[][][] \T1/ptm/m/n/10 for split-ting a vari-able ac-c
ord-ing to a group fac-tor; [][]\T1/zi4/m/n/10 factor[][][]\T1/ptm/m/n/10 , [][
]\T1/zi4/m/n/10 tabulate[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 table[][][]\T
1/ptm/m/n/10 ,
[113] [114] [115] [116] [117]
Underfull \hbox (badness 4479) in paragraph at lines 8027--8037
[][][]\T1/zi4/m/n/10 I[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 plot.data.frame
[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 print.data.frame[][][]\T1/ptm/m/n/10 
, [][]\T1/zi4/m/n/10 row.names[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 names[]
[][] \T1/ptm/m/n/10 (for the col-umn names),
[118] [119] [120] [121] [122]
Underfull \hbox (badness 1629) in paragraph at lines 8474--8486
[]\T1/ptm/m/n/10 A few times have spe-cific is-sues. First, the leap sec-onds a
re ig-nored, and real times

Underfull \hbox (badness 1609) in paragraph at lines 8474--8486
\T1/ptm/m/n/10 there is a prob-lem in the POSIX/C99 stan-dard with \T1/zi4/m/n/
10 "1969-12-31 23:59:59 UTC"\T1/ptm/m/n/10 , which

Underfull \hbox (badness 2426) in paragraph at lines 8474--8486
\T1/ptm/m/n/10 is \T1/zi4/m/n/10 -1 \T1/ptm/m/n/10 in cal-en-dar time and that 
value is on those OSes also used as an er-ror code.
[123] [124] [125] [126] [127] [128] [129] [130] [131] [132] [133]
Underfull \hbox (badness 1178) in paragraph at lines 9210--9214
[]\T1/ptm/m/n/10 If true, [][]\T1/zi4/m/n/10 list[][][]\T1/ptm/m/n/10 s and ato
mic vec-tors with non-[][]\T1/zi4/m/n/10 NA[][][] \T1/ptm/m/n/10 names (see [][
]\T1/zi4/m/n/10 names[][][]\T1/ptm/m/n/10 ) are de-
[134] [135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145]
[146] [147] [148] [149]
Underfull \hbox (badness 1735) in paragraph at lines 10358--10362
\T1/zi4/m/n/10 754-[]2008$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/n/10 https : / / 
en . wikipedia . org / wiki / Double _ precision$[][]\T1/ptm/m/n/10 , [][]$\T1/
zi4/m/n/10 https : / / en . wikipedia .
[150] [151] [152] [153] [154] [155] [156]
Underfull \hbox (badness 6396) in paragraph at lines 10797--10805
[]\T1/ptm/m/n/10 For the de-fault meth-ods, and when-ever there are equiv-a-len
t method def-i-ni-tions for

Underfull \hbox (badness 1946) in paragraph at lines 10797--10805
\T1/zi4/m/n/10 duplicated \T1/ptm/m/n/10 and \T1/zi4/m/n/10 anyDuplicated\T1/pt
m/m/n/10 , \T1/zi4/m/n/10 anyDuplicated(x,...) \T1/ptm/m/n/10 is a ``gen-er-al-
ized'' short-cut for
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[169] [170] [171]
Underfull \hbox (badness 4569) in paragraph at lines 11926--11930
[]\T1/ptm/m/n/10 When eval-u-at-ing ex-pres-sions in a data frame that has been
 passed as an ar-gu-ment

Underfull \hbox (badness 2401) in paragraph at lines 11926--11930
\T1/ptm/m/n/10 to a func-tion, the rel-e-vant en-clo-sure is of-ten the caller'
s en-vi-ron-ment, i.e., one needs
[172] [173] [174] [175] [176] [177] [178] [179] [180] [181] [182] [183]
[184] [185] [186] [187] [188] [189] [190] [191] [192] [193] [194] [195]
Underfull \hbox (badness 2253) in paragraph at lines 13605--13607
[]\T1/ptm/m/n/10 character vec-tors con-tain-ing file paths. Tilde-expansion is
 done: see
[196]
Underfull \hbox (badness 1565) in paragraph at lines 13678--13682
[][][]\T1/zi4/m/n/10 Sys.readlink[][][] \T1/ptm/m/n/10 to find out about sym-bo
lic links, [][]\T1/zi4/m/n/10 files[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 fi
le.access[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files[][][]\T1/ptm/m/n/
10 , and

Underfull \hbox (badness 4927) in paragraph at lines 13722--13724
[]\T1/ptm/m/n/10 It can also be used for en-vi-ron-ment paths such as \T1/zi4/m
/n/10 PATH \T1/ptm/m/n/10 and \T1/zi4/m/n/10 R_LIBS \T1/ptm/m/n/10 with \T1/zi4
/m/n/10 fsep =
[197] [198]
Underfull \hbox (badness 3148) in paragraph at lines 13815--13820
[][][]\T1/zi4/m/n/10 files[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files[
][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 help[][][]\T1/ptm/m/n/10 ; [][]\T1/zi4
/m/n/10 RShowDoc[][][] \T1/ptm/m/n/10 call \T1/zi4/m/n/10 file.show() \T1/ptm/m
/n/10 for \T1/zi4/m/n/10 type = "text"\T1/ptm/m/n/10 . Con-sider
[199]
Underfull \hbox (badness 1466) in paragraph at lines 13864--13868
[]\T1/ptm/m/n/10 character vec-tors, con-tain-ing file names or paths. For \T1/
zi4/m/n/10 file.copy \T1/ptm/m/n/10 and
[200]
Underfull \hbox (badness 2875) in paragraph at lines 13985--13996
[]\T1/ptm/m/n/10 A ver-sion of sym-bolic link-ing to files/directories was im-p
le-mented more re-cently, and
[201]
Underfull \hbox (badness 10000) in paragraph at lines 14028--14032
[][][]\T1/zi4/m/n/10 file.info[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 file.ac
cess[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 file.path[][][]\T1/ptm/m/n/10 , [
][]\T1/zi4/m/n/10 file.show[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 list.files
[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 unlink[][][]\T1/ptm/m/n/10 , [][]\T1/
zi4/m/n/10 basename[][][]\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 14039--14042
[][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Hard _ link$[][
] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wik
i /
[202] [203] [204] [205]
Underfull \hbox (badness 3965) in paragraph at lines 14328--14332
[]\T1/ptm/m/n/10 This is the same com-pu-ta-tion as for the em-pir-i-cal dis-tr
i-bu-tion func-tion, and in-deed,
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Underfull \hbox (badness 4429) in paragraph at lines 15104--15107
[]\T1/ptm/m/n/10 an atomic nu-mer-i-cal or char-ac-ter ob-ject, pos-si-bly [][]
\T1/zi4/m/n/10 complex[][][] \T1/ptm/m/n/10 only for
[218]
Underfull \hbox (badness 10000) in paragraph at lines 15210--15212
[]\T1/ptm/m/n/10 This works via \T1/zi4/m/n/10 prettyNum()\T1/ptm/m/n/10 , whic
h calls

Underfull \hbox (badness 1215) in paragraph at lines 15210--15212
\T1/zi4/m/n/10 .format.zeros(*,replace=replace.zero) \T1/ptm/m/n/10 three times
 in this case, see

Underfull \hbox (badness 10000) in paragraph at lines 15232--15237
[]\T1/ptm/m/n/10 For num-bers, \T1/zi4/m/n/10 formatC() \T1/ptm/m/n/10 calls \T
1/zi4/m/n/10 prettyNum() \T1/ptm/m/n/10 when needed which it-self calls

Underfull \hbox (badness 1558) in paragraph at lines 15232--15237
\T1/zi4/m/n/10 .format.zeros(*,replace=replace.zero)\T1/ptm/m/n/10 . (\T1/ptm/m
/it/10 ``when needed''\T1/ptm/m/n/10 : when \T1/zi4/m/n/10 zero.print \T1/ptm/m
/n/10 is not

Underfull \hbox (badness 10000) in paragraph at lines 15244--15248
[]\T1/zi4/m/n/10 formatC \T1/ptm/m/n/10 does not nec-es-sar-ily align the num-b
ers on the dec-i-mal point, so

Underfull \hbox (badness 2426) in paragraph at lines 15244--15248
\T1/zi4/m/n/10 formatC(c(6.11,13.1),digits = 2,format = "fg") \T1/ptm/m/n/10 gi
ves \T1/zi4/m/n/10 c("6.1"," 13")\T1/ptm/m/n/10 . If you want
[219]
Underfull \hbox (badness 2035) in paragraph at lines 15283--15287
[]\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/n/10 decimal.mark \T1/ptm/m/n/10 in
 \T1/zi4/m/n/10 formatC() \T1/ptm/m/n/10 was changed in \T1/phv/m/n/10 R \T1/pt
m/m/n/10 3.2.0: for use within
[220]
Underfull \vbox (badness 10000) has occurred while \output is active [221]
[222] [223] [224] [225] [226] [227] [228]
Underfull \hbox (badness 2452) in paragraph at lines 15882--15886
[]\T1/zi4/m/n/10 gctorture2 \T1/ptm/m/n/10 can also be in-voked via en-vi-ron-m
ent vari-ables at the start of the \T1/phv/m/n/10 R \T1/ptm/m/n/10 ses-

Underfull \hbox (badness 1147) in paragraph at lines 15882--15886
\T1/ptm/m/n/10 sion. \T1/zi4/m/n/10 R_GCTORTURE \T1/ptm/m/n/10 cor-re-sponds to
 the \T1/zi4/m/n/10 step \T1/ptm/m/n/10 ar-gu-ment, \T1/zi4/m/n/10 R_GCTORTURE_
WAIT \T1/ptm/m/n/10 to \T1/zi4/m/n/10 wait\T1/ptm/m/n/10 , and
[229] [230]
Underfull \hbox (badness 1092) in paragraph at lines 16055--16060
[][]\T1/zi4/m/n/10 library.dynam[][][]\T1/ptm/m/n/10 , or can be found af-ter t
he DLL has been loaded us-ing
[231] [232] [233]
Underfull \hbox (badness 6741) in paragraph at lines 16305--16309
\T1/ptm/m/n/10 Additionally, the list will have an ad-di-tional class, be-ing \
T1/zi4/m/n/10 CRoutine\T1/ptm/m/n/10 , \T1/zi4/m/n/10 CallRoutine\T1/ptm/m/n/10
 ,
[234] [235] [236] [237] [238] [239] [240] [241] [242]
Underfull \vbox (badness 10000) has occurred while \output is active [243]
[244] [245] [246] [247] [248] [249] [250] [251] [252]
Underfull \hbox (badness 1478) in paragraph at lines 17594--17597
[]\T1/ptm/m/n/10 A char-ac-ter vec-tor, or an ob-ject to be con-verted to a cha
r-ac-ter vec-tor
[253] [254] [255]
Underfull \hbox (badness 10000) in paragraph at lines 17849--17851
[]\T1/ptm/m/n/10 the `root' col-la-tion: see [][]$\T1/zi4/m/n/10 http : / / www
 . unicode . org / reports / tr35 /
[256] [257] [258] [259] [260] [261] [262] [263] [264]
Underfull \hbox (badness 1442) in paragraph at lines 18447--18449
[]\T1/ptm/m/n/10 the choice of de-fault graph-ics de-vice launched when needed 
and by [][]\T1/zi4/m/n/10 dev.new[][][]\T1/ptm/m/n/10 : see
[265]
Underfull \hbox (badness 2452) in paragraph at lines 18539--18555
[][][]\T1/zi4/m/n/10 as.character[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.c
omplex[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.double[][][]\T1/ptm/m/n/10 ,
 [][]\T1/zi4/m/n/10 as.integer[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.logi
cal[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 as.raw[][][]\T1/ptm/m/n/10 , [][]\
T1/zi4/m/n/10 as.vector[][][]\T1/ptm/m/n/10 ,
[266] [267] [268] [269] [270] [271]
Underfull \hbox (badness 1248) in paragraph at lines 18958--18961
[]\T1/zi4/m/n/10 is.atomic \T1/ptm/m/n/10 is true for the [][]atomic[][][] type
s (\T1/zi4/m/n/10 "logical"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "integer"\T1/ptm/m/n
/10 , \T1/zi4/m/n/10 "numeric"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "complex"\T1/ptm/
m/n/10 ,
[272] [273] [274] [275]
Underfull \hbox (badness 4739) in paragraph at lines 19216--19218
[]\T1/ptm/m/n/10 numeric scalar >= 0. Smaller dif-fer-ences are not con-sid-ere
d, see
[276] [277] [278] [279] [280] [281] [282]
Underfull \hbox (badness 1596) in paragraph at lines 19646--19651
\T1/ptm/m/n/10 trix or, if \T1/zi4/m/n/10 simplify = "array"\T1/ptm/m/n/10 , an
 ar-ray if ap-pro-pri-ate, by ap-ply-ing \T1/zi4/m/n/10 simplify2array()\T1/ptm
/m/n/10 .
[283] [284] [285] [286] [287] [288] [289] [290] [291]
Underfull \hbox (badness 2469) in paragraph at lines 20250--20255
[]\T1/ptm/m/n/10 In late 2017 a \T1/zi4/m/n/10 libcurl \T1/ptm/m/n/10 in-stal-l
a-tion was seen di-vided into two li-braries, \T1/zi4/m/n/10 libcurl \T1/ptm/m/
n/10 and
[292]
Underfull \hbox (badness 10000) in paragraph at lines 20264--20271
[][][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs / sslcerts . html$[][]
 \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 http : / / curl . haxx . se / docs /
[293] [294] [295]
Underfull \hbox (badness 1014) in paragraph at lines 20507--20512
[]\T1/ptm/m/n/10 Normally \T1/zi4/m/n/10 library \T1/ptm/m/n/10 re-turns (in-vi
s-i-bly) the list of at-tached pack-ages, but \T1/zi4/m/n/10 TRUE \T1/ptm/m/n/1
0 or \T1/zi4/m/n/10 FALSE \T1/ptm/m/n/10 if
[296] [297] [298] [299] [300] [301] [302] [303] [304] [305] [306]
Underfull \hbox (badness 1264) in paragraph at lines 21309--21314
[]\T1/ptm/m/n/10 character string. The fol-low-ing cat-e-gories should al-ways 
be sup-ported:
[307]
Underfull \hbox (badness 4441) in paragraph at lines 21338--21341
[]\T1/ptm/m/n/10 Note that set-ting cat-e-gory \T1/zi4/m/n/10 "LC_ALL" \T1/ptm/
m/n/10 sets only cat-e-gories \T1/zi4/m/n/10 "LC_COLLATE"\T1/ptm/m/n/10 , \T1/z
i4/m/n/10 "LC_CTYPE"\T1/ptm/m/n/10 ,
[308] [309] [310] [311] [312] [313] [314] [315] [316] [317]
Underfull \hbox (badness 6047) in paragraph at lines 22085--22087
[]\T1/ptm/m/n/10 The al-go-rithm used by \T1/zi4/m/n/10 make.unique \T1/ptm/m/n
/10 has the prop-erty that \T1/zi4/m/n/10 make.unique(c(A,B)) ==
[318] [319] [320] [321] [322] [323] [324] [325] [326] [327] [328] [329]
[330] [331] [332] [333]
Underfull \hbox (badness 1077) in paragraph at lines 23126--23132
\T1/zi4/m/n/10 / / en . wikipedia . org / wiki / Bzip2$[][]\T1/ptm/m/n/10 , [][
]$\T1/zi4/m/n/10 http : / / tukaani . org / xz/$[][] \T1/ptm/m/n/10 and [][]$\T
1/zi4/m/n/10 https : / / en . wikipedia .
[334] [335] [336] [337] [338] [339] [340] [341]
Underfull \hbox (badness 2790) in paragraph at lines 23631--23634
[]\T1/zi4/m/n/10 packageStartupMessage \T1/ptm/m/n/10 is a vari-ant whose mes-s
ages can be sup-pressed sep-a-rately by

Underfull \hbox (badness 1571) in paragraph at lines 23631--23634
\T1/zi4/m/n/10 suppressPackageStartupMessages\T1/ptm/m/n/10 . (They are still m
es-sages, so can be sup-pressed by
[342] [343] [344] [345]
Underfull \hbox (badness 1194) in paragraph at lines 23913--23916
[]\T1/ptm/m/n/10 The de-fault method for \T1/zi4/m/n/10 anyNA \T1/ptm/m/n/10 ha
n-dles atomic vec-tors with-out a class and \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 .
 It calls
[346] [347]
Underfull \hbox (badness 2368) in paragraph at lines 24119--24125
[]\T1/ptm/m/n/10 For an [][]\T1/zi4/m/n/10 environment[][][] env\T1/ptm/m/n/10 
, \T1/zi4/m/n/10 names(env) \T1/ptm/m/n/10 gives the names of the cor-re-spond-
ing list, i.e.,

Underfull \hbox (badness 4981) in paragraph at lines 24119--24125
\T1/zi4/m/n/10 names(as.list(env,all.names = TRUE)) \T1/ptm/m/n/10 which are al
so given by [][]\T1/zi4/m/n/10 ls[][][](env,all.names =
[348] [349] [350] [351] [352] [353]
Underfull \hbox (badness 10000) in paragraph at lines 24504--24507
[]\T1/ptm/m/n/10 optional [][]\T1/zi4/m/n/10 logical[][][] \T1/ptm/m/n/10 even-
tu-ally to be passed to \T1/zi4/m/n/10 print()\T1/ptm/m/n/10 , used by
[354] [355] [356] [357] [358] [359] [360] [361] [362]
Underfull \hbox (badness 10000) in paragraph at lines 25113--25115
[]\T1/zi4/m/n/10 isNamespaceLoaded(pkg) \T1/ptm/m/n/10 is equiv-a-lent to but m
ore ef-fi-cient than \T1/zi4/m/n/10 pkg %in%
[363] [364] [365] [366] [367] [368] [369] [370] [371] [372] [373] [374]
Underfull \hbox (badness 1038) in paragraph at lines 25953--25961
[]\T1/ptm/m/n/10 the pack-ages that are at-tached by de-fault when \T1/phv/m/n/
10 R \T1/ptm/m/n/10 starts up. Ini-tially

Underfull \hbox (badness 1735) in paragraph at lines 25953--25961
\T1/ptm/m/n/10 set from value of the en-vi-ron-ment vari-able \T1/zi4/m/n/10 R_
DEFAULT_PACKAGES\T1/ptm/m/n/10 , or if that is un-

Underfull \hbox (badness 1292) in paragraph at lines 25953--25961
\T1/ptm/m/n/10 set to \T1/zi4/m/n/10 c("datasets","utils","grDevices","graphics
","stats","methods")\T1/ptm/m/n/10 . (Set

Underfull \hbox (badness 1881) in paragraph at lines 25962--25965
[]\T1/ptm/m/n/10 integer value con-trol-ling the print-ing of lan-guage con-str
ucts which are

Underfull \hbox (badness 6220) in paragraph at lines 25981--25983
[]\T1/ptm/m/n/10 Extra command-line ar-gu-ment(s) for non-default meth-ods: see

[375]
Underfull \hbox (badness 2142) in paragraph at lines 26122--26126
[]\T1/ptm/m/n/10 the de-fault pa-per for-mat used by [][]\T1/zi4/m/n/10 postscr
ipt[][][]\T1/ptm/m/n/10 ; set by en-vi-ron-ment vari-able
[376]
Underfull \hbox (badness 1968) in paragraph at lines 26172--26177
[]\T1/ptm/m/n/10 the com-mand used by [][]\T1/zi4/m/n/10 postscript[][][] \T1/p
tm/m/n/10 for print-ing; set by en-vi-ron-ment vari-able
[377] [378] [379]
Underfull \hbox (badness 10000) in paragraph at lines 26460--26466
[]\T1/ptm/m/n/10 The URL of a Bio-con-duc-tor mir-ror for use by [][]\T1/zi4/m/
n/10 setRepositories[][][]\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 26460--26466
\T1/ptm/m/n/10 e.g. the de-fault `\T1/zi4/m/n/10 "https://bioconductor.org"\T1/
ptm/m/n/10 ' or the Eu-ro-pean mir-ror

Underfull \hbox (badness 10000) in paragraph at lines 26460--26466
\T1/ptm/m/n/10 `\T1/zi4/m/n/10 "https://bioconductor.statistik.tu-dortmund.de"\
T1/ptm/m/n/10 '. Can be set by

Underfull \hbox (badness 10000) in paragraph at lines 26473--26476
[]\T1/ptm/m/n/10 default Cc: ad-dress used by [][]\T1/zi4/m/n/10 create.post[][
][] \T1/ptm/m/n/10 (and hence[][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/n/10
 and

Underfull \hbox (badness 2689) in paragraph at lines 26499--26501
[]\T1/ptm/m/n/10 optional in-te-ger vec-tor for set-ting ports of the in-ter-na
l HTTP server, see
[380]
Underfull \hbox (badness 10000) in paragraph at lines 26534--26539
[]\T1/ptm/m/n/10 Used by [][]\T1/zi4/m/n/10 install.packages[][][] \T1/ptm/m/n/
10 (and in-di-rectly

Underfull \hbox (badness 2529) in paragraph at lines 26540--26551
\T1/ptm/m/n/10 in-di-rectly [][]\T1/zi4/m/n/10 update.packages[][][]\T1/ptm/m/n
/10 ) on plat-forms which sup-port bi-nary pack-ages. Pos-si-

Underfull \hbox (badness 2512) in paragraph at lines 26540--26551
\T1/ptm/m/n/10 ble val-ues are \T1/zi4/m/n/10 "never"\T1/ptm/m/n/10 , \T1/zi4/m
/n/10 "interactive" \T1/ptm/m/n/10 (which means ask in in-ter-ac-tive use and

Underfull \hbox (badness 7203) in paragraph at lines 26552--26555
[]\T1/ptm/m/n/10 default email-ing method used by [][]\T1/zi4/m/n/10 create.pos
t[][][] \T1/ptm/m/n/10 and hence [][]\T1/zi4/m/n/10 bug.report[][][] \T1/ptm/m/
n/10 and

Underfull \hbox (badness 10000) in paragraph at lines 26576--26581
[]\T1/zi4/m/n/10 "source" \T1/ptm/m/n/10 (the de-fault ex-cept un-der a CRAN ma
-cOS build),

Underfull \hbox (badness 2057) in paragraph at lines 26576--26581
\T1/zi4/m/n/10 "mac.binary.el-capitan" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "both"
 \T1/ptm/m/n/10 (the de-fault for CRAN ma-cOS builds).
[381] [382] [383] [384] [385] [386] [387]
Underfull \hbox (badness 10000) in paragraph at lines 27094--27097
[]\T1/zi4/m/n/10 str2expression(s) \T1/ptm/m/n/10 and \T1/zi4/m/n/10 str2lang(s
) \T1/ptm/m/n/10 re-turn spe-cial ver-sions of
[388]
Underfull \hbox (badness 7925) in paragraph at lines 27173--27177
[]\T1/ptm/m/n/10 for a [][]\T1/zi4/m/n/10 character[][][] \T1/ptm/m/n/10 vec-to
r \T1/zi4/m/n/10 s\T1/ptm/m/n/10 , \T1/zi4/m/n/10 str2expression(s) \T1/ptm/m/n
/10 cor-re-sponds to

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[][]\T1/zi4/m/n/10 parse[][][](text = s,keep.source=FALSE)\T1/ptm/m/n/10 , whic
h is al-ways of type ([][]\T1/zi4/m/n/10 typeof[][][]\T1/ptm/m/n/10 ) and [][]\
T1/zi4/m/n/10 class[][][]

