* using log directory 'd:/Rcompile/CRANpkg/local/2.13/mcmc.Rcheck' * using R version 2.13.2 (2011-09-30) * using platform: i386-pc-mingw32 (32-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'mcmc/DESCRIPTION' ... OK * this is package 'mcmc' version '0.8' * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking whether package 'mcmc' can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking for portable file names ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * loading checks for arch 'i386' ** checking whether the package can be loaded ... OK ** checking whether the package can be loaded with stated dependencies ... OK ** checking whether the package can be unloaded cleanly ... OK ** checking whether the namespace can be loaded with stated dependencies ... OK ** checking whether the namespace can be unloaded cleanly ... OK * loading checks for arch 'x64' ** checking whether the package can be loaded ... OK ** checking whether the package can be loaded with stated dependencies ... OK ** checking whether the package can be unloaded cleanly ... OK ** checking whether the namespace can be loaded with stated dependencies ... OK ** checking whether the namespace can be unloaded cleanly ... OK * checking for unstated dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of 'data' directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking sizes of PDF files under inst/doc ... NOTE 'qpdf' made some significant size reductions: compacted 'demo.pdf' from 1014Kb to 280Kb consider running tools::compactPDF() on these files * checking examples ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... OK * checking for unstated dependencies in tests ... OK * checking tests ... ** running tests for arch 'i386' OK Running 'circle.R' Comparing 'circle.Rout' to 'circle.Rout.save' ... OK Running 'initseq.R' Comparing 'initseq.Rout' to 'initseq.Rout.save' ...40c40,41 < Iso 0.0-10 --- > Iso 0.0-8 > Note: This package now has a NAMESPACE. Running 'logit.R' Comparing 'logit.Rout' to 'logit.Rout.save' ...67c67 < [1] 8.235190e-06 5.499507e-06 6.082246e-06 --- > [1] 8.242296e-06 5.499507e-06 6.082246e-06 Running 'logitbat.R' Comparing 'logitbat.Rout' to 'logitbat.Rout.save' ... OK Running 'logitfun.R' Comparing 'logitfun.Rout' to 'logitfun.Rout.save' ... OK Running 'logitfunarg.R' Comparing 'logitfunarg.Rout' to 'logitfunarg.Rout.save' ... OK Running 'logitidx.R' Comparing 'logitidx.Rout' to 'logitidx.Rout.save' ... OK Running 'logitlogidx.R' Comparing 'logitlogidx.Rout' to 'logitlogidx.Rout.save' ... OK Running 'logitmat.R' Comparing 'logitmat.Rout' to 'logitmat.Rout.save' ... OK Running 'logitnegidx.R' Comparing 'logitnegidx.Rout' to 'logitnegidx.Rout.save' ... OK Running 'logitsub.R' Comparing 'logitsub.Rout' to 'logitsub.Rout.save' ... OK Running 'logitsubbat.R' Comparing 'logitsubbat.Rout' to 'logitsubbat.Rout.save' ... OK Running 'logitvec.R' Comparing 'logitvec.Rout' to 'logitvec.Rout.save' ... OK Running 'saveseed.R' Comparing 'saveseed.Rout' to 'saveseed.Rout.save' ... OK Running 'temp-par-witch.R' Comparing 'temp-par-witch.Rout' to 'temp-par-witch.Rout.save' ...50c50 < [1] 0.6516291 0.3924419 0.3464789 0.2084433 0.1928375 0.5874317 --- > [1] 0.6335878 0.4974359 0.3245383 0.6022099 0.6129870 0.5913706 54,59c54,59 < [1,] NA 0.6650943 0.4607843 NA NA NA < [2,] 0.6346154 NA 0.5396825 0.2983871 NA NA < [3,] 0.4795918 0.5714286 NA 0.4148936 0.1030928 NA < [4,] NA 0.1980198 0.3193277 NA 0.2621359 0.3137255 < [5,] NA