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[]\T1/ptm/m/n/10 for a [][]\T1/zi4/m/n/10 character[][][] \T1/ptm/m/n/10 string
 \T1/zi4/m/n/10 s\T1/ptm/m/n/10 , \T1/zi4/m/n/10 str2lang(s) \T1/ptm/m/n/10 cor
-re-sponds to [][]\T1/zi4/m/n/10 parse[][][](text =
[389] [390] [391] [392] [393] [394] [395] [396] [397] [398] [399]
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[]\T1/ptm/m/n/10 character string (or \T1/zi4/m/n/10 NULL\T1/ptm/m/n/10 ) in-di
-cat-ing [][]\T1/zi4/m/n/10 NA[][][] \T1/ptm/m/n/10 val-ues in printed out-put,
 see
[400] [401] [402] [403] [404] [405] [406] [407] [408] [409] [410] [411]
[412] [413] [414] [415] [416] [417] [418] [419] [420] [421] [422] [423]
[424]
Underfull \hbox (badness 1533) in paragraph at lines 29593--29596
[]\T1/ptm/m/n/10 As with all com-piled code, mis-specifying these func-tions ca
n crash \T1/phv/m/n/10 R\T1/ptm/m/n/10 . Do in-clude the
[425] [426]
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[]\T1/ptm/m/n/10 If all com-po-nents are dif-fer-ent (and no \T1/zi4/m/n/10 NA\
T1/ptm/m/n/10 s), the ranks are well de-fined, with val-ues in
[427] [428] [429] [430] [431] [432] [433] [434] [435] [436] [437] [438]
[439] [440] [441] [442] [443] [444] [445] [446] [447] [448]
Underfull \hbox (badness 10000) in paragraph at lines 31299--31303
[]\T1/zi4/m/n/10 regexpr \T1/ptm/m/n/10 and \T1/zi4/m/n/10 gregexpr \T1/ptm/m/n
/10 sup-port `named cap-ture'. If groups are named, e.g.,

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\T1/zi4/m/n/10 "(?<first>[A-Z][a-z]+)" \T1/ptm/m/n/10 then the po-si-tions of t
he matches are also re-turned by name.
[449]
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[]\T1/ptm/m/n/10 The POSIX 1003.2 stan-dard at [][]$\T1/zi4/m/n/10 http : / / p
ubs . opengroup . org / onlinepubs / 9699919799 /
[450] [451] [452] [453] [454] [455] [456] [457]
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[]\T1/ptm/m/n/10 a vec-tor (atomic, not a list) for \T1/zi4/m/n/10 rle()\T1/ptm
/m/n/10 ; an ob-ject of class \T1/zi4/m/n/10 "rle" \T1/ptm/m/n/10 for
[458] [459] [460] [461] [462] [463] [464] [465] [466] [467] [468] [469]
[470] [471] [472] [473]
Underfull \hbox (badness 2261) in paragraph at lines 32999--33004
[]\T1/ptm/m/n/10 If \T1/zi4/m/n/10 strip.white \T1/ptm/m/n/10 is of length 1, i
t ap-plies to all fields; oth-er-wise, if
[474]
Underfull \hbox (badness 10000) in paragraph at lines 33026--33032
[]\T1/ptm/m/n/10 The es-capes which are in-ter-preted are the con-trol char-ac-
ters

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\T1/ptm/m/n/10 `\T1/zi4/m/n/10 \a,\b,\f,\n,\r,\t,\v\T1/ptm/m/n/10 ' and oc-tal 
and hex-adec-i-mal rep-re-sen-ta-tions like
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[487] [488]
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[]\T1/ptm/m/n/10 Encoded `\T1/zi4/m/n/10 file://\T1/ptm/m/n/10 ' URLs should be
 in the Win-dows stan-dard form,
[489] [490] [491] [492] [493] [494] [495] [496] [497] [498] [499] [500]
[501] [502] [503] [504] [505] [506] [507] [508] [509] [510] [511] [512]
[513] [514] [515] [516] [517] [518] [519]
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[]\T1/ptm/m/n/10 On front-ends which sup-port it, the com-mands his-tory is rea
d from the file spec-i-fied by

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[]\T1/ptm/m/n/10 The command-line op-tion `\T1/zi4/m/n/10 --vanilla\T1/ptm/m/n/
10 ' im-plies `\T1/zi4/m/n/10 --no-site-file\T1/ptm/m/n/10 ', `\T1/zi4/m/n/10 -
-no-init-file\T1/ptm/m/n/10 ',

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\T1/ptm/m/n/10 `\T1/zi4/m/n/10 --no-environ\T1/ptm/m/n/10 ' and (ex-cept for \T
1/zi4/m/n/10 R CMD\T1/ptm/m/n/10 ) `\T1/zi4/m/n/10 --no-restore\T1/ptm/m/n/10 '
 Un-der Win-dows, it also im-plies
[520]
Underfull \hbox (badness 10000) in paragraph at lines 36305--36311
[]\T1/ptm/m/n/10 On sys-tems with sub-architectures (mainly Win-dows), the file
s `\T1/zi4/m/n/10 Renviron.site\T1/ptm/m/n/10 '

Underfull \hbox (badness 10000) in paragraph at lines 36305--36311
\T1/ptm/m/n/10 and `\T1/zi4/m/n/10 Rprofile.site\T1/ptm/m/n/10 ' are looked for
 first in architecture-specific di-rec-to-ries,

Underfull \hbox (badness 1320) in paragraph at lines 36305--36311
\T1/ptm/m/n/10 e.g. `[][]\T1/ptm/m/sl/10 R_HOME[][][]\T1/zi4/m/n/10 /etc/i386/R
environ.site\T1/ptm/m/n/10 '. And e.g. `\T1/zi4/m/n/10 .Renviron.i386\T1/ptm/m/
n/10 ' will be used in
[521] [522] [523] [524] [525]
Underfull \hbox (badness 1142) in paragraph at lines 36668--36674
[]\T1/ptm/m/n/10 A char-ac-ter string. The de-fault for the \T1/zi4/m/n/10 form
at \T1/ptm/m/n/10 meth-ods is \T1/zi4/m/n/10 "%Y-%m-%d
[526] [527] [528] [529] [530] [531] [532] [533] [534] [535] [536] [537]
[538] [539] [540] [541] [542] [543] [544]
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[]\T1/ptm/m/n/10 integer code used in \T1/zi4/m/n/10 quantile(*,type=quantile.t
ype) \T1/ptm/m/n/10 for the de-fault
[545] [546] [547] [548] [549] [550] [551] [552] [553] [554]
Underfull \hbox (badness 1616) in paragraph at lines 38643--38648
\T1/zi4/m/n/10 system("id") \T1/ptm/m/n/10 is much more portable on Unix-alikes
, pro-vided only the POSIX op-tions
[555] [556] [557] [558] [559] [560] [561] [562]
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[]\T1/ptm/m/n/10 logical. If \T1/zi4/m/n/10 TRUE\T1/ptm/m/n/10 , func-tions kee
p their source in-clud-ing com-ments, see
[563] [564] [565] [566] [567] [568] [569] [570] [571] [572] [573] [574]
[575] [576]
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[]\T1/ptm/m/n/10 On 64-bit plat-forms \T1/zi4/m/n/10 bin \T1/ptm/m/n/10 can hav
e $\OT1/cmr/m/n/10 2[]$ \T1/ptm/m/n/10 or more el-e-ments (i.e., \T1/zi4/m/n/10
 length(bin) >
[577] [578] [579] [580]
Underfull \hbox (badness 10000) in paragraph at lines 40358--40361
[][][]\T1/zi4/m/n/10 getTaskCallbackNames[][][] [][]taskCallbackManager[][][] [
][]$https : / / developer . r-[]project . org /
[581] [582] [583]
Underfull \hbox (badness 10000) in paragraph at lines 40542--40546
[][][]\T1/zi4/m/n/10 addTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 r
emoveTaskCallback[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 taskCallbackManager[
][][]\T1/ptm/m/n/10 \ [][]$\T1/zi4/m/n/10 https : / / developer .
[584] [585] [586] [587] [588] [589] [590]
Underfull \hbox (badness 10000) in paragraph at lines 41117--41120
[][][]$\T1/zi4/m/n/10 https : / / en . wikipedia . org / wiki / Time _ zone$[][
] \T1/ptm/m/n/10 and [][]$\T1/zi4/m/n/10 https : / / data . iana . org / time-[
]zones /
[591] [592] [593] [594] [595] [596] [597] [598] [599] [600] [601] [602]
[603]
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[]\T1/zi4/m/n/10 try \T1/ptm/m/n/10 eval-u-ates an ex-pres-sion and traps any e
r-rors that oc-cur dur-ing the eval-u-a-tion. If

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\T1/ptm/m/n/10 an er-ror oc-curs then the er-ror mes-sage is printed to the [][
]\T1/zi4/m/n/10 stderr[][][] \T1/ptm/m/n/10 con-nec-tion un-less
[604] [605] [606] [607] [608] [609] [610]
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[]\T1/ptm/m/n/10 When a func-tion call-ing \T1/zi4/m/n/10 UseMethod("fun") \T1/
ptm/m/n/10 is ap-plied to an ob-ject with class at-tribute
[611] [612] [613] [614] [615] [616] [617] [618] [619] [620] [621]
Underfull \hbox (badness 3668) in paragraph at lines 43238--43240
[]\T1/ptm/m/n/10 logical, in-di-cat-ing if the call should be out-put im-me-di-
ately, even if
[622]
Underfull \hbox (badness 2401) in paragraph at lines 43366--43370
[]\T1/ptm/m/n/10 See the de-scrip-tion of [][]\T1/zi4/m/n/10 options[][][]("war
n") \T1/ptm/m/n/10 for the cir-cum-stances un-der which there is a
[623] [624] [625]
Underfull \hbox (badness 2111) in paragraph at lines 43555--43560
\T1/ptm/m/n/10 If [][]\T1/zi4/m/n/10 names[][][](.dimnames) \T1/ptm/m/n/10 is n
ot empty, these are used as col-umn names.

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[]\T1/ptm/m/n/10 If \T1/zi4/m/n/10 arr.ind == TRUE \T1/ptm/m/n/10 and \T1/zi4/m
/n/10 x \T1/ptm/m/n/10 is an [][]\T1/zi4/m/n/10 array[][][] \T1/ptm/m/n/10 (has
 a [][]\T1/zi4/m/n/10 dim[][][] \T1/ptm/m/n/10 at-tribute), the re-sult is
[626] [627] [628] [629] [630] [631] [632] [633] [634]
Underfull \hbox (badness 5417) in paragraph at lines 44158--44162
[]\T1/zi4/m/n/10 .packages() \T1/ptm/m/n/10 re-turns the names of the cur-rentl
y at-tached pack-ages \T1/ptm/m/it/10 in-vis-i-bly \T1/ptm/m/n/10 whereas
[635]
Underfull \hbox (badness 10000) in paragraph at lines 44219--44223
[]\T1/zi4/m/n/10 .standard_regexps \T1/ptm/m/n/10 re-turns a list of `stan-dard
' reg-exps, in-clud-ing el-e-ments named
[636]) (compiler-pkg.tex
Chapter 2.
[637] [638] [639] [640]) (datasets-pkg.tex
Chapter 3.
[641] [642] [643] [644] [645] [646]
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[648] [649] [650] [651] [652] [653] [654] [655]
Underfull \hbox (badness 1097) in paragraph at lines 1031--1035
[]\T1/ptm/m/n/10 MacDonell, W.R. (1902). On crim-i-nal an-thro-pom-e-try and th
e iden-ti-fi-ca-tion of crim-i-nals.
[656] [657] [658] [659] [660] [661] [662] [663] [664] [665] [666] [667]
[668] [669] [670] [671] [672] [673] [674] [675] [676] [677]
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[678] [679] [680] [681] [682] [683]
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[684]
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[686]
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[689] [690] [691] [692] [693] [694] [695] [696] [697] [698] [699]
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[700]
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[701] [702] [703] [704] [705] [706] [707] [708] [709] [710] [711] [712]
[713] [714] [715]) (grDevices-pkg.tex [716]
Chapter 4.
[717] [718] [719] [720]
Underfull \hbox (badness 3158) in paragraph at lines 282--286
[]\T1/ptm/m/n/10 numeric vec-tor of length 3, \T1/zi4/m/n/10 c(mi,ma,n.)\T1/ptm
/m/n/10 , with iden-ti-cal mean-ing to

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[]\T1/ptm/m/n/10 Apart from that, [][]\T1/zi4/m/n/10 axisTicks[][][]() \T1/ptm/
m/n/10 just calls the C func-tion \T1/zi4/m/n/10 CreateAtVector() \T1/ptm/m/n/1
0 in

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\T1/ptm/m/n/10 `\T1/zi4/m/n/10 <Rsrc>/src/main/plot.c\T1/ptm/m/n/10 ' which is 
also called by the base \T1/ptm/b/n/10 graph-ics \T1/ptm/m/n/10 pack-age func-t
ion
[721] [722] [723] [724] [725] [726] [727] [728] [729] [730] [731] [732]
[733]
Underfull \hbox (badness 5175) in paragraph at lines 1120--1122
[]\T1/ptm/m/n/10 There is cur-rently no doc-u-men-ta-tion about the al-go-rithm
. The source code is in
[734] [735] [736]
Underfull \hbox (badness 1852) in paragraph at lines 1322--1325
[]\T1/zi4/m/n/10 densCols \T1/ptm/m/n/10 com-putes and re-turns the set of col-
ors that will be used in plot-ting, call-ing
[737] [738] [739]
Underfull \hbox (badness 1490) in paragraph at lines 1528--1533
\T1/ptm/m/n/10 by [][]\T1/zi4/m/n/10 rasterImage[][][] \T1/ptm/m/n/10 and [][]\
T1/zi4/m/n/10 grid.raster[][][]\T1/ptm/m/n/10 ? Pos-si-ble val-ues \T1/zi4/m/n/
10 "no"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "yes" \T1/ptm/m/n/10 and
[740] [741] [742] [743] [744] [745]
Underfull \hbox (badness 1325) in paragraph at lines 1934--1944
\T1/zi4/m/n/10 "png48"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pngmono"\T1/ptm/m/n/10 ,
 \T1/zi4/m/n/10 "pnggray"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "pngalpha"\T1/ptm/m/n/
10 , \T1/zi4/m/n/10 "bmp16"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "bmp16m" "bmp256"\T1
/ptm/m/n/10 , \T1/zi4/m/n/10 "bmp32b"\T1/ptm/m/n/10 ,
[746]
Underfull \hbox (badness 10000) in paragraph at lines 2046--2048
[]\T1/ptm/m/n/10 The de-fault value when a de-vice is opened is taken from the 
set-ting of
[747] [748] [749]
Underfull \hbox (badness 6758) in paragraph at lines 2224--2227
[]\T1/ptm/m/n/10 Some other op-tions which can be use-ful (see your Ghostscript
 doc-u-men-ta-tion) are
[750] [751] [752] [753] [754] [755] [756] [757] [758]
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Underfull \hbox (badness 10000) in paragraph at lines 3384--3389
[]\T1/zi4/m/n/10 nclass.FD \T1/ptm/m/n/10 uses the Freedman-Diaconis choice bas
ed on the inter-quartile range
[767] [768] [769] [770] [771] [772]
Underfull \hbox (badness 10000) in paragraph at lines 3785--3788
[]\T1/ptm/m/n/10 For use with \T1/zi4/m/n/10 onefile = FALSE \T1/ptm/m/n/10 giv
e a C in-te-ger for-mat such as
[773] [774] [775] [776] [777] [778] [779] [780] [781] [782]
Underfull \hbox (badness 10000) in paragraph at lines 4514--4519
[][][]$\T1/zi4/m/n/10 https : / / www . adobe . com / content / dam / acom / en
 / devnet / actionscript / articles / PLRM . pdf$[][]

Underfull \hbox (badness 4181) in paragraph at lines 4514--4519
\T1/ptm/m/n/10 or PDF [][]$\T1/zi4/m/n/10 https : / / www . adobe . com / devne
t / acrobat / pdfs / pdf _ reference _ 1-[]7 . pdf$[][] \T1/ptm/m/n/10 and in
[783] [784] [785] [786]
Underfull \hbox (badness 3364) in paragraph at lines 4813--4815
[]\T1/ptm/m/n/10 The TIFF spec-i-fi-ca-tion, in-clud-ing ex-ten-sions, at [][]$
\T1/zi4/m/n/10 https : / / partners . adobe . com / public /
[787] [788]
Underfull \hbox (badness 1377) in paragraph at lines 4947--4952
[]\T1/ptm/m/n/10 a char-ac-ter string de-scrib-ing the color model: cur-rently 
al-lowed val-ues
[789]
Underfull \hbox (badness 1418) in paragraph at lines 5023--5030
\T1/ptm/m/n/10 it is one of \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4
/m/n/10 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/
zi4/m/n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm
/m/n/10 ,

Underfull \hbox (badness 1755) in paragraph at lines 5041--5043
[]\T1/ptm/m/n/10 Another type of fam-ily makes use of CID-keyed fonts for East 
Asian lan-guages -- see
[790] [791]
Underfull \hbox (badness 1377) in paragraph at lines 5152--5157
[]\T1/ptm/m/n/10 Color mod-els pro-vided for back-wards com-pat-i-bil-ity are \
T1/zi4/m/n/10 "rgb" \T1/ptm/m/n/10 (which is RGB+gray) and

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[]\T1/ptm/m/n/10 Support for Com-puter Mod-ern fonts is based on a con-tri-bu-t
ion by Brian D'Urso
[792] [793] [794]
Underfull \hbox (badness 2035) in paragraph at lines 5356--5365
[]\T1/ptm/m/n/10 Mappings for a num-ber of stan-dard Adobe fonts (and URW equiv
-a-lents) are also pro-

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\T1/ptm/m/n/10 vided: \T1/zi4/m/n/10 "AvantGarde"\T1/ptm/m/n/10 , \T1/zi4/m/n/1
0 "Bookman"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Courier"\T1/ptm/m/n/10 , \T1/zi4/m/
n/10 "Helvetica"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Helvetica-Narrow"\T1/ptm/m/n/1
0 ,

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\T1/zi4/m/n/10 "NewCenturySchoolbook"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "Palatino"
 \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "Times"\T1/ptm/m/n/10 ; \T1/zi4/m/n/10 "URWG
othic"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "URWBookman"\T1/ptm/m/n/10 ,
[795]
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[]\T1/zi4/m/n/10 BousungEG-Light-GB \T1/ptm/m/n/10 can be found at [][]$\T1/zi4
/m/n/10 ftp : / / ftp . gnu . org / pub / non-[]gnu /

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\T1/zi4/m/n/10 chinese-[]fonts-[]truetype/$[][]\T1/ptm/m/n/10 . Ken Lunde's CJK
V re-sources are at [][]$\T1/zi4/m/n/10 ftp : / / ftp . oreilly .
[796] [797]
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[]\T1/ptm/m/n/10 arguments \T1/zi4/m/n/10 onefile\T1/ptm/m/n/10 , \T1/zi4/m/n/1
0 family\T1/ptm/m/n/10 , \T1/zi4/m/n/10 title\T1/ptm/m/n/10 , \T1/zi4/m/n/10 fo
nts\T1/ptm/m/n/10 , \T1/zi4/m/n/10 encoding\T1/ptm/m/n/10 , \T1/zi4/m/n/10 bg\T
1/ptm/m/n/10 , \T1/zi4/m/n/10 fg\T1/ptm/m/n/10 , \T1/zi4/m/n/10 width\T1/ptm/m/
n/10 ,
[798] [799] [800] [801] [802] [803] [804] [805]
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[]\T1/zi4/m/n/10 rgb2hsv \T1/ptm/m/n/10 trans-forms col-ors from RGB space (red
/green/blue) into HSV space
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[]\T1/ptm/m/n/10 for cairo types, the type of anti-aliasing (if any) to be used
. One of
[818]
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[]\T1/zi4/m/n/10 "-*-mincho-%s-%s-*-*-%d-*-*-*-*-*-*-*" \T1/ptm/m/n/10 for CJK 
lan-guages and
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[]\T1/ptm/m/n/10 the font fam-ily to be used. This must be one of \T1/zi4/m/n/1
0 "AvantGarde"\T1/ptm/m/n/10 ,
[824] [825]
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[]\T1/ptm/m/n/10 multiplicities (pos-i-tive in-te-gers); i.e., \T1/zi4/m/n/10 n
umber[i] \T1/ptm/m/n/10 is the mul-ti-plic-ity of
[826] [827] [828]) (graphics-pkg.tex
Chapter 5.
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[][][]\T1/zi4/m/n/10 boxplot.default[][][] \T1/ptm/m/n/10 which al-ready works 
nowa-days with data.frames; [][]\T1/zi4/m/n/10 boxplot.formula[][][]\T1/ptm/m/n
/10 ,
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[862] [863] [864]
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\T1/ptm/m/n/10 be in as-cend-ing or-der. (The rest of this de-scrip-tion does n
ot ap-ply to
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[]\T1/ptm/m/n/10 a char-ac-ter string in-di-cat-ing if log-a-rith-mic axes are 
to be used, see
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[]\T1/ptm/b/it/10 R.O.\T1/ptm/m/n/10 ; size of de-fault char-ac-ter \T1/zi4/m/n
/10 (width,height) \T1/ptm/m/n/10 in user co-or-di-nate units.

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\T1/zi4/m/n/10 par("cxy") \T1/ptm/m/n/10 is \T1/zi4/m/n/10 par("cin")/par("pin"
) \T1/ptm/m/n/10 scaled to user co-or-di-nates. Note that
[902] [903]
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[904 <C:/projects/BUILD/R-source-win64/library/graphics/help/figures/mai.pdf>]
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[905 <C:/projects/BUILD/R-source-win64/library/graphics/help/figures/oma.pdf>]
[906]
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[]\T1/ptm/m/n/10 The five stan-dard dash-dot line types (\T1/zi4/m/n/10 lty = 2
:6\T1/ptm/m/n/10 ) cor-re-spond to
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[][] 
[930 <C:/projects/BUILD/R-source-win64/library/graphics/help/figures/pch.pdf>]
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[]\T1/ptm/m/n/10 For each \T1/zi4/m/n/10 i\T1/ptm/m/n/10 , a line seg-ment is d
rawn be-tween the point \T1/zi4/m/n/10 (x0[i],y0[i]) \T1/ptm/m/n/10 and the poi
nt
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[]\T1/ptm/m/n/10 Sub-title (at bot-tom) us-ing font, size and color

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[]\T1/ptm/m/n/10 X axis la-bel us-ing font, size and color
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s}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.8915 \HeaderA{units}{Graphical Units}{units}
                                               [963] [964] [965] [966])
(grid-pkg.tex
Chapter 6.
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[]\T1/ptm/m/n/10 Note that \T1/zi4/m/n/10 preDrawDetails \T1/ptm/m/n/10 and \T1
/zi4/m/n/10 postDrawDetails \T1/ptm/m/n/10 are also called in the cal-cu-la-tio
n of
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[][][]\T1/ptm/m/n/10 Grid[][][], [][]\T1/zi4/m/n/10 pushViewport[][][]\T1/ptm/m
/n/10 , [][]\T1/zi4/m/n/10 popViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10
 downViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 seekViewport[][][]\T1/pt
m/m/n/10 , [][]\T1/zi4/m/n/10 upViewport[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/
10 unit[][][]\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 Both func-tions cre-ate a seg-ments grob (a graph-i-cal ob-jec
t de-scrib-ing seg-ments), but only
[1037] [1038] [1039] [1040]
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[]\T1/ptm/m/n/10 A char-ac-ter or [][]ex-pres-sion[][][] vec-tor. Other ob-ject
s are co-erced by
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[]\T1/ptm/m/n/10 This can be use-ful for re-turn-ing to your start-ing point by
 do-ing some-thing like \T1/zi4/m/n/10 depth
[1069] [1070] [1071] [1072]) (methods-pkg.tex
Chapter 7.
[1073] [1074] [1075] [1076] [1077] [1078] [1079] [1080]
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[]\T1/ptm/m/n/10 The class \T1/zi4/m/n/10 "className" \T1/ptm/m/n/10 ex-tends \
T1/zi4/m/n/10 "character" \T1/ptm/m/n/10 and has a slot \T1/zi4/m/n/10 "package
"\T1/ptm/m/n/10 , also of class
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[]\T1/ptm/m/n/10 Two vir-tual classes are sup-plied to test for ref-er-ence ob-
jects: \T1/zi4/m/n/10 is(x,"refClass") \T1/ptm/m/n/10 tests

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[]\T1/ptm/m/n/10 The ar-gu-ment to \T1/zi4/m/n/10 insertSource \T1/ptm/m/n/10 c
an be an ob-ject of class

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\T1/ptm/m/n/10 file name is passed to \T1/zi4/m/n/10 insertSource \T1/ptm/m/n/1
0 it calls \T1/zi4/m/n/10 evalSource \T1/ptm/m/n/10 to ob-tain the
[1099] [1100] [1101]
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[]\T1/ptm/m/n/10 To re-strict the search to classes in a par-tic-u-lar pack-age
, use \T1/zi4/m/n/10 where =
[1102] [1103] [1104] [1105] [1106]
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[]\T1/ptm/m/n/10 As you might ex-pect [][]\T1/zi4/m/n/10 setGeneric[][][] \T1/p
tm/m/n/10 and [][]\T1/zi4/m/n/10 setGroupGeneric[][][] \T1/ptm/m/n/10 cre-ate o
b-jects of class
[1107] [1108]
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[]\T1/ptm/m/n/10 In \T1/zi4/m/n/10 getGenerics\T1/ptm/m/n/10 , if \T1/zi4/m/n/1
0 TRUE\T1/ptm/m/n/10 , the \T1/zi4/m/n/10 package \T1/ptm/m/n/10 slot of the re
-turned re-sult is in

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\T1/ptm/m/n/10 In ad-di-tion, \T1/zi4/m/n/10 removeGeneric \T1/ptm/m/n/10 re-mo
ves the func-tion it-self; \T1/zi4/m/n/10 removeMethods \T1/ptm/m/n/10 re-store
s the
[1109] [1110] [1111] [1112] [1113] [1114] [1115]
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[]\T1/zi4/m/n/10 getPackageName \T1/ptm/m/n/10 re-turns the character-string na
me of the pack-age (with-out the ex-tra-ne-ous
[1116] [1117] [1118] [1119] [1120]
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[]\T1/ptm/m/n/10 The \T1/zi4/m/n/10 initialize \T1/ptm/m/n/10 method for these 
classes takes spe-cial ar-gu-ments

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[]\T1/ptm/m/n/10 The
[1121] [1122]
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[] \T1/zi4/m/n/10 Pos <-setClass("Pos",slots = c(latitude = "numeric",longitude
 = "numeric",altitude
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[]\T1/ptm/m/n/10 class [][]\T1/zi4/m/n/10 MethodsList[][][] \T1/ptm/m/n/10 for 
the ob-jects defin-ing sets of meth-ods as-so-ci-ated with a par-tic-u-lar

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\T1/zi4/m/n/10 MethodDefinition\T1/ptm/m/n/10 , or an ex-ten-sion. Class [][]\T
1/zi4/m/n/10 MethodWithNext[][][] \T1/ptm/m/n/10 for an ex-ten-sion used by
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[]\T1/ptm/m/n/10 Object of class \T1/zi4/m/n/10 "PossibleMethod" \T1/ptm/m/n/10
 the method to use in re-sponse to a
[1145]
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[]\T1/ptm/m/n/10 arguments to spec-ify prop-er-ties of the new ob-ject, to be p
assed to
[1146] [1147] [1148]
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[]\T1/ptm/m/n/10 In ad-di-tion, the cur-rently avail-able gener-ics with meth-o
ds for this class are found (us-ing
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\T1/ptm/m/n/10 can be con-verted ex-plic-itly as \T1/zi4/m/n/10 externalRefMeth
od(f)\T1/ptm/m/n/10 , which re-turns an ob-ject of class
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l.7234 \aliasA{Ops}{S4groupGeneric}{Ops}
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                                                 [1167]
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[]\T1/ptm/m/n/10 The mem-bers of the group de-fined by a par-tic-u-lar generic 
can be ob-tained by call-ing
[1168] [1169]
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[]\T1/ptm/m/n/10 for \T1/zi4/m/n/10 .selectSuperClasses() \T1/ptm/m/n/10 only, 
a [][]\T1/zi4/m/n/10 list[][][] \T1/ptm/m/n/10 of class ex-ten-sions, typ-i-cal
ly
[1170] [1171] [1172] [1173] [1174] [1175] [1176] [1177] [1178] [1179] [1180]
[1181] [1182] [1183] [1184] [1185] [1186] [1187] [1188] [1189] [1190] [1191]
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[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/zi4/m/n/10 ne
w("signature",functionDef,...)\T1/ptm/m/n/10 . The
[1203] [1204] [1205] [1206] [1207] [1208] [1209]
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[]\T1/ptm/m/n/10 Each of the classes ex-tends the cor-re-spond-ing un-traced cl
ass, from the data part; e.g.,
[1210] [1211] [1212]) (parallel-pkg.tex
Chapter 8.

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[]\T1/ptm/m/n/10 There is sup-port for mul-ti-ple RNG streams with the `\T1/zi4
/m/n/10 "L\TS1/zi4/m/n/10 '\T1/zi4/m/n/10 Ecuyer-CMRG"\T1/ptm/m/n/10 ' [][]RNG[
][][]: see
[1213] [1214] [1215] [1216] [1217] [1218] [1219] [1220]
Underfull \hbox (badness 3386) in paragraph at lines 595--598
[]\T1/ptm/m/n/10 An in-te-ger vec-tor of length 7 as given by \T1/zi4/m/n/10 .R
andom.seed \T1/ptm/m/n/10 when the
[1221] [1222] [1223]) (splines-pkg.tex [1224]
Chapter 9.

Underfull \hbox (badness 10000) in paragraph at lines 22--24
[]\T1/ptm/m/n/10 Douglas M. Bates \T1/zi4/m/n/10 <bates@stat.wisc.edu> \T1/ptm/
m/n/10 and William N. Ven-ables
[1225] [1226] [1227] [1228] [1229] [1230] [1231] [1232] [1233] [1234] [1235]
[1236] [1237] [1238]) (stats-pkg.tex
Chapter 10.
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[1250] [1251]
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[]\T1/ptm/m/n/10 A fit-ted model ob-ject, for ex-am-ple from \T1/zi4/m/n/10 lm 
\T1/ptm/m/n/10 or \T1/zi4/m/n/10 aov\T1/ptm/m/n/10 , or a for-mula for
[1252] [1253] [1254] [1255] [1256] [1257] [1258]
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[]\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of 
\T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 ,
[1259] [1260]
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[]\T1/ptm/m/n/10 An ob-ject of class \T1/zi4/m/n/10 c("aov","lm") \T1/ptm/m/n/1
0 or for mul-ti-ple re-sponses of class
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[]\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of 
\T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 ,
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[1300] [1301] [1302]
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[]\T1/ptm/m/n/10 standardized resid-u-als, \T1/zi4/m/n/10 (observed -expected) 
/ sqrt(V)\T1/ptm/m/n/10 , where \T1/zi4/m/n/10 V \T1/ptm/m/n/10 is the
[1303] [1304] [1305] [1306] [1307]
Underfull \hbox (badness 3989) in paragraph at lines 4681--4688
[]\T1/ptm/m/n/10 a nu-meric vec-tor of length 2, equal to say $\OT1/cmr/m/n/10 
(\OML/cmm/m/it/10 g[]; g[]\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 , where $\OML/cmm/m/
it/10 g[] \OT1/cmr/m/n/10 =
[1308] [1309] [1310] [1311] [1312] [1313] [1314] [1315] [1316]
Underfull \hbox (badness 2556) in paragraph at lines 5317--5320
[]\T1/ptm/m/n/10 character; par-tially matched to \T1/zi4/m/n/10 "circular"\T1/
ptm/m/n/10 , \T1/zi4/m/n/10 "open"\T1/ptm/m/n/10 , \T1/zi4/m/n/10 "filter"\T1/p
tm/m/n/10 . For

Underfull \hbox (badness 2932) in paragraph at lines 5334--5336
[]\T1/ptm/m/n/10 Note that the usual def-i-ni-tion of con-vo-lu-tion of two se-
quences \T1/zi4/m/n/10 x \T1/ptm/m/n/10 and \T1/zi4/m/n/10 y \T1/ptm/m/n/10 is 
given by
[1317] [1318] [1319] [1320] [1321] [1322]
Underfull \hbox (badness 2503) in paragraph at lines 5726--5730
[]\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of 
\T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 ,
[1323] [1324] [1325] [1326] [1327] [1328] [1329] [1330] [1331] [1332] [1333]
[1334] [1335]
Underfull \hbox (badness 7081) in paragraph at lines 6520--6523
[]\T1/ptm/m/n/10 Objects of class \T1/zi4/m/n/10 "hclust" \T1/ptm/m/n/10 can be
 con-verted to class \T1/zi4/m/n/10 "dendrogram" \T1/ptm/m/n/10 us-ing method

Underfull \hbox (badness 10000) in paragraph at lines 6524--6526
[]\T1/zi4/m/n/10 rev.dendrogram \T1/ptm/m/n/10 sim-ply re-turns the den-dro-gra
m \T1/zi4/m/n/10 x \T1/ptm/m/n/10 with re-versed nodes, see also
[1336] [1337] [1338] [1339] [1340] [1341] [1342] [1343] [1344] [1345] [1346]
[1347]
Underfull \hbox (badness 10000) in paragraph at lines 7369--7372
[]\T1/ptm/m/n/10 optionally, the dis-tance method used; re-sult-ing from [][]\T
1/zi4/m/n/10 dist[][][]()\T1/ptm/m/n/10 , the
[1348] [1349] [1350] [1351] [1352] [1353] [1354] [1355] [1356] [1357] [1358]
[1359] [1360] [1361] [1362] [1363] [1364] [1365] [1366] [1367] [1368]
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[1370] [1371] [1372]
Underfull \hbox (badness 2626) in paragraph at lines 9048--9051
[]\T1/ptm/m/n/10 Either \T1/zi4/m/n/10 "convolution" \T1/ptm/m/n/10 or \T1/zi4/
m/n/10 "recursive" \T1/ptm/m/n/10 (and can be ab-bre-vi-ated). If
[1373] [1374]
Underfull \hbox (badness 2503) in paragraph at lines 9155--9159
[]\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of 
\T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 ,
[1375] [1376] [1377] [1378] [1379] [1380] [1381] [1382] [1383] [1384] [1385]
[1386] [1387] [1388] [1389] [1390] [1391] [1392] [1393]
Underfull \hbox (badness 4518) in paragraph at lines 10465--10470
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1394] [1395] [1396] [1397] [1398]
Underfull \hbox (badness 2142) in paragraph at lines 10825--10828
[]\T1/ptm/m/n/10 positive con-ver-gence tol-er-ance $\OML/cmm/m/it/10 $\T1/ptm
/m/n/10 ; the it-er-a-tions con-verge when $\OMS/cmsy/m/n/10 j\OML/cmm/m/it/10 
dev \OMS/cmsy/m/n/10 �

Underfull \hbox (badness 1253) in paragraph at lines 10844--10847
[]\T1/ptm/m/n/10 When \T1/zi4/m/n/10 trace \T1/ptm/m/n/10 is true, calls to [][
]\T1/zi4/m/n/10 cat[][][] \T1/ptm/m/n/10 pro-duce the out-put for each IWLS it-
er-a-tion. Hence,
[1399]
Underfull \hbox (badness 1708) in paragraph at lines 10906--10910
[]\T1/ptm/m/n/10 the type of resid-u-als which should be re-turned. The al-ter-
na-tives are:
[1400] [1401] [1402] [1403] [1404]
Underfull \hbox (badness 1694) in paragraph at lines 11302--11305
[]\T1/ptm/m/n/10 character vec-tors with row and col-umn la-bels to use; these 
de-fault to
[1405] [1406] [1407] [1408] [1409] [1410]
Underfull \hbox (badness 10000) in paragraph at lines 11629--11632
[]\T1/ptm/m/n/10 If one of $\OML/cmm/m/it/10 m; n; k$\T1/ptm/m/n/10 , ex-ceeds 
[][]\T1/zi4/m/n/10 .Machine[][][]$integer.max\T1/ptm/m/n/10 , cur-rently the eq
uiv-a-lent of

Underfull \hbox (badness 1281) in paragraph at lines 11629--11632
\T1/zi4/m/n/10 qhyper(runif(nn),m,n,k) \T1/ptm/m/n/10 is used, when a bi-no-mia
l ap-prox-i-ma-tion may be con-sid-er-ably
[1411] [1412]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.hat}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.11783 \aliasA{hat}{influence.measures}{hat}
                                              [1413] [1414]
Underfull \hbox (badness 1484) in paragraph at lines 11918--11920
[]\T1/ptm/m/n/10 The func-tion \T1/zi4/m/n/10 hat() \T1/ptm/m/n/10 ex-ists main
ly for S (ver-sion 2) com-pat-i-bil-ity; we rec-om-mend us-ing
[1415] [1416] [1417] [1418] [1419] [1420] [1421] [1422] [1423]
Underfull \hbox (badness 10000) in paragraph at lines 12511--12513
[]\T1/ptm/m/n/10 tolerance even-tu-ally passed to [][]\T1/zi4/m/n/10 solve.defa
ult[][][] \T1/ptm/m/n/10 when \T1/zi4/m/n/10 SSinit =
[1424] [1425] [1426] [1427] [1428]
Underfull \hbox (badness 2894) in paragraph at lines 12847--12851
[]\T1/ptm/m/n/10 logical or in-te-ger num-ber, cur-rently only used in the de-f
ault method
[1429] [1430] [1431] [1432] [1433] [1434] [1435] [1436] [1437] [1438] [1439]
[1440]
Underfull \hbox (badness 4518) in paragraph at lines 13597--13602
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1441] [1442] [1443] [1444] [1445] [1446] [1447] [1448] [1449]
Underfull \hbox (badness 4518) in paragraph at lines 14249--14254
[]\T1/ptm/m/n/10 an op-tional data frame, list or en-vi-ron-ment (or ob-ject co
-ercible by
[1450] [1451]
Underfull \hbox (badness 8151) in paragraph at lines 14387--14391
[]\T1/ptm/m/n/10 Only for the (de-fault) case \T1/zi4/m/n/10 (surface = "interp
olate",statistics =

Underfull \hbox (badness 1199) in paragraph at lines 14394--14396
[]\T1/ptm/m/n/10 the num-ber of it-er-a-tions used in ro-bust fit-ting, i.e. on
ly if \T1/zi4/m/n/10 family \T1/ptm/m/n/10 is
[1452] [1453] [1454] [1455] [1456] [1457] [1458] [1459] [1460] [1461] [1462]
[1463] [1464] [1465] [1466] [1467] [1468]
Underfull \hbox (badness 2503) in paragraph at lines 15465--15469
[]\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of 
\T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 ,
[1469] [1470] [1471] [1472] [1473] [1474] [1475]
Underfull \hbox (badness 4621) in paragraph at lines 15977--15983
[]\T1/zi4/m/n/10 model.offset \T1/ptm/m/n/10 and \T1/zi4/m/n/10 model.response 
\T1/ptm/m/n/10 are equiv-a-lent to \T1/zi4/m/n/10 model.extract(,"offset") \T1/
ptm/m/n/10 and
[1476] [1477] [1478] [1479] [1480] [1481] [1482] [1483] [1484] [1485] [1486]
[1487] [1488] [1489] [1490] [1491] [1492] [1493] [1494] [1495] [1496] [1497]
[1498] [1499] [1500] [1501] [1502]
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[1504] [1505] [1506] [1507] [1508] [1509] [1510] [1511] [1512] [1513] [1514]
[1515]
Underfull \hbox (badness 1377) in paragraph at lines 18576--18581
[]\T1/ptm/m/n/10 A vec-tor of scal-ing val-ues for the pa-ram-e-ters. Op-ti-miz
a-tion is per-formed on

Underfull \hbox (badness 1735) in paragraph at lines 18581--18584
[]\T1/ptm/m/n/10 A vec-tor of step sizes for the finite-difference ap-prox-i-ma
-tion to the gra-di-ent, on

Underfull \hbox (badness 2343) in paragraph at lines 18594--18598
[]\T1/ptm/m/n/10 Relative con-ver-gence tol-er-ance. The al-go-rithm stops if i
t is un-able to re-duce

Underfull \hbox (badness 3471) in paragraph at lines 18594--18598
\T1/ptm/m/n/10 the value by a fac-tor of \T1/zi4/m/n/10 reltol * (abs(val) + re
ltol) \T1/ptm/m/n/10 at a step. De-faults to
[1516]
Underfull \hbox (badness 2662) in paragraph at lines 18602--18606
[]\T1/ptm/m/n/10 The fre-quency of re-ports for the \T1/zi4/m/n/10 "BFGS"\T1/pt
m/m/n/10 , \T1/zi4/m/n/10 "L-BFGS-B" \T1/ptm/m/n/10 and \T1/zi4/m/n/10 "SANN" \
T1/ptm/m/n/10 meth-ods if
[1517] [1518]
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Overfull \hbox (15.73795pt too wide) in paragraph at lines 18827--18827
 []\T1/zi4/m/n/9 ## 1-D minimization: "Brent" or optimize() being preferred.. b
ut NM may be ok and "unavoidable",[] 

Overfull \hbox (3.75941pt too wide) in paragraph at lines 18830--18830
 []\T1/zi4/m/n/9 system.time(ro <- optim(1, function(x) (x-pi)^2, control=list(
warn.1d.NelderMead = FALSE)))[] 
[1520] [1521] [1522] [1523] [1524] [1525]
Underfull \hbox (badness 1337) in paragraph at lines 19252--19255
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
[1526] [1527] [1528] [1529] [1530] [1531] [1532] [1533] [1534]
Underfull \hbox (badness 3049) in paragraph at lines 19748--19752
[]\T1/ptm/m/n/10 In the Cook's dis-tance vs leverage/(1-leverage) plot, con-tou
rs of stan-dard-ized resid-u-als
[1535] [1536] [1537] [1538]
Underfull \hbox (badness 1194) in paragraph at lines 20006--20009
[]\T1/ptm/m/n/10 coverage prob-a-bil-ity for con-fi-dence in-ter-val. Plot-ting
 of the con-fi-dence
[1539] [1540] [1541] [1542] [1543]
Underfull \hbox (badness 2503) in paragraph at lines 20381--20384
[]\T1/ptm/m/n/10 indicates the al-ter-na-tive hy-poth-e-sis and must be one of 
\T1/zi4/m/n/10 "two.sided"\T1/ptm/m/n/10 ,
[1544]
Underfull \hbox (badness 3919) in paragraph at lines 20408--20410
[]\T1/ptm/m/n/10 the char-ac-ter string \T1/zi4/m/n/10 "Exact Poisson test" \T1
/ptm/m/n/10 or \T1/zi4/m/n/10 "Comparison of Poisson
[1545] [1546] [1547] [1548] [1549] [1550] [1551] [1552] [1553] [1554] [1555]
[1556] [1557] [1558] [1559] [1560]
Underfull \hbox (badness 10000) in paragraph at lines 21485--21491
[]\T1/ptm/m/n/10 For time-series pre-dic-tion, [][]\T1/zi4/m/n/10 predict.ar[][
][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/n/10 predict.Arima[][][]\T1/ptm/m/n/10 , [][]
\T1/zi4/m/n/10 predict.arima0[][][]\T1/ptm/m/n/10 ,
[1561] [1562] [1563] [1564] [1565] [1566] [1567] [1568] [1569] [1570] [1571]
[1572] [1573] [1574] [1575] [1576] [1577] [1578] [1579] [1580] [1581]
Underfull \hbox (badness 1337) in paragraph at lines 22834--22840
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
[1582] [1583] [1584] [1585] [1586] [1587] [1588] [1589] [1590]
Overfull \hbox (27.74408pt too wide) in paragraph at lines 23399--23399
 []  \T1/zi4/m/n/9 t(vapply(1:9, function(typ) quantile(x, prob=prob, type = ty
p, ...), quantile(x, prob, type=1)))[] 
[1591] [1592] [1593]
Underfull \hbox (badness 10000) in paragraph at lines 23650--23653
[]\T1/ptm/m/n/10 Optional vec-tor with clus-ter mem-ber-ships as re-turned by

Underfull \hbox (badness 4205) in paragraph at lines 23650--23653
\T1/zi4/m/n/10 cutree(hclust.obj,k = k)\T1/ptm/m/n/10 , can be spec-i-fied for 
ef-fi-ciency if al-ready
[1594] [1595] [1596] [1597] [1598] [1599] [1600] [1601] [1602]
Underfull \hbox (badness 10000) in paragraph at lines 24235--24238
[]\T1/ptm/m/n/10 Apart from the end val-ues, the re-sult \T1/zi4/m/n/10 y = run
med(x,k) \T1/ptm/m/n/10 sim-ply has \T1/zi4/m/n/10 y[j] =
[1603]
Underfull \hbox (badness 3690) in paragraph at lines 24287--24291
[][][]\T1/zi4/m/n/10 smoothEnds[][][] \T1/ptm/m/n/10 which im-ple-ments Tukey's
 end point rule and is called by de-fault from
[1604] [1605] [1606] [1607] [1608] [1609]
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[1611]
Underfull \hbox (badness 2165) in paragraph at lines 24777--24782
[]\T1/ptm/m/n/10 Each of the fol-low-ing are \T1/zi4/m/n/10 "selfStart" \T1/ptm
/m/n/10 mod-els (with ex-am-ples) [][]\T1/zi4/m/n/10 SSasymp[][][]\T1/ptm/m/n/1
0 , [][]\T1/zi4/m/n/10 SSasympOff[][][]\T1/ptm/m/n/10 ,
[1612] [1613] [1614]
Underfull \hbox (badness 1867) in paragraph at lines 24982--24984
[]\T1/ptm/m/n/10 potentially fur-ther ar-gu-ments passed to and from meth-ods. 
Passed to

Underfull \hbox (badness 10000) in paragraph at lines 24995--24999
\T1/ptm/m/n/10 where \T1/zi4/m/n/10 NN <-[][]nobs[][][](object,use.fallback = u
se.fallback) \T1/ptm/m/n/10 and \T1/zi4/m/n/10 PP
[1615] [1616] [1617] [1618] [1619] [1620] [1621] [1622] [1623] [1624] [1625]
[1626] [1627] [1628] [1629] [1630] [1631] [1632] [1633] [1634] [1635] [1636]
[1637]
Underfull \hbox (badness 3514) in paragraph at lines 26556--26561
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1638] [1639] [1640] [1641]
Overfull \hbox (2.23795pt too wide) in paragraph at lines 26790--26790
 []       \T1/zi4/m/n/9 quote({f(t[0.5]) == frac(phi[1],2)}~{} %=>% {}~~{t[0.5]
 == frac(log(2), e^{phi[2]})}),[] 

Underfull \hbox (badness 3514) in paragraph at lines 26826--26832
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1642] [1643] [1644] [1645]
Underfull \hbox (badness 3514) in paragraph at lines 27040--27045
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1646]
Underfull \hbox (badness 3514) in paragraph at lines 27127--27132
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1647]
Underfull \hbox (badness 3514) in paragraph at lines 27192--27197
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1648] [1649]
Underfull \hbox (badness 3514) in paragraph at lines 27286--27291
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 input\
T1/ptm/m/n/10 . It is the value of the ex-pres-sion
[1650]
Underfull \hbox (badness 6691) in paragraph at lines 27378--27383
[]\T1/ptm/m/n/10 a nu-meric vec-tor of the same length as \T1/zi4/m/n/10 x\T1/p
tm/m/n/10 . It is the value of the ex-pres-sion
[1651] [1652] [1653] [1654] [1655] [1656] [1657] [1658]
Underfull \hbox (badness 4024) in paragraph at lines 27908--27911
[]\T1/ptm/m/n/10 the span (in lags) of the loess win-dow for trend ex-trac-tion
, which
[1659] [1660] [1661] [1662] [1663] [1664] [1665] [1666] [1667] [1668]
Underfull \hbox (badness 5431) in paragraph at lines 28514--28516
[]\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/z
i4/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if
[1669] [1670] [1671]
Underfull \hbox (badness 5431) in paragraph at lines 28724--28727
[]\T1/ptm/m/n/10 the cor-re-la-tion ma-trix cor-re-spond-ing to the above \T1/z
i4/m/n/10 cov.unscaled\T1/ptm/m/n/10 , if
[1672] [1673] [1674] [1675] [1676]
Underfull \hbox (badness 1337) in paragraph at lines 29038--29042
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
[1677] [1678] [1679] [1680] [1681]
Underfull \hbox (badness 1616) in paragraph at lines 29340--29343
[]\T1/ptm/m/n/10 color, plot-ting char-ac-ter ex-pan-sion and type for par-tial
 resid-u-als, when
[1682] [1683] [1684] [1685] [1686] [1687] [1688] [1689] [1690] [1691] [1692]
[1693] [1694] [1695] [1696] [1697] [1698]
Underfull \hbox (badness 3557) in paragraph at lines 30470--30474
[]\T1/ptm/m/n/10 Setting \T1/zi4/m/n/10 extendInt \T1/ptm/m/n/10 to a non-\T1/z
i4/m/n/10 "no" \T1/ptm/m/n/10 string, means search-ing for the cor-rect \T1/zi4
/m/n/10 interval =
[1699] [1700] [1701] [1702] [1703] [1704]
Underfull \hbox (badness 1337) in paragraph at lines 30834--30838
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
[1705] [1706] [1707] [1708] [1709] [1710] [1711] [1712]
Underfull \hbox (badness 1337) in paragraph at lines 31361--31365
[]\T1/ptm/m/n/10 a char-ac-ter string spec-i-fy-ing the al-ter-na-tive hy-poth-
e-sis, must be one of
[1713] [1714] [1715] [1716] [1717] [1718] [1719] [1720] [1721]) (stats4-pkg.tex
[1722]
Chapter 11.
[1723] [1724] [1725] [1726] [1727] [1728]pdfTeX warning (ext4): destination wit
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l.407 ...Package \pkg{stats4}}{show.Rdash.methods}
                                                   [1729] [1730] [1731])
(tcltk-pkg.tex [1732]
Chapter 12.
[1733] [1734] [1735] [1736] [1737] [1738] [1739]
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Underfull \hbox (badness 1546) in paragraph at lines 660--667
[]\T1/zi4/m/n/10 tcl \T1/ptm/m/n/10 pro-vides a generic in-ter-face to call-ing
 any Tk or Tcl com-mand by sim-ply run-ning
[1741] [1742] [1743] [1744] [1745]
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[1747] [1748] [1749] [1750] [1751] [1752]) (tools-pkg.tex
Chapter 13.
[1753]

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[1754]
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[]\T1/zi4/m/n/10 assertWarning() \T1/ptm/m/n/10 as-serts that a warn-ing will b
e sig-nalled, but \T1/ptm/m/it/10 not \T1/ptm/m/n/10 an er-ror, whereas
[1755] [1756]
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[]\T1/ptm/m/n/10 At a min-i-mum, the en-vi-ron-ment should con-tain rou-tines t
o ren-der each of the 12 types

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\T1/ptm/m/n/10 of bib-li-o-graphic en-try sup-ported by [][]\T1/zi4/m/n/10 bibe
ntry[][][] \T1/ptm/m/n/10 as well as sev-eral other rou-tines de-

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\T1/zi4/m/n/10 formatIncollection\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatInProcee
dings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatManual\T1/ptm/m/n/10 , \T1/zi4/m/n/1
0 formatMastersthesis\T1/ptm/m/n/10 ,

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\T1/zi4/m/n/10 formatMisc\T1/ptm/m/n/10 , \T1/zi4/m/n/10 formatPhdthesis\T1/ptm
/m/n/10 , \T1/zi4/m/n/10 formatProceedings\T1/ptm/m/n/10 , \T1/zi4/m/n/10 forma
tTechreport \T1/ptm/m/n/10 and
[1757]
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[]\T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 or char-ac-ter; name of vi-gnette en-gine 
to use. Over-rides any
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\T1/ptm/m/n/10 giv-ing the repos-i-to-ries to use for lo-cat-ing re-verse de-pe
n-den-cies (de-
[1770]
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[]\T1/ptm/m/n/10 a log-i-cal in-di-cat-ing whether to also sum-ma-rize the re-v
erse de-pen-den-cies

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[]\T1/ptm/m/n/10 a char-ac-ter string giv-ing the path to the di-rec-tory of a 
pre-vi-ous

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[]\T1/ptm/m/n/10 Results and tim-ings can con-ve-niently be sum-ma-rized us-ing


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\T1/zi4/m/n/10 summarize_check_packages_in_dir_results \T1/ptm/m/n/10 and \T1/z
i4/m/n/10 summarize_check_packages_in_dir_timings\T1/ptm/m/n/10 ,
[1771] [1772] [1773] [1774] [1775]
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[]\T1/zi4/m/n/10 CRAN_memtest_notes() \T1/ptm/m/n/10 is now dep-re-cated, with 
its func-tion-al-ity in-te-grated into that of
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a
 sub-set of
[1778]
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor of \T1/phv/m/n/10 R \T1/ptm/m/n/10 li-br
ary trees, or \T1/zi4/m/n/10 NULL \T1/ptm/m/n/10 for all known trees (see
[1779] [1780] [1781]pdfTeX warning (ext4): destination with the same identifier
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l.1899 \aliasA{GSC}{find\_gs\_cmd}{GSC}
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                                                   [1782] [1783] [1784]
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 []\T1/zi4/m/n/9 writeLines(paste0("\\newcommand{\\logo}{\\if{html}{\\figure{Rl
ogo.svg}{options: width=100}",[] 
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of de-pen-den-cies, a
 sub-set of
[1789] [1790] [1791] [1792] [1793] [1794] [1795]

LaTeX Font Warning: Font shape `T1/zi4/m/sl' undefined
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[]\T1/zi4/m/sl/10 NULL \T1/ptm/m/n/10 or a named (by top-ics) char-ac-ter vec-t
or of links, as re-turned by
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[]\T1/ptm/m/n/10 additional ar-gu-ments use when prepar-ing the files to be run
,
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[]\T1/ptm/m/n/10 Where sup-ported (\T1/zi4/m/sl/10 texi2dvi \T1/ptm/m/n/10 5.0 
and later; \T1/zi4/m/sl/10 texify.exe \T1/ptm/m/n/10 from MiK-TeX), op-tion
[1813]
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[]\T1/ptm/m/n/10 a ma-trix spec-i-fy-ing all pack-ages in-stalled on the lo-cal
 sys-tem, as from
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[]\T1/ptm/m/n/10 Users should ex-pect sig-nif-i-cantly smaller speedups over \T
1/zi4/m/sl/10 write_PACKAGES \T1/ptm/m/n/10 in the \T1/zi4/m/sl/10 type ==
[1819]
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[]\T1/ptm/m/n/10 The re-main-ing steps are done only if file `\T1/zi4/m/sl/10 p
o/\T1/ptm/m/sl/10 pkgname\T1/zi4/m/sl/10 .pot\T1/ptm/m/n/10 ' al-ready ex-ists.
 The

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\T1/ptm/m/n/10 `\T1/zi4/m/sl/10 src/*.{c,cc,cpp,m,mm}\T1/ptm/m/n/10 ' files in 
the pack-age are ex-am-ined to cre-ate a file
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[]\T1/ptm/m/n/10 The de-fault cor-re-sponds to the fields needed by [][]\T1/zi4
/m/sl/10 available.packages[][][]\T1/ptm/m/n/10 :
[1823]
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[]\T1/ptm/m/n/10 For a re-mote repos-i-tory there is a trade-off be-tween down-
load speed and time spent by
[1824] [1825] [1826]) (utils-pkg.tex
Chapter 14.

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[]\T1/ptm/m/n/10 a nu-meric vec-tor or list with names par-tially match-ing `\T
1/zi4/m/sl/10 insertions\T1/ptm/m/n/10 ',
[1827] [1828] [1829] [1830] [1831]
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\T1/zi4/m/sl/10 c("vertical","horizontal","cascade","minimize","restore") \T1/p
tm/m/n/10 with
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[]\T1/ptm/m/n/10 Functions \T1/zi4/m/sl/10 aspell_package_Rd_files\T1/ptm/m/n/1
0 , \T1/zi4/m/sl/10 aspell_package_vignettes\T1/ptm/m/n/10 ,

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\T1/zi4/m/sl/10 aspell_package_R_files \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 aspel
l_package_C_files \T1/ptm/m/n/10 per-form spell check-ing on the
[1837] [1838]
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[]\T1/ptm/m/n/10 Argument \T1/zi4/m/sl/10 filters \T1/ptm/m/n/10 can be used to
 se-lect which of the pack-ages on the repos-i-to-

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\T1/ptm/m/n/10 ries are re-ported. It is called with its de-fault value (\T1/zi
4/m/sl/10 NULL\T1/ptm/m/n/10 ) by func-tions such as
[1839]
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[]\T1/ptm/m/n/10 Where pro-vided by the repos-i-tory, fields \T1/zi4/m/sl/10 "O
S_type"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "License"\T1/ptm/m/n/10 , \T1/zi4/m/sl/
10 "License_is_FOSS"\T1/ptm/m/n/10 ,
[1840] [1841] [1842]
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[]\T1/ptm/m/n/10 (\T1/ptm/m/it/10 deprecated\T1/ptm/m/n/10 , use \T1/zi4/m/sl/1
0 bibtex = T|F \T1/ptm/m/n/10 in-stead!) a num-ber, say $\OML/cmm/m/it/10 m$\T1
/ptm/m/n/10 , in-di-cat-

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\T1/ptm/m/n/10 ing that the bib-tex code should be given in ad-di-tion to the f
or-mat-

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\T1/ptm/m/n/10 ted tex \T1/ptm/m/it/10 when \T1/ptm/m/n/10 there are not more t
han $\OML/cmm/m/it/10 m$ \T1/ptm/m/n/10 en-tries. The de-fault is

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\T1/ptm/m/n/10 taken as [][]\T1/zi4/m/sl/10 getOption[][][]("citation.bibtex.ma
x",1) \T1/ptm/m/n/10 which is \T1/zi4/m/sl/10 1 \T1/ptm/m/n/10 typ-i-cally.

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\T1/ptm/m/n/10 For ex-am-ple, to see no bib-tex at all, you can change the de-f
ault by

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[]\T1/ptm/m/n/10 logical in-di-cat-ing if biben-tries should be sorted, us-ing
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[]\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T
1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to
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[]\T1/ptm/m/n/10 None for \T1/zi4/m/sl/10 chooseCRANmirror()\T1/ptm/m/n/10 , th
is func-tion is in-voked for its side ef-fect of up-dat-ing
[1859] [1860] [1861] [1862] [1863]pdfTeX warning (ext4): destination with the s
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l.2566 ... the Clipboard in MS Windows}{clipboard}
                                                   [1864] [1865]
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[]\T1/ptm/m/n/10 A [][]\T1/zi4/m/sl/10 list[][][] \T1/ptm/m/n/10 or [][]\T1/zi4
/m/sl/10 array[][][]\T1/ptm/m/n/10 , see the \T1/zi4/m/sl/10 simplify \T1/ptm/m
/n/10 ar-gu-ment above. In the lat-ter case, the iden-tity
[1866] [1867] [1868] [1869] [1870] [1871]
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[]\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .tab\T1/ptm/m/n/10 ', `\T1/zi4/
m/sl/10 .txt\T1/ptm/m/n/10 ' or `\T1/zi4/m/sl/10 .TXT\T1/ptm/m/n/10 ' are read 
us-ing [][]\T1/zi4/m/sl/10 read.table[][][](...,header =

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[]\T1/ptm/m/n/10 files end-ing `\T1/zi4/m/sl/10 .csv\T1/ptm/m/n/10 ' or `\T1/zi
4/m/sl/10 .CSV\T1/ptm/m/n/10 ' are read us-ing [][]\T1/zi4/m/sl/10 read.table[]
[][](...,header = TRUE,sep =
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[]\T1/ptm/m/n/10 The level of de-tail pro-vided dur-ing trans-fer can be set by
 the \T1/zi4/m/sl/10 quiet \T1/ptm/m/n/10 ar-gu-ment and the
[1883]
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[]\T1/ptm/m/n/10 Usernames and pass-words can be set for HTTP proxy trans-fers 
via en-vi-ron-ment vari-able
[1884] [1885]
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[]\T1/ptm/m/n/10 additional ar-gu-ments to be passed to [][]\T1/zi4/m/sl/10 dow
nload.file[][][] \T1/ptm/m/n/10 and
[1886] [1887] [1888] [1889] [1890] [1891] [1892] [1893] [1894] [1895] [1896]pdf
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l.4850 ...mat Unordered and Ordered Lists}{format}
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ation with the same identifier (name{Rfn.format.1}) has been already used, dupl
icate ignored
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l.4850 ...mat Unordered and Ordered Lists}{format}
                                                   [1897] [1898] [1899]
[1900] [1901] [1902] [1903] [1904]
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[]\T1/ptm/m/n/10 This func-tion will search for Win-dows han-dles, for pass-ing
 to ex-ter-nal GUIs or to the
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[]\T1/ptm/m/n/10 additional named ar-gu-ments such as \T1/zi4/m/sl/10 method \T
1/ptm/m/n/10 and \T1/zi4/m/sl/10 ccaddress \T1/ptm/m/n/10 to pass to
[1914]
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[]\T1/ptm/m/n/10 a char-ac-ter string to be matched in the help page `key-words
'. `Key-

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\T1/ptm/m/n/10 words' are re-ally cat-e-gories: the stan-dard cat-e-gories are 
listed in file
[1915] [1916] [1917]
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[]\T1/ptm/m/n/10 One of the links on the in-dex page is the HTML pack-age in-de
x,
[1918]
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[]\T1/ptm/m/n/10 a char-ac-ter vec-tor list-ing the types of doc-u-men-ta-tion 
to search. See
[1919]
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[]\T1/ptm/m/n/10 For de-tails of the lock-ing which is done, see the sec-tion `
Lock-ing' in the help for
[1920] [1921] [1922]
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[]\T1/ptm/m/n/10 a ma-trix as re-turned by [][]\T1/zi4/m/sl/10 available.packag
es[][][] \T1/ptm/m/n/10 list-ing pack-ages avail-able

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\T1/ptm/m/n/10 used if \T1/zi4/m/sl/10 repos = NULL\T1/ptm/m/n/10 . Can also be
 a char-ac-ter vec-tor, a sub-set of

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[]\T1/ptm/m/n/10 an op-tional char-ac-ter vec-tor of ad-di-tional op-tion(s) to
 be

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\T1/ptm/m/n/10 passed to \T1/zi4/m/sl/10 R CMD INSTALL \T1/ptm/m/n/10 for a sou
rce pack-age in-stall. E.g.,
[1923]
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[]\T1/ptm/m/n/10 An al-ter-na-tive (and the cur-rent de-fault) is \T1/zi4/m/sl/
10 "both" \T1/ptm/m/n/10 which means `use bi-nary if avail-

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\T1/ptm/m/n/10 able and cur-rent, oth-er-wise try source'. The ac-tion if there
 are source pack-ages

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\T1/ptm/m/n/10 which are pre-ferred but may con-tain code which needs to be com
-piled is con-trolled by

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[][]\T1/zi4/m/sl/10 getOption[][][]("install.packages.compile.from.source")\T1/
ptm/m/n/10 . \T1/zi4/m/sl/10 type = "both" \T1/ptm/m/n/10 will be silently
[1924]
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[]\T1/ptm/m/n/10 Using pack-ages with \T1/zi4/m/sl/10 type = "source" \T1/ptm/m
/n/10 al-ways works pro-vided the pack-age con-tains no
[1925]
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[][][]\T1/zi4/m/sl/10 update.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10
 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 download.packages
[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 installed.packages[][][]\T1/ptm/m/n/
10 ,
[1926] [1927] [1928] [1929] [1930] [1931] [1932] [1933] [1934] [1935] [1936]
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[1948]
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[]\T1/ptm/m/n/10 for \T1/zi4/m/sl/10 asDateBuilt()\T1/ptm/m/n/10 , a [][]\T1/zi
4/m/sl/10 character[][][] \T1/ptm/m/n/10 string as from
[1949]
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[]\T1/ptm/m/n/10 If a `\T1/zi4/m/sl/10 DESCRIPTION\T1/ptm/m/n/10 ' file for the
 given pack-age is found and can suc-cess-fully be read,
[1950] [1951] [1952] [1953] [1954] [1955] [1956]
Underfull \hbox (badness 1248) in paragraph at lines 8977--8981
[]\T1/zi4/m/sl/10 R CMD build \T1/ptm/m/n/10 builds \T1/phv/m/n/10 R \T1/ptm/m/
n/10 source tar-balls. The name(s) of the pack-ages are taken from the
[1957]
Underfull \hbox (badness 1789) in paragraph at lines 9055--9057
[]\T1/ptm/m/n/10 See `Writ-ing R Ex-ten-sions' and the `R for Win-dows FAQ' for
 more dis-cus-sion of the
[1958] [1959] [1960] [1961] [1962] [1963] [1964] [1965] [1966]
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[]\T1/ptm/m/n/10 The name \T1/zi4/m/sl/10 "clipboard" \T1/ptm/m/n/10 may also b
e used on Win-dows, in which case
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[][][]\T1/zi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 type.conve
rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for 
read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i
dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/zi4/m/sl/10 read.t
able[][][]\T1/ptm/m/n/10 ;
[1972] [1973] [1974] [1975] [1976] [1977] [1978] [1979]
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[][][]\T1/zi4/m/sl/10 scan[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 type.conve
rt[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 read.fwf[][][] \T1/ptm/m/n/10 for 
read-ing \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ixed \T1/ptm/m/it/10 w\T1/ptm/m/n/10 i
dth \T1/ptm/m/it/10 f\T1/ptm/m/n/10 ormatted in-put; [][]\T1/zi4/m/sl/10 write.
table[][][]\T1/ptm/m/n/10 ;
[1980]
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[]\T1/ptm/m/n/10 The `hive' con-tain-ing the key. The ab-bre-vi-a-tions are for


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\T1/zi4/m/sl/10 HKEY_LOCAL_MACHINE\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 HKEY_CLASSES
_ROOT\T1/ptm/m/n/10 . \T1/zi4/m/sl/10 HKEY_CURRENT_USER\T1/ptm/m/n/10 ,
[1981] [1982] [1983] [1984] [1985] [1986] [1987]
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[]\T1/ptm/m/n/10 Wikipedia con-trib-u-tors (2006). Ro-man nu-mer-als. Wikipedia
, The Free En-cy-clo-pe-dia.

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[][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / w / index . php ? title
 = Roman _ numerals & oldid = 78252134$[][]\T1/ptm/m/n/10 . Ac-
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[]\T1/ptm/m/n/10 If `\T1/zi4/m/sl/10 --default-packages\T1/ptm/m/n/10 ' is not 
used, then \T1/zi4/m/sl/10 Rscript \T1/ptm/m/n/10 checks the en-vi-ron-ment var
i-able

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 []\T1/zi4/m/n/9 Rscript --default-packages=methods,datasets,utils,grDevices,gr
aphics,stats -e \TS1/zi4/m/n/9 '\T1/zi4/m/n/9 sessionInfo()\TS1/zi4/m/n/9 '[] 
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[][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Ctags$[][]\T1/
ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 https : / / www . gnu . org / software / emac
s / manual /
[1997] [1998] [1999]
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[]\T1/ptm/m/n/10 The de-fault for \T1/zi4/m/sl/10 stylepath \T1/ptm/m/n/10 is n
ow taken from the en-vi-ron-ment vari-able
[2000]
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[]\T1/ptm/m/n/10 If you wish to over-ride this de-fault be-hav-ior en-tirely, y
ou can add a
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[]\T1/ptm/m/n/10 Before each code chunk is eval-u-ated, zero or more hook func-
tions can be ex-e-cuted. If
[2003]
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[]\T1/ptm/m/n/10 The file `\T1/zi4/m/sl/10 Rconsole\T1/ptm/m/n/10 ' con-fig-ure
s the R GUI (\T1/zi4/m/sl/10 Rgui\T1/ptm/m/n/10 ) con-sole un-der MS Win-dows a
nd

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\T1/ptm/m/n/10 (strip-ping any trail-ing slash), oth-er-wise to the Win-dows `p
er-sonal' di-rec-tory, oth-er-wise to
[2004] [2005] [2006] [2007] [2008] [2009]
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[]\T1/ptm/m/n/10 A Bio-con-duc-tor mir-ror can be se-lected by set-ting [][]\T1
/zi4/m/sl/10 options[][][]("BioC_mirror")\T1/ptm/m/n/10 , e.g. via

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[]\T1/ptm/m/n/10 Repository `\T1/zi4/m/sl/10 CRAN\T1/ptm/m/n/10 ' is treated sp
e-cially: the value is taken from the cur-rent set-ting of
[2010] [2011] [2012]
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[]\T1/ptm/m/n/10 Convert file paths to the short form. This is an in-ter-face t
o the Win-dows API call
[2013] [2014] [2015] [2016] [2017]
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[]\T1/ptm/m/n/10 logical; if \T1/zi4/m/sl/10 TRUE \T1/ptm/m/n/10 (de-fault), []
[]\T1/zi4/m/sl/10 deparse[][][](control = <S>) \T1/ptm/m/n/10 will not have

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[]\T1/ptm/m/n/10 the page width to be used. The de-fault is the cur-rently ac-t
ive
[2018]
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[2020] [2021] [2022] [2023]
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[]\T1/ptm/m/n/10 If \T1/zi4/m/sl/10 syntax = NULL \T1/ptm/m/n/10 (the de-fault)
 then the avail-able syn-tax ob-jects are con-sulted in turn,

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\T1/ptm/m/n/10 and se-lected if their \T1/zi4/m/sl/10 extension \T1/ptm/m/n/10 
com-po-nent matches (as a reg-exp) the file name. Ob-
[2024] [2025] [2026] [2027]
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[]\T1/ptm/m/n/10 When ar-gu-ment \T1/zi4/m/sl/10 tar \T1/ptm/m/n/10 is set to t
he com-mand \T1/zi4/m/sl/10 tar \T1/ptm/m/n/10 on ma-cOS, en-vi-ron-ment vari-a
ble

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[][][]$\T1/zi4/m/sl/10 https : / / en . wikipedia . org / wiki / Tar _ (file _ 
format)$[][]\T1/ptm/m/n/10 , [][]$\T1/zi4/m/sl/10 http : / / pubs . opengroup .
 org /

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\T1/zi4/m/sl/10 onlinepubs / 9699919799 / utilities / pax . html # tag _ 20 _ 9
2 _ 13 _ 06$[][] \T1/ptm/m/n/10 for the way the POSIX
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[]\T1/ptm/m/n/10 Arguments such as \T1/zi4/m/sl/10 destdir \T1/ptm/m/n/10 and \
T1/zi4/m/sl/10 dependencies \T1/ptm/m/n/10 to be passed to

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[][]\T1/zi4/m/sl/10 install.packages[][][] \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 i
gnore_repo_cache\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 max_repo_cache_age \T1/ptm/m/n
/10 and
[2037]
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[]\T1/ptm/m/n/10 character, in-di-cat-ing the type of pack-age to down-load and
 in-stall. See

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[][][]\T1/zi4/m/sl/10 install.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/1
0 available.packages[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 download.package
s[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 installed.packages[][][]\T1/ptm/m/n
/10 ,
[2038] [2039] [2040] [2041] [2042] [2043] [2044] [2045] [2046] [2047] [2048]
[2049]
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[]\T1/ptm/m/n/10 To write a Unix-style file on Win-dows, use a bi-nary con-nec-
tion e.g. \T1/zi4/m/sl/10 file =
[2050] [2051] [2052]) [2053] [2054] (KernSmooth-pkg.tex
Chapter 15.
[2055] [2056] [2057] [2058] [2059] [2060] [2061] [2062] [2063] [2064])
(MASS-pkg.tex
Chapter 16.
[2065] [2066] [2067] [2068] [2069] [2070] [2071] [2072] [2073] [2074] [2075]
[2076] [2077] [2078] [2079] [2080] [2081] [2082] [2083] [2084] [2085] [2086]
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[]\T1/ptm/m/n/10 further ar-gu-ments for \T1/zi4/m/sl/10 plot \T1/ptm/m/n/10 an
d graph-i-cal pa-ram-e-ters. Note that
[2102] [2103] [2104]
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\T1/zi4/m/sl/10 "geometric"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "log-normal"\T1/ptm
/m/n/10 , \T1/zi4/m/sl/10 "lognormal"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "logistic
"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "negative
[2105] [2106]
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[]\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i-
na-tor ex-ceeds
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[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
rm \T1/zi4/m/sl/10 response ~
[2132]
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[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
rm \T1/zi4/m/sl/10 response ~
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[2144] [2145] [2146] [2147] [2148] [2149]pdfTeX warning (ext4): destination wit
h the same identifier (name{Rfn.npk}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.6111 ...sical N, P, K Factorial Experiment}{npk}
                                                  pdfTeX warning (ext4): destin
ation with the same identifier (name{Rfn.npk.1}) has been already used, duplica
te ignored
<to be read again> 
                   \relax 
l.6111 ...sical N, P, K Factorial Experiment}{npk}
                                                   [2150] [2151] [2152]
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[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
rm \T1/zi4/m/sl/10 response ~
[2163]
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[]\T1/ptm/m/n/10 The log-log and com-ple-men-tary log-log links are the in-crea
s-ing func-tions $\OML/cmm/m/it/10 F[]\OT1/cmr/m/n/10 (\OML/cmm/m/it/10 p\OT1/c
mr/m/n/10 ) =
[2164] [2165] [2166]
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\T1/ptm/m/n/10 only the first \T1/zi4/m/sl/10 dimen \T1/ptm/m/n/10 dis-crim-i-n
ant com-po-nents are used (ex-cept for
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[]\T1/ptm/m/n/10 An early ter-mi-na-tion cri-te-rion. If any par-tial de-nom-i-
na-tor ex-ceeds
[2176] [2177] [2178] [2179] [2180] [2181] [2182] [2183] [2184] [2185] [2186]
[2187] [2188] [2189] [2190] [2191] [2192] [2193] [2194] [2195] [2196] [2197]
[2198] [2199] [2200] [2201] [2202] [2203] [2204] [2205] [2206] [2207] [2208]
[2209] [2210] [2211] [2212]) (Matrix-pkg.tex
Chapter 17.

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[]\T1/ptm/m/n/10 Note that the cur-rent im-ple-men-ta-tion de-tails are sub-jec
t to change, and if you

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\T1/ptm/m/n/10 con-sider work-ing with these classes, please con-tact the pack-
age main-tain-ers
[2213]
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[]\T1/ptm/m/n/10 This is cur-rently ex-per-i-men-tal and not yet used for our o
wn code. Please con-tact us
[2214] [2215] [2216] [2217]
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[]\T1/ptm/m/n/10 logical; if true the re-sult will be sym-met-ric (in-her-it-in
g from class
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[]\T1/ptm/m/n/10 The value of \T1/zi4/m/sl/10 bdiag() \T1/ptm/m/n/10 in-heris f
rom class [][]\T1/zi4/m/sl/10 CsparseMatrix[][][]\T1/ptm/m/n/10 , whereas \T1/z
i4/m/sl/10 .bdiag() \T1/ptm/m/n/10 re-turns a
[2220] [2221] [2222] [2223] [2224]
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[]\T1/zi4/m/sl/10 signature(from = "CHMfactor",to = "sparseMatrix") \T1/ptm/m/n
/10 (or equiv-a-lently, \T1/zi4/m/sl/10 to =
[2225] [2226]pdfTeX warning (ext4): destination with the same identifier (name{
Rfn.chol}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1134 ...- 'Matrix' S4 Generic and Methods}{chol}
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ation with the same identifier (name{Rfn.chol.1}) has been already used, duplic
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<to be read again> 
                   \relax 
l.1134 ...- 'Matrix' S4 Generic and Methods}{chol}
                                                  
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\T1/ptm/m/n/10 sider [][]\T1/zi4/m/sl/10 Cholesky[][][]() \T1/ptm/m/n/10 in suc
h sit-u-a-tions, since \T1/zi4/m/sl/10 chol(x,pivot=TRUE) \T1/ptm/m/n/10 uses t
he same al-go-rithm
[2227pdfTeX warning (ext4): destination with the same identifier (name{Rfn.chol
,dsCMatrix.Rdash.method}) has been already used, duplicate ignored

\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.1209 \item[chol]
                   \code{signature(x = "dgeMatrix")}: works viapdfTeX warning (
ext4): destination with the same identifier (name{Rfn.chol,lsCMatrix.Rdash.meth
od}) has been already used, duplicate ignored

\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.1209 \item[chol]
                   \code{signature(x = "dgeMatrix")}: works viapdfTeX warning (
ext4): destination with the same identifier (name{Rfn.chol,nsCMatrix.Rdash.meth
od}) has been already used, duplicate ignored

\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
                                                  \fi \fi 
l.1209 \item[chol]
                   \code{signature(x = "dgeMatrix")}: works via] [2228]
[2229]
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[]\T1/ptm/m/n/10 This is a generic func-tion with spe-cial meth-ods for dif-fer
-ent types of ma-tri-ces. Use
[2230] [2231]
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[]\T1/ptm/m/n/10 Class \T1/zi4/m/sl/10 "MatrixFactorization" \T1/ptm/m/n/10 and
 \T1/zi4/m/sl/10 "dtrMatrix"\T1/ptm/m/n/10 , di-rectly. Class \T1/zi4/m/sl/10 "
dgeMatrix"\T1/ptm/m/n/10 , by class

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[]\T1/ptm/m/n/10 Both these fac-tor-iza-tions can \T1/ptm/m/it/10 di-rectly \T1
/ptm/m/n/10 be treated as (tri-an-gu-lar) ma-tri-ces, as they ex-tend
[2232]pdfTeX warning (ext4): destination with the same identifier (name{Rfn.col
Sums}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.1623 ... Row and Column Sums and Means}{colSums}
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ation with the same identifier (name{Rfn.colSums.1}) has been already used, dup
licate ignored
<to be read again> 
                   \relax 
l.1623 ... Row and Column Sums and Means}{colSums}
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ation with the same identifier (name{Rfn.colMeans}) has been already used, dupl
icate ignored
<to be read again> 
                   \relax 
l.1624 \aliasA{colMeans}{colSums}{colMeans}
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ith the same identifier (name{Rfn.rowMeans}) has been already used, duplicate i
gnored
<to be read again> 
                   \relax 
l.1645 \aliasA{rowMeans}{colSums}{rowMeans}
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                   \relax 
l.1656 \aliasA{rowSums}{colSums}{rowSums}
                                          [2233] [2234] [2235]
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[]\T1/ptm/m/n/10 a num-ber $\OML/cmm/m/it/10 > \OT1/cmr/m/n/10 0$\T1/ptm/m/n/10
 , the es-ti-mated (1-norm) con-di-tion num-ber $[]$; when
[2236] [2237] [2238] [2239] [2240]
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[]\T1/ptm/m/n/10 Objects can be cre-ated by calls of the form \T1/zi4/m/sl/10 n
ew("dgCMatrix",...)\T1/ptm/m/n/10 , more typ-i-cally via
[2241] [2242] [2243] [2244]
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[]\T1/ptm/m/n/10 However this means that a ma-trix typ-i-cally can tbe stored i
n more than one pos-si-ble
[2245] [2246]
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[]\T1/zi4/m/sl/10 Diagonal() \T1/ptm/m/n/10 re-turns an ob-ject of class [][]\T
1/zi4/m/sl/10 ddiMatrix[][][] \T1/ptm/m/n/10 or [][]\T1/zi4/m/sl/10 ldiMatrix[]
[][] \T1/ptm/m/n/10 (with ``su-per-class''
[2247]
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[]\T1/zi4/m/sl/10 signature(x = "diagonalMatrix")\T1/ptm/m/n/10 : all these gro
up meth-ods re-turn a
[2248] [2249] [2250]
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[]\T1/zi4/m/sl/10 signature(x = "dMatrix",digits = "numeric")\T1/ptm/m/n/10 : t
his group con-tains [][]\T1/zi4/m/sl/10 round[][][]() \T1/ptm/m/n/10 and

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[][][]\T1/zi4/m/sl/10 drop0[][][](x,tol=1e-10) \T1/ptm/m/n/10 is some-times pre
fer-able to (and more ef-fi-cient than)
[2251] [2252]
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[]\T1/ptm/m/n/10 a Ma-trix like \T1/zi4/m/sl/10 x \T1/ptm/m/n/10 but with no ex
-plicit ze-ros, i.e., \T1/zi4/m/sl/10 !any(x@x == 0)\T1/ptm/m/n/10 , al-ways in
-her-it-ing from
[2253] [2254] [2255] [2256] [2257]
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[]\T1/zi4/m/sl/10 signature(x = "dspMatrix",type = "character")\T1/ptm/m/n/10 ,
 or \T1/zi4/m/sl/10 x = "dsyMatrix" \T1/ptm/m/n/10 or \T1/zi4/m/sl/10 type =

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[]\T1/zi4/m/sl/10 signature(x = "dspMatrix",type = "character")\T1/ptm/m/n/10 ,
 or \T1/zi4/m/sl/10 x = "dsyMatrix" \T1/ptm/m/n/10 or \T1/zi4/m/sl/10 type =
[2258] [2259]
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[]\T1/ptm/m/n/10 Class \T1/zi4/m/sl/10 "dgCMatrix"\T1/ptm/m/n/10 , di-rectly. C
lass \T1/zi4/m/sl/10 "triangularMatrix"\T1/ptm/m/n/10 , di-rectly. Class \T1/zi
4/m/sl/10 "dMatrix"\T1/ptm/m/n/10 ,
[2260] [2261]
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[]\T1/zi4/m/sl/10 signature(x = "dtpMatrix",logarithm = "logical")\T1/ptm/m/n/1
0 : the [][]\T1/zi4/m/sl/10 determinant[][][](x)
[2262] [2263] [2264] [2265] [2266] [2267]
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 [] \T1/zi4/m/n/9 readHB(gzcon(url("http://www.cise.ufl.edu/research/sparse/RB/
Boeing/msc00726.tar.gz"))))[] 

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 [] \T1/zi4/m/n/9 readMM(gzcon(url("ftp://math.nist.gov/pub/MatrixMarket2/Harwe
ll-Boeing/counterx/jgl009.mtx.gz"))))[] 
[2268] [2269]
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[]\T1/ptm/m/n/10 a string spec-i-fy-ing how the \T1/zi4/m/sl/10 zero.print \T1/
ptm/m/n/10 codes should be aligned, see
[2270] [2271] [2272] [2273] [2274]
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[]\T1/ptm/m/n/10 color for the bor-der of each rect-an-gle. \T1/zi4/m/sl/10 NA 
\T1/ptm/m/n/10 means no bor-der is drawn.

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\T1/ptm/m/n/10 When \T1/zi4/m/sl/10 NULL \T1/ptm/m/n/10 as by de-fault, \T1/zi4
/m/sl/10 border.col <-if(lwd < .01) NA else NULL \T1/ptm/m/n/10 is

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[]\T1/ptm/m/n/10 All meth-ods cur-rently end up call-ing the method for the [][
]\T1/zi4/m/sl/10 dgTMatrix[][][] \T1/ptm/m/n/10 class. Use
[2275]
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 []\T1/zi4/m/n/9 image(USCounties, c(1,100), c(1,100), useAbs=FALSE, lwd=3, bor
der.col = adjustcolor("skyblue", 1/2))[] 
[2276]
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[]\T1/ptm/m/n/10 While ``row-indexing'' (of more than one row \T1/ptm/m/it/10 o
r \T1/ptm/m/n/10 us-ing \T1/zi4/m/sl/10 drop=FALSE\T1/ptm/m/n/10 ) stays within
 the

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[]\T1/zi4/m/sl/10 signature(x = "matrix",y = "indMatrix") \T1/ptm/m/n/10 and ot
her sig-na-tures (use
[2277]
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[]\T1/zi4/m/sl/10 signature(from = "numeric",to = "indMatrix")\T1/ptm/m/n/10 : 
a user con-ve-nience, to al-low

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[]\T1/zi4/m/sl/10 signature(from = "indMatrix",to = "matrix")\T1/ptm/m/n/10 : c
o-er-cion to a tra-di-tional
[2278] [2279] [2280] [2281] [2282]
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[]\T1/zi4/m/sl/10 isTriangular(M) \T1/ptm/m/n/10 re-turns a [][]\T1/zi4/m/sl/10
 logical[][][] \T1/ptm/m/n/10 in-di-cat-ing if \T1/zi4/m/sl/10 M \T1/ptm/m/n/10
 is a tri-an-gu-lar ma-trix. Anal-o-gously,
[2283] [2284] [2285] [2286]
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[]\T1/zi4/m/sl/10 signature(x = "ndenseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally
 equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2287]
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[]\T1/ptm/m/n/10 Class \T1/zi4/m/sl/10 "ldenseMatrix"\T1/ptm/m/n/10 , di-rectly
. Class \T1/zi4/m/sl/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/zi4/m/sl/10 "lde
nseMatrix"\T1/ptm/m/n/10 . Class
[2288]
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[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/zi4/m/sl/10 t[][][]() \T1/ptm/m/n/10
 and co-er-cion meth-ods (for [][]\T1/zi4/m/sl/10 as[][][](.)\T1/ptm/m/n/10 ); 
use, e.g.,
[2289]
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[]\T1/zi4/m/sl/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-call
y equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2290]
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[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/zi4/m/sl/10 t[][][]() \T1/ptm/m/n/10
 and co-er-cion meth-ods (for [][]\T1/zi4/m/sl/10 as[][][](.)\T1/ptm/m/n/10 ; u
se, e.g.,
[2291]
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[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/zi4/m/sl/10 t[][][]() \T1/ptm/m/n/10
 and co-er-cion meth-ods (for [][]\T1/zi4/m/sl/10 as[][][](.)\T1/ptm/m/n/10 ; u
se, e.g.,
[2292]
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[]\T1/zi4/m/sl/10 lu() \T1/ptm/m/n/10 is a generic func-tion with spe-cial meth
-ods for dif-fer-ent types of ma-tri-ces. Use
[2293] [2294] [2295]
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[]\T1/ptm/m/n/10 Note that when the re-sult-ing ma-trix is di-ag-o-nal (``math-
e-mat-i-cally''),
[2296]
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[]\T1/ptm/m/n/10 Most of the time, the func-tion works via a tra-di-tional (\T1
/ptm/m/it/10 full\T1/ptm/m/n/10 ) [][]\T1/zi4/m/sl/10 matrix[][][]\T1/ptm/m/n/1
0 . How-ever,
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[]\T1/zi4/m/sl/10 signature(x = "Matrix")\T1/ptm/m/n/10 : sim-ply de-fined as \
T1/zi4/m/sl/10 prod(dim(x)) \T1/ptm/m/n/10 (and hence of mode

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[]\T1/zi4/m/sl/10 signature(object = "Matrix")\T1/ptm/m/n/10 : draws an [][]\T1
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                   \relax 
l.7044 ...*\%}{matrix-products}{.Rpcent.*.Rpcent.}
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l.7152 ...A{crossprod}{matrix-products}{crossprod}
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\AtBegShi@Output ...ipout \box \AtBeginShipoutBox 
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[]\T1/zi4/m/sl/10 signature(x = "dtrMatrix",y = "matrix") \T1/ptm/m/n/10 and ot
her sig-na-tures (use

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\T1/zi4/m/sl/10 showMethods("%*%",class="dtrMatrix")\T1/ptm/m/n/10 ): ma-trix m
ul-ti-pli-ca-tion. Mul-ti-pli-ca-tion of

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[]\T1/zi4/m/sl/10 signature(x = "CsparseMatrix",y = "missing") \T1/ptm/m/n/10 r
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[]\T1/zi4/m/sl/10 signature(x = "TsparseMatrix",y = "missing") \T1/ptm/m/n/10 r
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[]\T1/zi4/m/sl/10 signature(x = "dtrMatrix",y = "matrix") \T1/ptm/m/n/10 and ot
her sig-na-tures, see
[2301] [2302]
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[]\T1/ptm/m/n/10 classes in-her-it-ing from \T1/zi4/m/sl/10 "MatrixFactorizatio
n"\T1/ptm/m/n/10 , such as [][]\T1/zi4/m/sl/10 LU[][][]\T1/ptm/m/n/10 , [][]\T1
/zi4/m/sl/10 Cholesky[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 CHMfactor[][][]
\T1/ptm/m/n/10 , and
[2303]
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[]\T1/zi4/m/sl/10 signature(x = "ndenseMatrix")\T1/ptm/m/n/10 , se-man-ti-cally
 equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2304]
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[]\T1/ptm/m/n/10 logical in-di-cat-ing if \T1/zi4/m/sl/10 X <-(X + t(X))/2 \T1/
ptm/m/n/10 should be done, af-ter \T1/zi4/m/sl/10 X
[2305] [2306]
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[]\T1/ptm/m/n/10 Class \T1/zi4/m/sl/10 "ndenseMatrix"\T1/ptm/m/n/10 , di-rectly
. Class \T1/zi4/m/sl/10 "lMatrix"\T1/ptm/m/n/10 , by class \T1/zi4/m/sl/10 "nde
nseMatrix"\T1/ptm/m/n/10 . Class

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[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/zi4/m/sl/10 t[][][]() \T1/ptm/m/n/10
 and co-er-cion meth-ods (for [][]\T1/zi4/m/sl/10 as[][][](.)\T1/ptm/m/n/10 ); 
use, e.g.,
[2308] [2309]
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[]\T1/ptm/m/n/10 fast sim-ple meth-ods
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l.8154 \HeaderA{norm}{Matrix Norms}{norm}
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l.8154 \HeaderA{norm}{Matrix Norms}{norm}
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[]\T1/zi4/m/sl/10 signature(x = "lsparseMatrix")\T1/ptm/m/n/10 , se-man-ti-call
y equiv-a-lent to \T1/ptm/b/n/10 base \T1/ptm/m/n/10 func-tion
[2313]
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[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/zi4/m/sl/10 t[][][]() \T1/ptm/m/n/10
 and co-er-cion meth-ods (for [][]\T1/zi4/m/sl/10 as[][][](.)\T1/ptm/m/n/10 ; u
se, e.g.,
[2314]
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[]\T1/ptm/m/n/10 Currently, mainly [][]\T1/zi4/m/sl/10 t[][][]() \T1/ptm/m/n/10
 and co-er-cion meth-ods (for [][]\T1/zi4/m/sl/10 as[][][](.)\T1/ptm/m/n/10 ; u
se, e.g.,
[2315]
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[]\T1/zi4/m/sl/10 signature(x = "matrix",y = "pMatrix") \T1/ptm/m/n/10 and othe
r sig-na-tures (use

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[]\T1/zi4/m/sl/10 signature(from = "numeric",to = "pMatrix")\T1/ptm/m/n/10 : a 
user con-ve-nience, to al-low
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l.8956 \aliasA{qr}{qr-methods}{qr}
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l.9252 ... the Reciprocal Condition Number}{rcond}
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[2328]
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[]\T1/ptm/m/n/10 The al-go-rithm first sam-ples ``en-coded'' $\OT1/cmr/m/n/10 (
\OML/cmm/m/it/10 i; j\OT1/cmr/m/n/10 )$\T1/ptm/m/n/10 s with-out re-place-ment,
 via one di-men-sional

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\T1/ptm/m/n/10 in-dices, if not \T1/zi4/m/sl/10 symmetric [][]sample.int[][][](
nrow*ncol,nnz)\T1/ptm/m/n/10 , then---if \T1/zi4/m/sl/10 rand.x \T1/ptm/m/n/10 
is not \T1/zi4/m/sl/10 NULL\T1/ptm/m/n/10 ---

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\T1/ptm/m/n/10 gets \T1/zi4/m/sl/10 x <-rand.x(nnz) \T1/ptm/m/n/10 and calls []
[]\T1/zi4/m/sl/10 sparseMatrix[][][](i=i,j=j,x=x,..)\T1/ptm/m/n/10 . When \T1/z
i4/m/sl/10 rand.x=NULL\T1/ptm/m/n/10 ,
[2329] [2330] [2331] [2332]pdfTeX warning (ext4): destination with the same ide
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                                            [2333]
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[]\T1/ptm/m/n/10 with ex-tra ar-gu-ment list \T1/zi4/m/sl/10 ( sparse =
[2334]
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[]\T1/ptm/m/n/10 , and sim-i-lar \T1/zi4/m/sl/10 b\T1/ptm/m/n/10 , in-clud-ing 
\T1/zi4/m/sl/10 "missing"\T1/ptm/m/n/10 , and

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[]\T1/ptm/m/n/10 Construct a sparse model or ``de-sign'' ma-trix, form a for-mu
la and data frame
[2335]
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[]\T1/ptm/m/n/10 character string or \T1/zi4/m/sl/10 NULL \T1/ptm/m/n/10 or (co
-er-ca-ble to)

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[]\T1/ptm/m/n/10 should fac-tors have un-used lev-els dropped? The de-fault for

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[]\T1/zi4/m/sl/10 signature(from = "factor",to = "sparseMatrix")\T1/ptm/m/n/10 
: Co-er-cion of a fac-tor to

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\T1/zi4/m/sl/10 "sparseMatrix" \T1/ptm/m/n/10 pro-duces the ma-trix of in-di-ca
-tor \T1/ptm/b/n/10 rows \T1/ptm/m/n/10 stored as an ob-ject of class
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                                            [2345] [2346]
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[]\T1/ptm/m/n/10 vector of the non zero en-tries; may be miss-ing in which case
 a
[2347] [2348]
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[]\T1/zi4/m/sl/10 signature(x = "sparseVector") \T1/ptm/m/n/10 re-peat \T1/zi4/
m/sl/10 x\T1/ptm/m/n/10 , with the same ar-gu-ment list
[2349]
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[2351] [2352]
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[]\T1/ptm/m/n/10 The va-lid-ity checks do not re-quire a sym-met-ric \T1/zi4/m/
sl/10 Dimnames \T1/ptm/m/n/10 slot, so it can be
[2353]
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[]\T1/ptm/m/n/10 These are generic func-tions with sev-eral meth-ods for dif-fe
r-ent ma-trix classes, use e.g.,
[2354] [2355]
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[]\T1/ptm/m/n/10 For con-ve-nience, meth-ods for some op-er-a-tions such as \T1
/zi4/m/sl/10 %*% \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 crossprod \T1/ptm/m/n/10 ar
e de-fined
[2356]
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[]\T1/ptm/m/n/10 Note that \T1/zi4/m/sl/10 new(.)\T1/ptm/m/n/10 , [][]\T1/zi4/m
/sl/10 spMatrix[][][] \T1/ptm/m/n/10 or [][]\T1/zi4/m/sl/10 sparseMatrix[][][] 
\T1/ptm/m/n/10 con-struc-tors for \T1/zi4/m/sl/10 "dgTMatrix" \T1/ptm/m/n/10 (a
nd other
[2357] [2358] [2359] [2360] [2361] [2362]
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[]\T1/ptm/m/n/10 is cur-rently a sim-ple fall-back
[2363] [2364] [2365]) (boot-pkg.tex [2366]
Chapter 18.
[2367] [2368] [2369] [2370] [2371] [2372] [2373] [2374] [2375] [2376]
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[]\T1/ptm/m/n/10 Where random-number gen-er-a-tion is done in the worker pro-ce
sses, the de-fault be-haviour
[2377]
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[]\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi
-cient boot-strap sim-u-la-tion.
[2378]
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[2380]
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[]\T1/ptm/m/n/10 A vec-tor of char-ac-ter strings rep-re-sent-ing the type of i
n-ter-

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\T1/ptm/m/n/10 vals re-quired. The value should be any sub-set of the val-ues

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\T1/zi4/m/sl/10 c("norm","basic","stud","perc","bca") \T1/ptm/m/n/10 or sim-ply
 \T1/zi4/m/sl/10 "all" \T1/ptm/m/n/10 which will
[2381]
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[]\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est. The de-fa
ult value is
[2382] [2383] [2384] [2385]
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[]\T1/ptm/m/n/10 Rawlings, J.O. (1988) \T1/ptm/m/it/10 Ap-plied Re-gres-sion An
al-y-sis\T1/ptm/m/n/10 . Wadsworth and Brooks/Cole Statis-
[2386] [2387] [2388] [2389] [2390] [2391]
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[]\T1/ptm/m/n/10 The sim-u-la-tion type. Pos-si-ble types are \T1/zi4/m/sl/10 "
ordinary" \T1/ptm/m/n/10 (case re-sam-pling),
[2392] [2393]
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[]\T1/ptm/m/n/10 The length of time (in months) that the res-i-dent spent at Ch
an-ning House.
[2395] [2396] [2397] [2398]
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[]\T1/ptm/m/n/10 The ob-served value of the statis-tic of in-ter-est on the ori
g-i-nal data set
[2399]
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[]\T1/ptm/m/n/10 Davison, A.C., Hink-ley, D.V. and Schecht-man, E. (1986) Ef-fi
-cient boot-strap sim-u-la-tion.
[2400] [2401]
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[]\T1/ptm/m/n/10 The un-bi-ased es-ti-ma-tor uses a mul-ti-plier of \T1/zi4/m/s
l/10 n/((n-1)*(n-2)) \T1/ptm/m/n/10 where \T1/zi4/m/sl/10 n \T1/ptm/m/n/10 is t
he sam-ple

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\T1/ptm/m/n/10 size, if \T1/zi4/m/sl/10 unbiased \T1/ptm/m/n/10 is \T1/zi4/m/sl
/10 FALSE \T1/ptm/m/n/10 then a mul-ti-plier of \T1/zi4/m/sl/10 1/n \T1/ptm/m/n
/10 is used. This is mul-ti-plied by
[2402] [2403] [2404] [2405] [2406] [2407] [2408] [2409] [2410] [2411] [2412]
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[2424]
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[]\T1/ptm/m/n/10 The quan-tiles at which the plots are re-quired. The de-fault 
is
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[]\T1/ptm/m/n/10 The in-dex of the statis-tic of in-ter-est within the out-put 
of a call to
[2436] [2437] [2438] [2439]
Underfull \hbox (badness 2293) in paragraph at lines 5235--5238
[]\T1/ptm/m/n/10 An in-te-ger giv-ing the num-ber of classes to be used in the 
boot-strap

Underfull \hbox (badness 1668) in paragraph at lines 5235--5238
\T1/ptm/m/n/10 his-togram. The de-fault is the in-te-ger be-tween 10 and 100 cl
os-est to
[2440] [2441] [2442] [2443] [2444] [2445] [2446] [2447] [2448] [2449] [2450]
Underfull \hbox (badness 4954) in paragraph at lines 6018--6021
[]\T1/ptm/m/n/10 The re-turned value is an ob-ject of class \T1/zi4/m/sl/10 "sa
ddle.distn"\T1/ptm/m/n/10 . See the help file for
[2451] [2452] [2453] [2454] [2455] [2456] [2457] [2458] [2459]
Underfull \hbox (badness 1596) in paragraph at lines 6739--6743
[]\T1/ptm/m/n/10 A char-ac-ter string in-di-cat-ing the type of sec-ond ar-gu-m
ent ex-pected by
[2460] [2461] [2462] [2463] [2464] [2465] [2466] [2467] [2468] [2469])
(class-pkg.tex [2470]
Chapter 19.
[2471] [2472] [2473] [2474] [2475] [2476] [2477] [2478] [2479] [2480] [2481]
[2482] [2483] [2484] [2485] [2486]) (cluster-pkg.tex
Chapter 20.
[2487] [2488] [2489] [2490] [2491]
Underfull \vbox (badness 7777) has occurred while \output is active [2492]
[2493] [2494] [2495] [2496]
Underfull \hbox (badness 4144) in paragraph at lines 688--691
[]\T1/ptm/m/n/10 Setting this to \T1/zi4/m/sl/10 FALSE \T1/ptm/m/n/10 saves mem
-ory (and hence time), but dis-ables
[2497]
Underfull \hbox (badness 1412) in paragraph at lines 771--776
[]\T1/ptm/m/n/10 Kaufman and Rousseeuw (see [][]\T1/zi4/m/sl/10 agnes[][][]\T1/
ptm/m/n/10 ), orig-i-nally. Met-ric \T1/zi4/m/sl/10 "jaccard"\T1/ptm/m/n/10 : K
amil Ko-zlowski
[2498] [2499]
Underfull \hbox (badness 10000) in paragraph at lines 864--866
[]\T1/ptm/m/n/10 list with sil-hou-ette width in-for-ma-tion for the best sam-p
le, see
[2500] [2501]
Underfull \hbox (badness 10000) in paragraph at lines 975--977
[]\T1/ptm/m/n/10 simply cor-re-sponds to the global max-i-mum, i.e., is

Underfull \hbox (badness 1342) in paragraph at lines 989--993
[]\T1/ptm/m/n/10 This, the de-fault, has been pro-posed by Mar-tin Maech-ler in
 2012,
[2502] [2503] [2504]
Underfull \hbox (badness 6110) in paragraph at lines 1190--1194
[]\T1/ptm/m/n/10 when \T1/zi4/m/sl/10 x \T1/ptm/m/n/10 does not have a \T1/zi4/
m/sl/10 diss \T1/ptm/m/n/10 nor a \T1/zi4/m/sl/10 data \T1/ptm/m/n/10 com-po-ne
nt, e.g., for
[2505] [2506] [2507]
Underfull \hbox (badness 10000) in paragraph at lines 1459--1462

[2508] [2509]
Underfull \hbox (badness 2503) in paragraph at lines 1571--1574
[]\T1/ptm/m/n/10 an ob-ject of class \T1/zi4/m/sl/10 "hclust" \T1/ptm/m/n/10 or
 \T1/zi4/m/sl/10 "twins"\T1/ptm/m/n/10 , i.e., typ-i-cally the re-sult of
[2510] [2511] [2512] [2513] [2514] [2515] [2516] [2517]
Underfull \hbox (badness 10000) in paragraph at lines 2162--2165


Underfull \hbox (badness 10000) in paragraph at lines 2176--2182
[][][]\T1/zi4/m/sl/10 predict.ellipsoid[][][] \T1/ptm/m/n/10 which is also the 
[][]\T1/zi4/m/sl/10 predict[][][] \T1/ptm/m/n/10 method for \T1/zi4/m/sl/10 ell
ipsoid \T1/ptm/m/n/10 ob-jects.
[2518] [2519] [2520] [2521]
Underfull \hbox (badness 6675) in paragraph at lines 2411--2413
[]\T1/ptm/m/n/10 list with sil-hou-ette in-for-ma-tion of the near-est crisp cl
us-ter-ing, see
[2522] [2523] [2524] [2525] [2526] [2527] [2528]
Underfull \hbox (badness 2980) in paragraph at lines 2902--2906
[][][]\T1/zi4/m/sl/10 agnes[][][] \T1/ptm/m/n/10 for back-ground and ref-er-enc
es; [][]\T1/zi4/m/sl/10 pam.object[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 cl
ara[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 daisy[][][]\T1/ptm/m/n/10 , [][]\
T1/zi4/m/sl/10 partition.object[][][]\T1/ptm/m/n/10 ,
[2529] [2530] [2531] [2532] [2533]
Underfull \hbox (badness 1142) in paragraph at lines 3243--3246
[]\T1/ptm/m/n/10 graphical pa-ram-e-ters (see [][]\T1/zi4/m/sl/10 par[][][]\T1/
ptm/m/n/10 ) may also be sup-plied and are passed to
[2534] [2535]
Underfull \hbox (badness 1142) in paragraph at lines 3362--3365
[]\T1/ptm/m/n/10 graphical pa-ram-e-ters (see [][]\T1/zi4/m/sl/10 par[][][]\T1/
ptm/m/n/10 ) may also be sup-plied and are passed to
[2536] [2537] [2538] [2539]
Underfull \hbox (badness 2582) in paragraph at lines 3585--3590
[][][]\T1/zi4/m/sl/10 partition.object[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/1
0 clusplot.partition[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 clusplot.default
[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 pam[][][]\T1/ptm/m/n/10 , [][]\T1/zi
4/m/sl/10 pam.object[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 clara[][][]\T1/p
tm/m/n/10 ,
[2540]
Underfull \hbox (badness 3209) in paragraph at lines 3647--3652
[]\T1/ptm/m/n/10 Note that cur-rently the method func-tion sim-ply calls \T1/zi
4/m/sl/10 plot([][]as.hclust[][][](x),...)\T1/ptm/m/n/10 , which

Underfull \hbox (badness 8019) in paragraph at lines 3647--3652
\T1/ptm/m/n/10 dis-patches to [][]\T1/zi4/m/sl/10 plot.hclust[][][](..)\T1/ptm/
m/n/10 . If more flex-i-ble plots are needed, con-sider \T1/zi4/m/sl/10 xx
[2541] [2542] [2543] [2544]
Underfull \hbox (badness 10000) in paragraph at lines 3939--3941
[]\T1/ptm/m/n/10 a \T1/zi4/m/sl/10 dissimilarity \T1/ptm/m/n/10 ob-ject or a \T
1/zi4/m/sl/10 summary.dissimilarity \T1/ptm/m/n/10 one for
[2545] [2546] [2547] [2548]
Underfull \hbox (badness 2626) in paragraph at lines 4163--4168
[]\T1/ptm/m/n/10 arguments passed [][]\T1/zi4/m/sl/10 barplot[][][]()\T1/ptm/m/
n/10 ; note that the de-fault used to be \T1/zi4/m/sl/10 col =
[2549]
Underfull \hbox (badness 1383) in paragraph at lines 4241--4246
[]\T1/ptm/m/n/10 While \T1/zi4/m/sl/10 silhouette() \T1/ptm/m/n/10 is \T1/ptm/m
/it/10 in-trin-sic \T1/ptm/m/n/10 to the [][]\T1/zi4/m/sl/10 partition[][][] \T
1/ptm/m/n/10 clus-ter-ings, and hence has a (triv-ial)
[2550] [2551] [2552] [2553] [2554] [2555] [2556]
Underfull \hbox (badness 10000) in paragraph at lines 4684--4686
[]\T1/ptm/m/n/10 Sample data set ac-com-pa-ny-ing the ref-er-ence be-low (file 
`\T1/zi4/m/sl/10 xclara.dat\T1/ptm/m/n/10 ' in side
[2557] [2558]) (codetools-pkg.tex
Chapter 21.
[2559] [2560] [2561] [2562] [2563]) (foreign-pkg.tex [2564]
Chapter 22.
[2565] [2566] [2567] [2568] [2569] [2570] [2571] [2572]
Underfull \hbox (badness 10000) in paragraph at lines 506--515
[]\T1/ptm/m/n/10 character: what to do with du-pli-cated value la-bels for dif-
fer-

Underfull \hbox (badness 10000) in paragraph at lines 506--515
\T1/ptm/m/n/10 ent lev-els. For \T1/zi4/m/sl/10 "append" \T1/ptm/m/n/10 (the de
-fault), the first orig-i-nal value

Underfull \hbox (badness 10000) in paragraph at lines 506--515
\T1/ptm/m/n/10 la-bel is kept while fur-ther du-pli-cated la-bels are re-named 
to
[2573]
Overfull \hbox (6.73795pt too wide) in paragraph at lines 625--625
 []\T1/zi4/m/n/9 ### Expect lots of warnings as value labels (corresponding to 
R factor labels) are uncomplete,[] 
[2574] [2575] [2576]
Underfull \hbox (badness 10000) in paragraph at lines 813--814

[2577] [2578] [2579] [2580] [2581] [2582] [2583]
Underfull \hbox (badness 10000) in paragraph at lines 1267--1273
[]\T1/ptm/m/n/10 The work for this func-tion is done by \T1/zi4/m/sl/10 foreign
:::writeForeignStata\T1/ptm/m/n/10 ,
[2584] [2585]) (lattice-pkg.tex [2586]
Chapter 23.
[2587] [2588] [2589] [2590] [2591] [2592] [2593] [2594] [2595] [2596] [2597]
[2598] [2599] [2600] [2601] [2602]
Underfull \hbox (badness 1062) in paragraph at lines 1398--1402
\T1/ptm/m/n/10 no-ta-tion for the x and y axes re-spec-tively. See doc-u-men-ta
-tion for
[2603]
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Underfull \hbox (badness 1803) in paragraph at lines 1566--1583
[][][]\T1/zi4/m/sl/10 Lattice[][][] \T1/ptm/m/n/10 for an overview of the pack-
age, as well as [][]\T1/zi4/m/sl/10 barchart.table[][][]\T1/ptm/m/n/10 , [][]\T
1/zi4/m/sl/10 print.trellis[][][]\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 1566--1583
[][]\T1/zi4/m/sl/10 panel.stripplot[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 p
anel.superpose[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 panel.loess[][][]\T1/p
tm/m/n/10 , [][]\T1/zi4/m/sl/10 panel.average[][][]\T1/ptm/m/n/10 , [][]\T1/zi4
/m/sl/10 strip.default[][][]\T1/ptm/m/n/10 ,
[2605] [2606] [2607]
Underfull \hbox (badness 3009) in paragraph at lines 1725--1727
[]\T1/ptm/m/n/10 additional ar-gu-ments passed to [][]\T1/zi4/m/sl/10 xyplot[][
][]\T1/ptm/m/n/10 , which may pass them on to

Underfull \hbox (badness 6808) in paragraph at lines 1755--1759
[]\T1/ptm/m/n/10 graphical ar-gu-ments, which are pro-cessed and even-tu-ally p
assed to
[2608] [2609] [2610] [2611] [2612]
Underfull \hbox (badness 10000) in paragraph at lines 2141--2144
[]\T1/ptm/m/n/10 When \T1/zi4/m/sl/10 breaks \T1/ptm/m/n/10 is un-spec-i-fied, 
the value of
[2613] [2614] [2615] [2616] [2617] [2618] [2619] [2620] [2621] [2622]
Underfull \hbox (badness 2781) in paragraph at lines 2848--2850
[]\T1/ptm/m/n/10 A color ramp spec-i-fi-ca-tion, as in the \T1/zi4/m/sl/10 col.
regions \T1/ptm/m/n/10 ar-gu-ment in
[2623]
Underfull \hbox (badness 2486) in paragraph at lines 2959--2963
[]\T1/ptm/m/n/10 Other use-ful ar-gu-ments are men-tioned in the help page for 
the de-fault panel func-tion
[2624] [2625] [2626] [2627] [2628] [2629] [2630]pdfTeX warning (ext4): destinat
ion with the same identifier (name{Rfn.parallel}) has been already used, duplic
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<to be read again> 
                   \relax 
l.3431 \aliasA{parallel}{B\_08\_splom}{parallel}
                                                 [2631] [2632] [2633] [2634]
[2635] [2636] [2637]
Underfull \hbox (badness 5696) in paragraph at lines 3922--3926
[]\T1/ptm/m/n/10 A pos-si-ble use of this ar-gu-ment is to change the de-fault 
set-tings

Underfull \hbox (badness 10000) in paragraph at lines 3922--3926
\T1/ptm/m/n/10 by spec-i-fy-ing \T1/zi4/m/sl/10 lattice.options(default.theme =
 "col.whitebg")\T1/ptm/m/n/10 .

Underfull \hbox (badness 2435) in paragraph at lines 3922--3926
\T1/ptm/m/n/10 For back-compatibility, this is ini-tially (when lat-tice is loa
ded) set to
[2638] [2639]
Underfull \hbox (badness 1173) in paragraph at lines 4061--4065
[]\T1/ptm/m/n/10 A char-ac-ter string giv-ing the name of a com-po-nent. If un-
spec-i-fied in

Underfull \hbox (badness 3219) in paragraph at lines 4088--4090
[]\T1/ptm/m/n/10 A log-i-cal flag, in-di-cat-ing whether a warn-ing should be i
s-sued when
[2640] [2641] [2642]
Underfull \hbox (badness 3492) in paragraph at lines 4284--4294
[]\T1/ptm/m/n/10 A color spec-i-fi-ca-tion. \T1/zi4/m/sl/10 col \T1/ptm/m/n/10 
is used for com-po-nents \T1/zi4/m/sl/10 "plot.symbol"\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 4309--4312
[]\T1/ptm/m/n/10 fill color, ap-pli-ca-ble for com-po-nents \T1/zi4/m/sl/10 plo
t.symbol\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 plot.polygon\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 4312--4314
[]\T1/ptm/m/n/10 border color, ap-pli-ca-ble for com-po-nents \T1/zi4/m/sl/10 p
lot.polygon \T1/ptm/m/n/10 and
[2643] [2644] [2645] [2646] [2647] [2648] [2649] [2650] [2651] [2652]
Underfull \hbox (badness 6157) in paragraph at lines 5035--5038
[]\T1/zi4/m/sl/10 plot.shingle \T1/ptm/m/n/10 dis-plays the ranges of shin-gles
 via rect-an-gles. \T1/zi4/m/sl/10 print.shingle \T1/ptm/m/n/10 and
[2653] [2654] [2655] [2656] [2657] [2658]
Underfull \hbox (badness 10000) in paragraph at lines 5486--5489
[]\T1/ptm/m/n/10 logical, spec-i-fy-ing whether the la-bels etc should be hor-i
-zon-tal.

Underfull \hbox (badness 5592) in paragraph at lines 5486--5489
\T1/zi4/m/sl/10 horizontal=FALSE \T1/ptm/m/n/10 is use-ful for strips on the le
ft of pan-els us-ing
[2659] [2660] [2661] [2662] [2663]
Underfull \hbox (badness 4805) in paragraph at lines 5846--5850
[]\T1/ptm/m/n/10 logical, whether the view-port be-ing as-signed fo-cus should 
be high-

Underfull \hbox (badness 10000) in paragraph at lines 5857--5864
[]\T1/ptm/m/n/10 For \T1/zi4/m/sl/10 panel.identify.qqmath\T1/ptm/m/n/10 , ex-t
ra pa-ram-e-ters are passed on to

Underfull \hbox (badness 1226) in paragraph at lines 5857--5864
\T1/zi4/m/sl/10 panel.identify\T1/ptm/m/n/10 . For \T1/zi4/m/sl/10 panel.identi
fy\T1/ptm/m/n/10 , ex-tra ar-gu-ments are treated as

Underfull \hbox (badness 2418) in paragraph at lines 5857--5864
\T1/ptm/m/n/10 graph-i-cal pa-ram-e-ters and are used for la-belling. For \T1/z
i4/m/sl/10 trellis.focus

Underfull \hbox (badness 10000) in paragraph at lines 5857--5864
\T1/ptm/m/n/10 and \T1/zi4/m/sl/10 trellis.switchFocus\T1/ptm/m/n/10 , these ar
e used (in com-bi-na-tion with

Underfull \hbox (badness 1259) in paragraph at lines 5857--5864
[][]\T1/zi4/m/sl/10 lattice.options[][][]\T1/ptm/m/n/10 ) for high-light-ing th
e cho-sen view-port if so re-quested.
[2664] [2665] [2666] [2667]
Underfull \hbox (badness 4242) in paragraph at lines 6157--6162
[]\T1/ptm/m/n/10 Graphical pa-ram-e-ters for the bars. By de-fault, the trel-li
s pa-ram-e-

Underfull \hbox (badness 2529) in paragraph at lines 6157--6162
\T1/ptm/m/n/10 ter \T1/zi4/m/sl/10 plot.polygon \T1/ptm/m/n/10 is used if there
 is no group-ing vari-able, oth-er-wise
[2668] [2669]
Underfull \hbox (badness 2310) in paragraph at lines 6273--6278
[]\T1/ptm/m/n/10 Creates Box and Whisker plot of \T1/zi4/m/sl/10 x \T1/ptm/m/n/
10 for ev-ery level of \T1/zi4/m/sl/10 y \T1/ptm/m/n/10 (or the other way round
 if
[2670] [2671] [2672] [2673] [2674] [2675] [2676] [2677] [2678] [2679] [2680]
Underfull \hbox (badness 3168) in paragraph at lines 7055--7059
\T1/ptm/m/n/10 to know what ar-gu-ments this func-tion is passed when called. U
se
[2681] [2682] [2683] [2684]
Underfull \hbox (badness 2012) in paragraph at lines 7326--7329
[]\T1/ptm/m/n/10 Further ar-gu-ments, of-ten graph-i-cal pa-ram-e-ters, even-tu
-ally passed on to
[2685] [2686]
Underfull \hbox (badness 3333) in paragraph at lines 7498--7500
[]\T1/ptm/m/n/10 default colours are ob-tained from \T1/zi4/m/sl/10 plot.symbol
 \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 plot.line \T1/ptm/m/n/10 us-ing
[2687] [2688] [2689]
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[2691] [2692]
Underfull \hbox (badness 1436) in paragraph at lines 7912--7918
[]\T1/ptm/m/n/10 A log-i-cal flag de-ter-min-ing whether the de-fault graph-i-c
al pa-ram-e-ters for
[2693] [2694] [2695] [2696] [2697] [2698] [2699] [2700]
Underfull \hbox (badness 10000) in paragraph at lines 8470--8473
[]\T1/ptm/m/n/10 Extra ar-gu-ments. Passed down to \T1/zi4/m/sl/10 panel.superp
ose \T1/ptm/m/n/10 from
[2701]
Underfull \hbox (badness 1092) in paragraph at lines 8516--8518
[]\T1/ptm/m/n/10 Deepayan Sarkar \T1/zi4/m/sl/10 <Deepayan.Sarkar@R-project.org
> \T1/ptm/m/n/10 (\T1/zi4/m/sl/10 panel.superpose.2 \T1/ptm/m/n/10 orig-i-nally
 con-
[2702] [2703]
Underfull \hbox (badness 3895) in paragraph at lines 8677--8680
[]\T1/ptm/m/n/10 details of his-togram cal-cu-la-tions. \T1/zi4/m/sl/10 type \T
1/ptm/m/n/10 has a dif-fer-ent mean-ing in
[2704]
Underfull \hbox (badness 1515) in paragraph at lines 8753--8757
[]\T1/ptm/m/n/10 numeric vec-tor of length two, rep-re-sent-ing prob-a-bil-i-ti
es. If used with
[2705] [2706]
Underfull \hbox (badness 6316) in paragraph at lines 8859--8864
[]\T1/ptm/m/n/10 which packet (counted ac-cord-ing to the packet or-der, de-scr
ibed in

Underfull \hbox (badness 5908) in paragraph at lines 8876--8879
[]\T1/ptm/m/n/10 list, sim-i-lar to those pro-duced by \T1/zi4/m/sl/10 xscale.c
omponents.default \T1/ptm/m/n/10 and
[2707] [2708] [2709] [2710]
Overfull \hbox (1.94879pt too wide) in paragraph at lines 9164--9168
[]\T1/ptm/m/n/10 returns a list with sev-eral com-po-nents, in-clud-ing \T1/zi4
/m/sl/10 left,right,left.name,right.name,condition
[2711] [2712] [2713] [2714] [2715] [2716] [2717]
Underfull \hbox (badness 2310) in paragraph at lines 9622--9626
[]\T1/ptm/m/n/10 Factor with lev-els \T1/zi4/m/sl/10 "Svansota"\T1/ptm/m/n/10 ,
 \T1/zi4/m/sl/10 "No. 462"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "Manchuria"\T1/ptm/m
/n/10 , \T1/zi4/m/sl/10 "No. 475"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "Velvet"\T1/p
tm/m/n/10 ,

Underfull \hbox (badness 3701) in paragraph at lines 9627--9630
[]\T1/ptm/m/n/10 Factor with 6 lev-els: \T1/zi4/m/sl/10 "Grand Rapids"\T1/ptm/m
/n/10 , \T1/zi4/m/sl/10 "Duluth"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "University Fa
rm"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "Morris"\T1/ptm/m/n/10 ,
[2718] [2719] [2720]pdfTeX warning (ext4): destination with the same identifier
 (name{Rfn.melanoma}) has been already used, duplicate ignored
<to be read again> 
                   \relax 
l.9853 \aliasA{melanoma}{H\_melanoma}{melanoma}
                                                [2721] [2722] [2723]
Underfull \hbox (badness 4144) in paragraph at lines 10077--10080
[]\T1/ptm/m/n/10 Rural Health Re-form Pol-icy Re-search Cen-ter. _Ex-plor-ing R
u-ral and Ur-ban Mor-tal-

Underfull \hbox (badness 1509) in paragraph at lines 10077--10080
\T1/ptm/m/n/10 ity Dif-fer-ences_, Au-gust 2015 Bethesda, MD. [][]$\T1/zi4/m/sl
/10 https : / / ruralhealth . und . edu / projects /
[2724] [2725]) (mgcv-pkg.tex [2726]
Chapter 24.
[2727] [2728] [2729]
Underfull \hbox (badness 1142) in paragraph at lines 171--175
\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from

Underfull \hbox (badness 1043) in paragraph at lines 196--201
\T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known 
scale.
[2730] [2731] [2732] [2733]
Underfull \hbox (badness 10000) in paragraph at lines 365--372
[][][]\T1/zi4/m/sl/10 mgcv.parallel[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 m
gcv-package[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 gamObject[][][]\T1/ptm/m/
n/10 , [][]\T1/zi4/m/sl/10 gam.models[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10
 smooth.terms[][][]\T1/ptm/m/n/10 ,

Underfull \hbox (badness 7168) in paragraph at lines 365--372
[][]\T1/zi4/m/sl/10 linear.functional.terms[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m
/sl/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 te[][][] [][]predict.gam[][]
[]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 plot.gam[][][]\T1/ptm/m/n/10 , [][]\T1/z
i4/m/sl/10 summary.gam[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 gam.side[][][]
\T1/ptm/m/n/10 ,
[2734] [2735] [2736] [2737] [2738] [2739] [2740]
Underfull \hbox (badness 1158) in paragraph at lines 753--755
[]\T1/ptm/m/n/10 Choosing the ba-sis di-men-sion, and check-ing the choice, whe
n us-ing pe-nal-ized re-gres-sion
[2741]
Underfull \hbox (badness 1259) in paragraph at lines 816--817
[]\T1/ptm/m/n/10 Wood, S.N. (2017) Gen-er-al-ized Ad-di-tive Mod-els: An In-tro
-duc-tion with R (2nd edi-tion).
[2742]
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[2744] [2745] [2746] [2747] [2748] [2749] [2750] [2751] [2752] [2753] [2754]
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Underfull \hbox (badness 1142) in paragraph at lines 2239--2243
\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
[2766]
Underfull \hbox (badness 1043) in paragraph at lines 2265--2270
\T1/ptm/m/n/10 un-known scale pa-ram-e-ter and Mal-lows' Cp/UBRE/AIC for known 
scale.
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[2786] [2787]
Underfull \hbox (badness 10000) in paragraph at lines 3584--3588
[]\T1/ptm/m/n/10 Random ef-fects can be added to \T1/zi4/m/sl/10 gam \T1/ptm/m/
n/10 mod-els us-ing \T1/zi4/m/sl/10 s(...,bs="re") \T1/ptm/m/n/10 terms (see
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Underfull \hbox (badness 1184) in paragraph at lines 3870--3874
[]\T1/ptm/m/n/10 list of the square root penal-ties: last en-try is root of fix
ed penalty, if
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[2804]
Underfull \hbox (badness 1142) in paragraph at lines 4591--4595
\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
[2805]
Underfull \hbox (badness 1231) in paragraph at lines 4692--4694
[]\T1/zi4/m/sl/10 gamm \T1/ptm/m/n/10 per-forms poorly with bi-nary data, since
 it uses PQL. It is bet-ter to use \T1/zi4/m/sl/10 gam \T1/ptm/m/n/10 with
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Underfull \hbox (badness 2181) in paragraph at lines 5064--5065
[]\T1/ptm/m/n/10 one sided for-mula con-tain-ing vari-ables needed for pre-dic-
tion, used by
[2812] [2813] [2814] [2815] [2816] [2817] [2818]
Underfull \hbox (badness 10000) in paragraph at lines 5453--5454
[]\T1/ptm/m/n/10 A pre-fit gam ob-ject, as pro-duced by \T1/zi4/m/sl/10 gam(...
,fit=FALSE) \T1/ptm/m/n/10 or
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[2822] [2823] [2824] [2825] [2826] [2827]
Underfull \hbox (badness 1142) in paragraph at lines 5956--5960
\T1/ptm/m/n/10 ates re-quired by the for-mula. By de-fault the vari-ables are t
aken from
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[2832] [2833] [2834]
Underfull \hbox (badness 1087) in paragraph at lines 6326--6327
[]\T1/ptm/m/n/10 If \T1/zi4/m/sl/10 rho \T1/ptm/m/n/10 and \T1/zi4/m/sl/10 thet
a \T1/ptm/m/n/10 were sup-plied then deriva-tives are w.r.t. these. In this cas
e, and if
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Underfull \vbox (badness 10000) has occurred while \output is active [2839]
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Underfull \hbox (badness 1242) in paragraph at lines 7272--7273
[]\T1/ptm/m/n/10 Development of mgcv ver-sion 1.8 was part funded by EP-SRC gra
nts EP/K005251/1 and
[2851] [2852] [2853] [2854] [2855] [2856] [2857] [2858] [2859] [2860] [2861]
Underfull \hbox (badness 6001) in paragraph at lines 7912--7914
[]\T1/ptm/m/n/10 Simon N. Wood \T1/zi4/m/sl/10 <simon.wood@r-project.org> \T1/p
tm/m/n/10 mod-i-fied from Ven-ables and Rip-ley's
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Underfull \hbox (badness 1038) in paragraph at lines 8661--8664
[]\T1/ptm/m/n/10 The fol-low-ing func-tions are pro-vided: \T1/zi4/m/sl/10 Dim.
pdIndot\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 coef.pdIdnot\T1/ptm/m/n/10 , \T1/zi4/m/
sl/10 corMatrix.pdIdnot\T1/ptm/m/n/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 8661--8664
\T1/zi4/m/sl/10 logDet.pdIdnot\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 pdConstruct.pdId
not\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 pdFactor.pdIdnot\T1/ptm/m/n/10 , \T1/zi4/m/
sl/10 pdMatrix.pdIdnot\T1/ptm/m/n/10 ,
[2874]
Underfull \hbox (badness 10000) in paragraph at lines 8717--8720
[]\T1/ptm/m/n/10 These func-tions (\T1/zi4/m/sl/10 pdTens\T1/ptm/m/n/10 , \T1/z
i4/m/sl/10 pdConstruct.pdTens\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 pdFactor.pdTens\T
1/ptm/m/n/10 , \T1/zi4/m/sl/10 pdMatrix.pdTens\T1/ptm/m/n/10 ,
[2875] [2876] [2877] [2878] [2879] [2880] [2881] [2882] [2883] [2884] [2885]
Underfull \hbox (badness 1852) in paragraph at lines 9387--9390
[]\T1/ptm/m/n/10 To fa-cil-i-tate plot-ting with [][]\T1/zi4/m/sl/10 termplot[]
[][]\T1/ptm/m/n/10 , if \T1/zi4/m/sl/10 object \T1/ptm/m/n/10 pos-sesses an at-
tribute \T1/zi4/m/sl/10 "para.only" \T1/ptm/m/n/10 and
[2886] [2887] [2888]
Underfull \hbox (badness 1852) in paragraph at lines 9551--9554
[]\T1/ptm/m/n/10 To fa-cil-i-tate plot-ting with [][]\T1/zi4/m/sl/10 termplot[]
[][]\T1/ptm/m/n/10 , if \T1/zi4/m/sl/10 object \T1/ptm/m/n/10 pos-sesses an at-
tribute \T1/zi4/m/sl/10 "para.only" \T1/ptm/m/n/10 and
[2889] [2890]
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[2892]
Underfull \hbox (badness 1205) in paragraph at lines 9780--9782
[]\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a
tes at which

Underfull \hbox (badness 2689) in paragraph at lines 9780--9782
\T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are 
as for

Underfull \hbox (badness 1975) in paragraph at lines 9786--9791
[]\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f
i-ca-tion ob-jects of class
[2893]
Underfull \hbox (badness 1205) in paragraph at lines 9870--9872
[]\T1/ptm/m/n/10 A data frame con-tain-ing the val-ues of the (named) co-vari-a
tes at which

Underfull \hbox (badness 2689) in paragraph at lines 9870--9872
\T1/ptm/m/n/10 the smooth term is to be eval-u-ated. Ex-act re-quire-ments are 
as for
[2894] [2895] [2896]
Underfull \hbox (badness 1253) in paragraph at lines 10069--10071
[]\T1/ptm/m/n/10 Note that the op-ti-mized smooth-ing pa-ram-e-ter se-lec-tion 
cri-te-rion re-ported is one of GCV,
[2897] [2898] [2899] [2900]
Underfull \hbox (badness 4792) in paragraph at lines 10255--10258
[]\T1/ptm/m/n/10 Alternatively, but less straight-for-wardly, the \T1/zi4/m/sl/
10 paraPen \T1/ptm/m/n/10 ar-gu-ment to [][]\T1/zi4/m/sl/10 gam[][][] \T1/ptm/m
/n/10 can be used:

Underfull \hbox (badness 10000) in paragraph at lines 10255--10258
\T1/ptm/m/n/10 see [][]\T1/zi4/m/sl/10 gam.models[][][]\T1/ptm/m/n/10 . If smoo
th-ing pa-ram-e-ter es-ti-ma-tion is by ML or REML (e.g.
[2901]
Underfull \hbox (badness 10000) in paragraph at lines 10350--10353
[]\T1/ptm/m/n/10 the type of resid-u-als wanted. Usu-ally one of \T1/zi4/m/sl/1
0 "deviance"\T1/ptm/m/n/10 ,
[2902] [2903] [2904] [2905] [2906] [2907] [2908] [2909] [2910] [2911] [2912]
Underfull \hbox (badness 3861) in paragraph at lines 10978--10981
[]\T1/ptm/m/n/10 INTERNAL rou-tine to ap-ply ini-tial Sl re-parameterization to
 model ma-trix X, or, if
[2913] [2914]
Underfull \hbox (badness 1320) in paragraph at lines 11084--11089
\T1/ptm/m/n/10 and \T1/zi4/m/sl/10 b.orig = D*b.repara \T1/ptm/m/n/10 (where \T
1/zi4/m/sl/10 b.orig \T1/ptm/m/n/10 is the orig-i-nal pa-ram-e-ter vec-tor). If
 ma-
[2915] [2916]
Underfull \hbox (badness 1975) in paragraph at lines 11190--11195
[]\T1/ptm/m/n/10 Smooth terms in a GAM for-mula are turned into smooth spec-i-f
i-ca-tion ob-jects of class
[2917]
Underfull \hbox (badness 1762) in paragraph at lines 11279--11291
\T1/ptm/m/n/10 plate re-gres-sion splines: see [][]\T1/zi4/m/sl/10 tprs[][][]\T
1/ptm/m/n/10 ); \T1/zi4/m/sl/10 ts.smooth.spec \T1/ptm/m/n/10 (thin plate re-gr
es-sion splines with
[2918] [2919] [2920]
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Underfull \hbox (badness 7667) in paragraph at lines 11491--11497
[][][]\T1/zi4/m/sl/10 gam[][][] \T1/ptm/m/n/10 can use adap-tive smooths of one
 or two vari-ables, spec-i-fied via terms like

Underfull \hbox (badness 10000) in paragraph at lines 11532--11533
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2922] [2923] [2924] [2925] [2926] [2927]
Underfull \hbox (badness 10000) in paragraph at lines 11808--11810
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2928] [2929]
Underfull \hbox (badness 10000) in paragraph at lines 11936--11937
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2930] [2931]
Underfull \hbox (badness 1436) in paragraph at lines 12074--12081
\T1/ptm/m/n/10 nest-ing of the smooth within the fac-tor. Note how-ever that: i
) \T1/zi4/m/sl/10 gamm \T1/ptm/m/n/10 only al-lows one
[2932] [2933]
Underfull \hbox (badness 10000) in paragraph at lines 12168--12169
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2934] [2935] [2936] [2937] [2938] [2939] [2940] [2941] [2942] [2943]
Underfull \hbox (badness 10000) in paragraph at lines 12754--12760
[]\T1/ptm/m/n/10 A smooth spec-i-fi-ca-tion ob-ject as pro-duced by a

Underfull \hbox (badness 1292) in paragraph at lines 12754--12760
\T1/zi4/m/sl/10 s(...,bs="so",xt=list(bnd=bnd,...)) \T1/ptm/m/n/10 term in a \T
1/zi4/m/sl/10 gam \T1/ptm/m/n/10 for-mula. Note
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Underfull \vbox (badness 10000) has occurred while \output is active [2948]
[2949]
Underfull \hbox (badness 10000) in paragraph at lines 13097--13098
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2950] [2951] [2952] [2953]
Underfull \hbox (badness 3895) in paragraph at lines 13358--13361
[][][]\T1/zi4/m/sl/10 gam[][][] \T1/ptm/m/n/10 can use isotropic smooths of any
 num-ber of vari-ables, spec-i-fied via terms like
[2954]
Underfull \hbox (badness 10000) in paragraph at lines 13403--13405
[]\T1/ptm/m/n/10 a smooth spec-i-fi-ca-tion ob-ject, usu-ally gen-er-ated by a 
term
[2955] [2956] [2957] [2958]
Underfull \hbox (badness 1371) in paragraph at lines 13620--13626
[]\T1/zi4/m/sl/10 bs="ad" \T1/ptm/m/n/10 Uni-vari-ate and bi-vari-ate adap-tive
 smooths are avail-able (see

Underfull \hbox (badness 10000) in paragraph at lines 13660--13664
[][][]\T1/zi4/m/sl/10 s[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 te[][][]\T1/p
tm/m/n/10 , [][]\T1/zi4/m/sl/10 t2[][][] [][]tprs[][][]\T1/ptm/m/n/10 ,[][]\T1/
zi4/m/sl/10 Duchon.spline[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 cubic.regre
ssion.spline[][][]\T1/ptm/m/n/10 ,[][]\T1/zi4/m/sl/10 p.spline[][][]\T1/ptm/m/n
/10 ,

Underfull \hbox (badness 10000) in paragraph at lines 13660--13664
[][]\T1/zi4/m/sl/10 mrf[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 soap[][][]\T1
/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 Spherical.Spline[][][]\T1/ptm/m/n/10 , [][]\T
1/zi4/m/sl/10 adaptive.smooth[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 user.de
fined.smooth[][][]\T1/ptm/m/n/10 ,

Overfull \hbox (46.8009pt too wide) in paragraph at lines 13660--13664
[][]\T1/zi4/m/sl/10 smooth.construct.re.smooth.spec[][][]\T1/ptm/m/n/10 , [][]\
T1/zi4/m/sl/10 smooth.construct.gp.smooth.spec[][][]\T1/ptm/m/n/10 ,[][]\T1/zi4
/m/sl/10 factor.smooth.interaction[][][] 
[2959] [2960] [2961] [2962]
Underfull \hbox (badness 2326) in paragraph at lines 13865--13872
[]\T1/ptm/m/n/10 These wrap-per func-tions ex-ist to al-low smooths spec-i-fied
 us-ing [][]\T1/zi4/m/sl/10 smooth.construct[][][] \T1/ptm/m/n/10 and
[2963]
Underfull \hbox (badness 2158) in paragraph at lines 13950--13950
[]\T1/ptm/m/it/10 Extract smooth-ing pa-ram-e-ter es-ti-ma-tor co-vari-ance ma-
trix from
[2964] [2965] [2966] [2967] [2968] [2969] [2970] [2971] [2972] [2973] [2974]
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[2976] [2977] [2978] [2979] [2980] [2981] [2982] [2983] [2984] [2985] [2986]
[2987] [2988] [2989] [2990]
Underfull \hbox (badness 1796) in paragraph at lines 15594--15597
[]\T1/ptm/m/n/10 other op-tions to pass on to [][]\T1/zi4/m/sl/10 persp[][][]\T
1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 image[][][] \T1/ptm/m/n/10 or [][]\T1/zi4/m/
sl/10 contour[][][]\T1/ptm/m/n/10 . In par-tic-u-lar
[2991] [2992] [2993] [2994] [2995] [2996]) (nlme-pkg.tex
Chapter 25.
[2997] [2998] [2999] [3000] [3001] [3002] [3003] [3004] [3005] [3006] [3007]
[3008] [3009] [3010] [3011] [3012] [3013] [3014] [3015] [3016] [3017] [3018]
[3019] [3020] [3021] [3022] [3023] [3024] [3025] [3026]
Underfull \hbox (badness 2875) in paragraph at lines 1994--2000
[]\T1/ptm/m/n/10 an op-tional log-i-cal value or one-sided for-mula, in-di-cat-
ing a co-vari-ate

Underfull \hbox (badness 1466) in paragraph at lines 1994--2000
\T1/ptm/m/n/10 that is in-ner to the \T1/zi4/m/sl/10 displayLevel \T1/ptm/m/n/1
0 group-ing fac-tor. If equal to \T1/zi4/m/sl/10 TRUE\T1/ptm/m/n/10 ,
[3027] [3028] [3029] [3030]
Underfull \hbox (badness 10000) in paragraph at lines 2256--2262
[][][]\T1/zi4/m/sl/10 ACF.lme[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 corARMA
[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 corClasses[][][]\T1/ptm/m/n/10 , [][
]\T1/zi4/m/sl/10 Dim.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 Initi
alize.corStruct[][][]\T1/ptm/m/n/10 ,
[3031] [3032] [3033] [3034] [3035] [3036] [3037] [3038] [3039] [3040] [3041]
[3042] [3043] [3044] [3045] [3046] [3047] [3048] [3049] [3050] [3051] [3052]
[3053] [3054] [3055] [3056] [3057] [3058] [3059] [3060] [3061] [3062] [3063]
Underfull \hbox (badness 1067) in paragraph at lines 4414--4419
\T1/ptm/m/n/10 ma-trix), \T1/zi4/m/sl/10 fitted \T1/ptm/m/n/10 (fit-ted val-ues
), and \T1/zi4/m/sl/10 residuals \T1/ptm/m/n/10 (resid-u-als). De-faults to
[3064] [3065] [3066] [3067] [3068] [3069] [3070] [3071] [3072] [3073] [3074]
[3075]
Underfull \hbox (badness 10000) in paragraph at lines 5160--5164
[][][]\T1/zi4/m/sl/10 getCovariate.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/
m/sl/10 getCovariate.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 getCo
variate.varFunc[][][]\T1/ptm/m/n/10 ,
[3076] [3077] [3078] [3079] [3080] [3081] [3082]
Underfull \hbox (badness 10000) in paragraph at lines 5592--5595
[][][]\T1/zi4/m/sl/10 getGroupsFormula[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/1
0 getGroups.data.frame[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 getGroups.gls[
][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 getGroups.lmList[][][]\T1/ptm/m/n/10 
,
[3083] [3084] [3085] [3086] [3087] [3088] [3089]
Underfull \hbox (badness 10000) in paragraph at lines 5973--5978
[][][]\T1/zi4/m/sl/10 getGroupsFormula.gls[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/
sl/10 getGroupsFormula.lmList[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 getGrou
psFormula.lme[][][]\T1/ptm/m/n/10 ,
[3090] [3091] [3092] [3093]
Underfull \hbox (badness 1490) in paragraph at lines 6243--6254
[][][]\T1/zi4/m/sl/10 corClasses[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 glsC
ontrol[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 glsObject[][][]\T1/ptm/m/n/10 
, [][]\T1/zi4/m/sl/10 glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 plot.
gls[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 predict.gls[][][]\T1/ptm/m/n/10 ,
 [][]\T1/zi4/m/sl/10 qqnorm.gls[][][]\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
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[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
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[][][]\T1/zi4/m/sl/10 formula[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 gapply[
][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 gsummary[][][]\T1/ptm/m/n/10 , [][]\T
1/zi4/m/sl/10 lme[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 plot.nffGroupedData
[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 plot.nfnGroupedData[][][]\T1/ptm/m/n
/10 ,
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[][][]\T1/zi4/m/sl/10 Initialize.corStruct[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/
sl/10 Initialize.lmeStruct[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 Initialize
.glsStruct[][][]\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
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l.8572 \aliasA{sigma}{lmeObject}{sigma}
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[][][]\T1/zi4/m/sl/10 lm[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 lme.lmList[]
[][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 plot.lmList[][][]\T1/ptm/m/n/10 , [][]
\T1/zi4/m/sl/10 pooledSD[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 predict.lmLi
st[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 residuals.lmList[][][]\T1/ptm/m/n/
10 ,
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[][][]\T1/zi4/m/sl/10 lme[][][]\T1/ptm/m/n/10 ,[][]\T1/zi4/m/sl/10 gls[][][]\T1
/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 logLik.corStruct[][][]\T1/ptm/m/n/10 , [][]\T
1/zi4/m/sl/10 logLik.glsStruct[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 logLik
.lmeStruct[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 logLik.lmList[][][]\T1/ptm
/m/n/10 ,
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l.9686 ...rA{Matrix}{Assign Matrix Values}{Matrix}
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l.9686 ...rA{Matrix}{Assign Matrix Values}{Matrix}
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[]\T1/ptm/m/n/10 optionally, any of the fol-low-ing: (i) a two-sided for-mula o
f the form
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[][][]\T1/zi4/m/sl/10 nlmeControl[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 nlm
e.nlsList[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 nlmeObject[][][]\T1/ptm/m/n
/10 , [][]\T1/zi4/m/sl/10 nlsList[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 nlm
eStruct[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 pdClasses[][][]\T1/ptm/m/n/10
 , [][]\T1/zi4/m/sl/10 reStruct[][][]\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 relative step for nu-mer-i-cal deriva-tives cal-cu-la-tions. D
e-fault is
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[]\T1/ptm/m/n/10 an op-tional log-i-cal func-tion or func-tion. If \T1/zi4/m/sl
/10 TRUE \T1/ptm/m/n/10 and ei-ther \T1/zi4/m/sl/10 inner \T1/ptm/m/n/10 or
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[]\T1/ptm/m/n/10 an op-tional nu-meric vec-tor with the lim-its for the y-axis.
 De-faults to
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l.15177 ...Extract Random Effects}{random.effects}
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l.15177 ...Extract Random Effects}{random.effects}
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\T1/ptm/m/n/10 ma-trix), \T1/zi4/m/sl/10 fitted \T1/ptm/m/n/10 (fit-ted val-ues
), and \T1/zi4/m/sl/10 residuals \T1/ptm/m/n/10 (resid-u-als). De-faults to
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\T1/ptm/m/n/10 Op-tions in-clude \T1/zi4/m/sl/10 "response" \T1/ptm/m/n/10 for 
the "raw" resid-u-als (ob-served - fit-ted),
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[]\T1/ptm/m/n/10 an op-tional log-i-cal value used to con-trol the amount of ou
t-put in the
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\T1/zi4/m/sl/10 Symmetry" \T1/ptm/m/n/10 for \T1/zi4/m/sl/10 pdCompSymm\T1/ptm/
m/n/10 , \T1/zi4/m/sl/10 "Diagonal" \T1/ptm/m/n/10 for \T1/zi4/m/sl/10 pdDiag\T
1/ptm/m/n/10 , \T1/zi4/m/sl/10 "Multiple of

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\T1/zi4/m/sl/10 an Identity" \T1/ptm/m/n/10 for \T1/zi4/m/sl/10 pdIdent\T1/ptm/
m/n/10 , \T1/zi4/m/sl/10 "General Positive-Definite,Natural

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\T1/zi4/m/sl/10 Parametrization" \T1/ptm/m/n/10 for \T1/zi4/m/sl/10 pdNatural\T
1/ptm/m/n/10 , \T1/zi4/m/sl/10 "General Positive-Definite" \T1/ptm/m/n/10 for
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\T1/ptm/m/n/10 for \T1/zi4/m/sl/10 varComb\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "Con
stant plus power of covariate" \T1/ptm/m/n/10 for \T1/zi4/m/sl/10 varConstPower
\T1/ptm/m/n/10 ,
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[][][]\T1/zi4/m/sl/10 Variogram.corExp[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/1
0 Variogram.corGaus[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 Variogram.corLin[
][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 Variogram.corRatio[][][]\T1/ptm/m/n/1
0 ,

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[][]\T1/zi4/m/sl/10 Variogram.corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl
/10 Variogram.corSpher[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 Variogram.defa
ult[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 Variogram.gls[][][]\T1/ptm/m/n/10
 ,
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[][][]\T1/zi4/m/sl/10 corSpatial[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 Vari
ogram[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 Variogram.default[][][]\T1/ptm/
m/n/10 , [][]\T1/zi4/m/sl/10 Variogram.corExp[][][]\T1/ptm/m/n/10 , [][]\T1/zi4
/m/sl/10 Variogram.corGaus[][][]\T1/ptm/m/n/10 ,
[3274] [3275] [3276] [3277] [3278] [3279] [3280] [3281] [3282] [3283] [3284]
[3285] [3286]) (nnet-pkg.tex
Chapter 26.
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l.47 ...t Multinomial Log-linear Models}{multinom}
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[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for re-gres-sion mod-els, of the fo
rm \T1/zi4/m/sl/10 response ~
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Chapter 27.
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Chapter 28.
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[3342] [3343]) (survival-pkg.tex [3344]
Chapter 29.
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l.326 ... Myelogenous Leukemia survival data}{aml}
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l.326 ... Myelogenous Leukemia survival data}{aml}
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[]\T1/ptm/m/n/10 F.J. Anscombe (1949). Trans-for-ma-tions of Pois-son, bi-no-mi
al and negative-binomial data.
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l.1178 ...erapy for Stage B/C colon cancer}{colon}
                                                  
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[]\T1/ptm/m/n/10 Often used to add the ex-pected sur-vival curve(s) to a Kaplan
-Meier plot gen-er-ated with
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e the note in
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[]\T1/ptm/m/n/10 an ob-ject of class \T1/zi4/m/sl/10 "summary.survfit"\T1/ptm/m
/n/10 , which is the re-sult of the
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[]\T1/ptm/m/n/10 type of resid-u-als, with choices of \T1/zi4/m/sl/10 "response
"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "deviance"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "d
fbeta"\T1/ptm/m/n/10 ,
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l.5866 ...ata from a soldering experiment}{solder}
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[]\T1/ptm/m/n/10 a for-mula ex-pres-sion as for other sur-vival mod-els, of the
 form
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\T1/ptm/m/n/10 op-tion does not cre-ate a curve, rather it re-trieves the pre-d
icted sur-vival
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[][][]\T1/zi4/m/sl/10 survfit.formula[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10
 survfit.coxph[][][]\T1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 survfit.object[][][]\T
1/ptm/m/n/10 , [][]\T1/zi4/m/sl/10 print.survfit[][][]\T1/ptm/m/n/10 , [][]\T1/
zi4/m/sl/10 plot.survfit[][][]\T1/ptm/m/n/10 ,
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[]\T1/ptm/m/n/10 One of \T1/zi4/m/sl/10 "none"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 
"plain"\T1/ptm/m/n/10 , \T1/zi4/m/sl/10 "log" \T1/ptm/m/n/10 (the de-fault), \T
1/zi4/m/sl/10 "log-log" \T1/ptm/m/n/10 or
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[]\T1/ptm/m/n/10 survival times, for time de-pen-dent pre-dic-tion. It gives th
e time range
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[]| \T1/zi4/m/it/10 smooth.construct.tensor.smooth.spec\T1/ptm/m/n/10 , 
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[]\T1/zi4/m/it/10 [,CsparseMatrix,index,index,logical-method 

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[]\T1/zi4/m/it/10 %*%,lsparseMatrix,lsparseMatrix-method 
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[3540]
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[3541] [3542] [3543]
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Chapter 1 (R-FAQ.aux) [1] Chapter 2 [2] [3] [4] [5] [6] [7] [8] [9] Chapter 3
[10] [11] [12] [13] [14] [15] [16] [17] [18] Chapter 4 [19] Chapter 5 [20]
[21] [22] [23] [24] Chapter 6 [25] [26] Chapter 7 [27] [28] [29] [30] [31]
[32] [33] [34] [35] [36] [37] [38]
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[39] [40] [41]
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@texttt download.file()[] @textrm func-tion), a down-load method is cho-sen bas
ed on the
[42] Chapter 8 [43] Chapter 9 [44] [45] Chapter 10 [46] [47] [48] )
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[3] [4] [5] [6] [7] [8] [9] [10] [11] [12] Chapter 3 [13] [14]
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[17] [18] Chapter 4 [19] [20]
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@texttt capitan.fw.pkg[]@textrm , @texttt org.r-project.R.el-capitan.GUI.pkg[]@
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[21] Chapter 5 [22] Chapter 6 [23] [24] [25] [26] [27] [28] [29] [30]
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[38] [39]
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[40] [41] [42] [43] [44] [45] [46] [47] Appendix B [48] [49] [50] [51] [52]
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[61] [62] [63] [64] [65]
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[66] [67] Appendix D [68] [69] [70] (Function and variable index) [71]
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[1] Chapter 2 [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] Chapter 3 [13]
[14]
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@texttt capitan.fw.pkg[]@textrm , @texttt org.r-project.R.el-capitan.GUI.pkg[]@
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[21] Chapter 5 [22] Chapter 6 [23] [24] [25] [26] [27] [28] [29] [30]
Chapter 7 [31] [32] [33] Chapter 8 [34] Chapter 9 [35] [36] Appendix A [37]
[38] [39]
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[40] [41] [42] [43] [44] [45] [46] [47] Appendix B [48] [49] [50] [51] [52]
[53] Appendix C [54] [55] [56] [57] [58]
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[61] [62] [63] [64] [65]
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[66] [67] Appendix D [68] [69] [70] (Function and variable index) [71]
(Concept index) [72] (Environment variable index) [73] [74] )
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[1] [2] Chapter 1 [3]
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(see the transcript file for additional information)<C:/Program Files/MiKTeX 2.
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ype1/public/amsfonts/cm/cmbx12.pfb><C:/Program Files/MiKTeX 2.9/fonts/type1/pub
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[1] [2] Chapter 1 [3]
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[4] [5] [6] Chapter 2 [7] [8] [9] [10] [11] [12] Chapter 3 [13] [14] Chapter 4
[15] [16] [17] [18] [19] [20] Chapter 5 [21] Chapter 6 [22] Chapter 7 [23]
[24] [25] [26] Chapter 8 [27] Chapter 9 [28] Appendix A [29]
(Function and variable index) [30] [31] (Concept index) [32] [33] )
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[]@textrm The `@texttt Depends[]@textrm '[], `@texttt Imports[]@textrm '[], `@t
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[]@textrm '[] and
[6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21]
[22] [23] [24] [25] [26]
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[27] [28] [29]
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[62] [63] [64] [65] [66] Chapter 2 [67] [68] [69] [70] [71] [72] [73] [74]
[75] [76] [77] [78]
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[81] [82] [83] [84] Chapter 3 [85] [86] [87] [88] [89] [90] [91] [92]
Chapter 4 [93] [94] [95] [96] [97]
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[98] [99] [100]
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[101] [102]
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[119] [120] [121] [122] [123] [124] [125]
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[148] [149] Chapter 6 [150] [151] [152] [153] [154] [155] [156] [157] [158]
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[164] [165] [166] [167] [168]
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Chapter 7 [169] [170] Chapter 8 [171] [172] [173]
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[6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21]
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[108] Chapter 5 [109] [110] [111] [112] [113] [114] [115] [116] [117] [118]
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[119] [120] [121] [122] [123] [124] [125]
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" -lpackB[] 
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[]@textrm Functions @texttt any_duplicated[] @textrm and @texttt any_duplicated
3[] @textrm are fast ver-sions of R's
[135] [136] [137] [138] [139] [140] [141] [142] [143] [144] [145] [146]
[147]
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[148] [149] Chapter 6 [150] [151] [152] [153] [154] [155] [156] [157] [158]
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[164] [165] [166] [167] [168]
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[]@textrm The graph-ics sys-tems are ex-posed in head-ers @texttt R_ext/Graphic
sEngine.h[]@textrm , @texttt R_
Chapter 7 [169] [170] Chapter 8 [171] [172] [173]
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[175] [176] [177] [178] [179] [180]
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[181] [182]
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-core\R32[] @textrm or
(Function and variable index) [183] [184] [185] [186]
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[2] [3] [4] [5] Chapter 2 [6] [7] [8] [9] [10] [11] Chapter 3 [12] [13]
[14] Chapter 4 [15] [16] Chapter 5 [17] [18] [19] [20] [21] [22] [23] [24]
Chapter 6 [25] [26] [27] [28] Chapter 7 [29] [30] [31] Chapter 8 [32] [33] <./i
mages/hist.pdf> [34] <./images/ecdf.pdf> <./images/QQ.pdf> [35] [36] <./images/
ice.pdf> [37] [38] Chapter 9 [39] [40] Chapter 10 [41] [42] [43] [44] [45]
[46] [47] [48] [49] Chapter 11 [50] [51] [52] [53] [54] [55] [56] [57] [58]
[59] [60] [61] Chapter 12 [62] [63] [64] [65] [66] [67] [68] [69] [70] <./image
s/fig11.pdf> [71] <./images/fig12.pdf> [72] [73] [74] [75] Chapter 13 [76]
[77] Chapter 14 [78] [79]
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[80] Appendix A [81] [82] [83] Appendix B [84] [85] [86] [87] [88] [89]
[90] Appendix C [91] [92] Appendix D [93]
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(R-intro.toc) (R-intro.toc) (Preface) (R-intro.aux) Chapter 1 [1]
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[2] [3] [4] [5] Chapter 2 [6] [7] [8] [9] [10] [11] Chapter 3 [12] [13]
[14] Chapter 4 [15] [16] Chapter 5 [17] [18] [19] [20] [21] [22] [23] [24]
Chapter 6 [25] [26] [27] [28] Chapter 7 [29] [30] [31] Chapter 8 [32] [33] <./i
mages/hist.pdf> [34] <./images/ecdf.pdf> <./images/QQ.pdf> [35] [36] <./images/
ice.pdf> [37] [38] Chapter 9 [39] [40] Chapter 10 [41] [42] [43] [44] [45]
[46] [47] [48] [49] Chapter 11 [50] [51] [52] [53] [54] [55] [56] [57] [58]
[59] [60] [61] Chapter 12 [62] [63] [64] [65] [66] [67] [68] [69] [70] <./image
s/fig11.pdf> [71] <./images/fig12.pdf> [72] [73] [74] [75] Chapter 13 [76]
[77] Chapter 14 [78] [79]
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[80] Appendix A [81] [82] [83] Appendix B [84] [85] [86] [87] [88] [89]
[90] Appendix C [91] [92] Appendix D [93] [94] [95] Appendix E [96] [97]
Appendix F [98] [99] )
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[16] [17] [18] [19] [20] [21] Chapter 2 [22] [23] [24] [25] [26] Chapter 3
[27] [28] Chapter 4 [29] [30] Chapter 5 [31] Chapter 6 [32] [33] [34] [35]
[36] [37] [38] [39] [40] [41] [42] Chapter 7 [43]
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@textrm ing been built and in-stalled as a Mac macOS `frame-work'. Specif-i-cal
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@textrm frame-works can con-tain mul-ti-ple ver-sions of R. It even-tu-ally re-
solves to
[44] Chapter 8 [45] [46]
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hoice of
[47] [48] [49] [50] [51] [52]
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 []@textrm Optionally check if ei-ther ar-gu-ment of the bi-nary op-er-a-tors @
texttt &&[] @textrm and
[53] [54] Chapter 9 [55] [56] Chapter 10 [57] Chapter 11 [58] Chapter 12
[59] [60] (Function and variable index) [61]
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[63] )
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[16] [17] [18] [19] [20] [21] Chapter 2 [22] [23] [24] [25] [26] Chapter 3
[27] [28] Chapter 4 [29] [30] Chapter 5 [31] Chapter 6 [32] [33] [34] [35]
[36] [37] [38] [39] [40] [41] [42] Chapter 7 [43]
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 []@textrm Optionally check if ei-ther ar-gu-ment of the bi-nary op-er-a-tors @
texttt &&[] @textrm and
[53] [54] Chapter 9 [55] [56] Chapter 10 [57] Chapter 11 [58] Chapter 12
[59] [60] (Function and variable index) [61] [62] (Concept index) [63] [64] )
(see the transcript file for additional information)<C:/Program Files/MiKTeX 2.
9/fonts/type1/public/amsfonts/cm/cmb10.pfb><C:/Program Files/MiKTeX 2.9/fonts/t
ype1/public/amsfonts/cm/cmbx12.pfb><C:/Program Files/MiKTeX 2.9/fonts/type1/pub
lic/amsfonts/cm/cmmi10.pfb><C:/Program Files/MiKTeX 2.9/fonts/type1/public/amsf
onts/cm/cmmi12.pfb><C:/Program Files/MiKTeX 2.9/fonts/type1/public/amsfonts/cm/
cmmi9.pfb><C:/Program Files/MiKTeX 2.9/fonts/type1/public/amsfonts/cm/cmr10.pfb
><C:/Program Files/MiKTeX 2.9/fonts/type1/public/amsfonts/cm/cmr7.pfb><C:/Progr
am Files/MiKTeX 2.9/fonts/type1/public/amsfonts/cm/cmr8.pfb><C:/Program Files/M
iKTeX 2.9/fonts/type1/public/amsfonts/cm/cmr9.pfb><C:/Program Files/MiKTeX 2.9/
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pe1/public/amsfonts/cm/cmsltt10.pfb><C:/Program Files/MiKTeX 2.9/fonts/type1/pu
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TEXINDEX=C:/Rtools/bin/texindex.exe texify --pdf --texinfo="@set UseExternalXrefs " R-lang.texi
texify: warning: running with administrator privileges
miktex-pdftex: warning: running with administrator privileges
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Loading texinfo [version 2019-02-16.14]: pdf, fonts, markup, glyphs,
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[3] [4] [5] [6] [7] Chapter 3 [8] [9] [10] [11] [12] [13] [14] [15] [16]
[17] [18] [19] [20] Chapter 4 [21] [22] [23] [24] Chapter 5 [25] [26] [27]
[28] [29] [30] Chapter 6 [31] [32] [33] [34] [35] [36] [37] [38] Chapter 7
[39] Chapter 8 [40] [41] Chapter 9 [42] [43] Chapter 10 [44] [45]
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[]@textrm Up-to-date in-for-ma-tion on the cur-rently ac-cepted for-mats can be
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[46] [47] [48] [49] [50] (Function and Variable Index) [51]
No file R-lang.vrs.
(Concept Index) [52]
No file R-lang.cps.
Appendix A [53] [54] )
(see the transcript file for additional information)<C:/Program Files/MiKTeX 2.
9/fonts/type1/public/amsfonts/cm/cmb10.pfb><C:/Program Files/MiKTeX 2.9/fonts/t
ype1/public/amsfonts/cm/cmbx12.pfb><C:/Program Files/MiKTeX 2.9/fonts/type1/pub
lic/amsfonts/cm/cmmi10.pfb><C:/Program Files/MiKTeX 2.9/fonts/type1/public/amsf
onts/cm/cmr10.pfb><C:/Program Files/MiKTeX 2.9/fonts/type1/public/amsfonts/cm/c
mr7.pfb><C:/Program Files/MiKTeX 2.9/fonts/type1/public/amsfonts/cm/cmr9.pfb><C
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m Files/MiKTeX 2.9/fonts/type1/public/amsfonts/cm/cmsltt10.pfb><C:/Program File
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Output written on R-lang.pdf (57 pages, 372285 bytes).
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("C:\Program Files\MiKTeX 2.9\tex/texinfo/texinfo\texinfo.tex"
Loading texinfo [version 2019-02-16.14]: pdf, fonts, markup, glyphs,
page headings, tables, conditionals, indexing, sectioning, toc, environments,
defuns, macros, cross references, insertions, (epsf.tex
This is `epsf.tex' v2.7.4 <14 February 2011>
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iKTeX/2.9/pdftex/config/pdftex.map}] [2] (R-lang.toc [-1] [-2]) [-3]
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Chapter 2 [1] [2]
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[3] [4] [5] [6] [7] Chapter 3 [8] [9] [10] [11] [12] [13] [14] [15] [16]
[17] [18] [19] [20] Chapter 4 [21] [22] [23] [24] Chapter 5 [25] [26] [27]
[28] [29] [30] Chapter 6 [31] [32] [33] [34] [35] [36] [37] [38] Chapter 7
[39] Chapter 8 [40] [41] Chapter 9 [42] [43] Chapter 10 [44] [45]
Underfull \hbox (badness 10000) in paragraph at lines 4341--4343
[]@textrm Up-to-date in-for-ma-tion on the cur-rently ac-cepted for-mats can be
 found by
[46] [47] [48] [49] [50] (Function and Variable Index) [51] [52]
(Concept Index) [53] Appendix A [54] [55] )
(see the transcript file for additional information)<C:/Program Files/MiKTeX 2.
9/fonts/type1/public/amsfonts/cm/cmb10.pfb><C:/Program Files/MiKTeX 2.9/fonts/t
ype1/public/amsfonts/cm/cmbx12.pfb><C:/Program Files/MiKTeX 2.9/fonts/type1/pub
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rm -f -R R-3.6.1
mkdir R-3.6.1
cp -pR ../../../bin ../../../modules R-3.6.1
mkdir -p R-3.6.1/library
cp -pR  ../../../library/base  ../../../library/tools  ../../../library/utils  ../../../library/grDevices  ../../../library/graphics  ../../../library/stats  ../../../library/datasets  ../../../library/methods  ../../../library/grid  ../../../library/splines  ../../../library/stats4  ../../../library/tcltk  ../../../library/compiler  ../../../library/parallel  ../../../library/MASS  ../../../library/lattice  ../../../library/Matrix  ../../../library/nlme  ../../../library/survival  ../../../library/boot  ../../../library/cluster  ../../../library/codetools  ../../../library/foreign  ../../../library/KernSmooth  ../../../library/rpart  ../../../library/class  ../../../library/nnet  ../../../library/spatial  ../../../library/mgcv  ../../../library/translations R-3.6.1/library
rm -f R-3.6.1/library/*/MD5
rm -f R-3.6.1/*/Makefile.in
mkdir -p R-3.6.1/etc/x64
cp -p ../../../etc/Rprofile.site ../../../etc/Rconsole ../../../etc/Rdevga ../../../etc/rgb.txt ../../../etc/repositories ../../../etc/Rcmd_environ R-3.6.1/etc
if test -f "../../../etc/curl-ca-bundle.crt"; then \
  cp -p "../../../etc/curl-ca-bundle.crt" R-3.6.1/etc; \
fi
cp -p ../../../etc/x64/Makeconf R-3.6.1/etc/x64
mkdir -p R-3.6.1/doc
cp -p ../../../doc/CRAN_mirrors.csv R-3.6.1/doc
cp -p ../../../doc/BioC_mirrors.csv R-3.6.1/doc
mkdir -p R-3.6.1/doc/manual/images
cp -pR ../../../doc/html R-3.6.1/doc
cp -p ../../../doc/manual/*.html ../../../doc/manual/*.pdf \
  R-3.6.1/doc/manual
cp -p ../../../doc/manual/images/*.png R-3.6.1/doc/manual/images
rm -f R-3.6.1/doc/manual/R-FAQ.pdf
rm -f R-3.6.1/doc/html/R-admin.html 
rm -f R-3.6.1/doc/html/index-default.html
cp -p ../../../COPYING ../../../README R-3.6.1
cp -p ../../../doc/AUTHORS ../../../doc/COPYING ../../../doc/FAQ ../../../doc/RESOURCES ../../../doc/THANKS ../../../doc/CHANGES ../../../doc/NEWS ../../../doc/NEWS.0 ../../../doc/NEWS.1 ../../../doc/NEWS.2 R-3.6.1/doc
cp -p ../COPYRIGHTS ../README.Rterm ../../../doc/manual/rw-FAQ R-3.6.1/doc
cp -p R-3.6.1/doc/CHANGES R-3.6.1
sed -e s/@RWVER@/R-3.6.1/g \
  -e s/@RVER@//g \
  -e "s/@FULLVERSION@/`cat ../../../VERSION`/g" ../README > R-3.6.1/README.R-3.6.1
sed -e 3,5d ../README.packages > R-3.6.1/doc/README.packages
zip -q dosfiles.zip R-3.6.1/* R-3.6.1/doc/*
unzip -qao dosfiles.zip
rm -f dosfiles.zip
cp -p ../../../doc/NEWS.pdf R-3.6.1/doc
cp -p ../../../doc/NEWS.rds ../../../doc/CHANGES.rds R-3.6.1/doc
mkdir -p R-3.6.1/share \
  R-3.6.1/src/library R-3.6.1/src/gnuwin32
cp ../../../doc/html/logo.jpg ../../../doc/html/Rlogo.svg R-3.6.1/doc/html
cp ../../../doc/KEYWORDS* R-3.6.1/doc
cp -pR ../../../include R-3.6.1
cp -pR ../../../share/R ../../../share/dictionaries ../../../share/encodings ../../../share/licenses ../../../share/make ../../../share/Rd ../../../share/texmf ../../../share/zoneinfo R-3.6.1/share
(cd ..; make --no-print-directory PKGDIR=. pkgclean-windlgs)
cp -pR ../windlgs R-3.6.1/src/library
sed -e 's!^BINPREF [?]= .*!BINPREF ?= c:/Rtools/mingw_64/bin/!' \
  ../../../etc/x64/Makeconf > R-3.6.1/etc/x64/Makeconf
mkdir R-3.6.1/tests
make --no-print-directory -C ../../../tests -f Makefile.win \
  INST_TO=../src/gnuwin32/installer/R-3.6.1/tests install-tests
find R-3.6.1 -name .svn -prune -exec rm -Rf \{\} \;
find R-3.6.1 -name \*~ -delete
echo "make.packages.html(.Library,temp=FALSE,verbose=FALSE)" | R-3.6.1/bin/x64/Rterm.exe --vanilla --slave LC_COLLATE=C
cp -pRf ../../../Tcl R-3.6.1
rm -f R-3.6.1/Tcl*/lib/*.lib
------------ including 32-bit files
(cd "C:/projects/BUILD/R-source-win32"; zip -qr9X 32bit */i386 library/*/libs/i386 bin/R.exe bin/Rscript.exe)
unzip -qo "C:/projects/BUILD/R-source-win32/32bit" -d R-3.6.1
rm "C:/projects/BUILD/R-source-win32/32bit.zip"
mkdir -p R-3.6.1/Tcl
cp -pRf "C:/projects/BUILD/R-source-win32/Tcl/bin" "C:/projects/BUILD/R-source-win32/Tcl/lib" R-3.6.1/Tcl
for f in MASS lattice Matrix nlme survival boot cluster codetools foreign KernSmooth rpart class nnet spatial mgcv; do \
   sed -e 's/Archs: x64/Archs: i386, x64/' \
             ../../../library/${f}/DESCRIPTION \
             > R-3.6.1/library/${f}/DESCRIPTION; \
done
sed -e 's!^BINPREF [?]= .*!BINPREF ?= c:/Rtools/mingw_32/bin/!' \
  C:/projects/BUILD/R-source-win32/etc/i386/Makeconf > R-3.6.1/etc/i386/Makeconf
for f in ; do \
  cp "$f" R-3.6.1/bin/i386; \
done
for f in ; do \
  cp "$f" R-3.6.1/bin/x64; \
done
adding MD5 checksums
../../../bin/x64/Rscript JRins.R \
  R-3.6.1 R-3.6.1 0 \
  1 R-core "C:/Program Files (x86)/Inno Setup 6"
"C:/Program Files (x86)/Inno Setup 6/iscc" R.iss > R-3.6.1.log 2>&1
rm -Rf R.iss *.log R.wxs files.wxs R.wixobj uuidgen.o uuidgen.exe uuids
rm -Rf R-3.6.1
make -C cran all
cp ../../../doc/html/CHANGES.html CHANGES.R-3.6.1.html
cp ../../../doc/html/NEWS.html NEWS.R-3.6.1.html
cp ../installer/R-3.6.1-win*.exe .
(echo 'cat(md5sum("R-3.6.1-win.exe"), "*R-3.6.1-win.exe")' \
         | ../../../bin/x64/rterm.exe --vanilla --slave R_DEFAULT_PACKAGES=tools > md5sum.txt)
cp ../../../doc/html/rw-FAQ.html .	
cp release.html release.htm
sed -e s/@RWVER@/R-3.6.1/g \
  -e s/@RVER@/3.6.1/g \
  -e "s/@FULLVERSION@/`cat ../../../VERSION`/g" ../README > README.R-3.6.1
sed -e s/@RWVER@/R-3.6.1/g \
  -e s/@RVER@/3.6.1/g \
  -e "s/@FULLVERSION@/`cat ../../../VERSION`/g" ReadMe.in > ReadMe	  
echo set target=R-3.6.1 >target.cmd