NA 0.1870504 0.2608696 NA 0.2615385 < [6,] NA NA NA 0.3333333 0.3173653 NA --- > [1,] NA 0.7050691 0.5497382 NA NA NA > [2,] 0.7522936 NA 0.5547445 0.6287879 NA NA > [3,] 0.5794393 0.5865385 NA 0.5308642 0.5476190 NA > [4,] NA 0.6666667 0.5505618 NA 0.8271605 0.6836735 > [5,] NA NA 0.5438596 0.8925620 NA 0.8373984 > [6,] NA NA NA 0.8390805 0.9022989 NA 75c75 < [1] 0.5492308 0.4800000 0.5569231 0.7692308 0.9246154 0.7707692 --- > [1] 0.54923077 0.40923077 0.39538462 0.09692308 0.12923077 0.60000000 77c77 < [1] 0.03584574 0.05019272 0.05510132 0.04774849 0.02586413 0.05737443 --- > [1] 0.03482043 0.04817350 0.05463694 0.02855536 0.02113093 0.05130821 88,93c88,93 < [1,] 0.5033010 0.01344527 < [2,] 0.5122330 0.02468881 < [3,] 0.4968932 0.03692207 < [4,] 0.5283495 0.04713313 < [5,] 0.4582524 0.04742925 < [6,] 0.4192233 0.05931187 --- > [1,] 0.5231068 0.01389634 > [2,] 0.5361165 0.02213288 > [3,] 0.4904854 0.03961204 > [4,] 0.5652427 0.04909165 > [5,] 0.4056311 0.05106757 > [6,] 0.2450485 0.05108284 Running 'temp-par.R' Comparing 'temp-par.Rout' to 'temp-par.Rout.save' ...19c19 < -2.0371 -0.6337 0.2394 0.6685 1.9599 --- > -2.0371 -0.6337 0.2394 0.6686 1.9599 32,34c32,34 < Null deviance: 134.602 on 99 degrees of freedom < Residual deviance: 86.439 on 96 degrees of freedom < AIC: 94.439 --- > Null deviance: 134.60 on 99 degrees of freedom > Residual deviance: 86.44 on 96 degrees of freedom > AIC: 94.44 Running 'temp-ser-witch.R' Comparing 'temp-ser-witch.Rout' to 'temp-ser-witch.Rout.save' ... OK Running 'temp-ser.R' Comparing 'temp-ser.Rout' to 'temp-ser.Rout.save' ...19c19 < -2.0371 -0.6337 0.2394 0.6685 1.9599 --- > -2.0371 -0.6337 0.2394 0.6686 1.9599 32,34c32,34 < Null deviance: 134.602 on 99 degrees of freedom < Residual deviance: 86.439 on 96 degrees of freedom < AIC: 94.439 --- > Null deviance: 134.60 on 99 degrees of freedom > Residual deviance: 86.44 on 96 degrees of freedom > AIC: 94.44 ** running tests for arch 'x64' OK Running 'circle.R' Comparing 'circle.Rout' to 'circle.Rout.save' ... OK Running 'initseq.R' Comparing 'initseq.Rout' to 'initseq.Rout.save' ...40c40,41 < Iso 0.0-10 --- > Iso 0.0-8 > Note: This package now has a NAMESPACE. Running 'logit.R' Comparing 'logit.Rout' to 'logit.Rout.save' ... OK Running 'logitbat.R' Comparing 'logitbat.Rout' to 'logitbat.Rout.save' ... OK Running 'logitfun.R' Comparing 'logitfun.Rout' to 'logitfun.Rout.save' ... OK Running 'logitfunarg.R' Comparing 'logitfunarg.Rout' to 'logitfunarg.Rout.save' ... OK Running 'logitidx.R' Comparing 'logitidx.Rout' to 'logitidx.Rout.save' ... OK Running 'logitlogidx.R' Comparing 'logitlogidx.Rout' to 'logitlogidx.Rout.save' ... OK Running 'logitmat.R' Comparing 'logitmat.Rout' to 'logitmat.Rout.save' ... OK Running 'logitnegidx.R' Comparing 'logitnegidx.Rout' to 'logitnegidx.Rout.save' ... OK Running 'logitsub.R' Comparing 'logitsub.Rout' to 'logitsub.Rout.save' ... OK Running 'logitsubbat.R' Comparing 'logitsubbat.Rout' to 'logitsubbat.Rout.save' ... OK Running 'logitvec.R' Comparing 'logitvec.Rout' to 'logitvec.Rout.save' ... OK Running 'saveseed.R' Comparing 'saveseed.Rout' to 'saveseed.Rout.save' ... OK Running 'temp-par-witch.R' Comparing 'temp-par-witch.Rout' to 'temp-par-witch.Rout.save' ...50c50 < [1] 0.6118980 0.4083333 0.2890625 0.5093333 0.4365482 0.6274510 --- > [1] 0.6335878 0.4974359 0.3245383 0.6022099 0.6129870 0.5913706 54,59c54,59 < [1,] NA 0.6000000 0.4254144 NA NA NA < [2,] 0.5526316 NA 0.6153846 0.4384615 NA NA < [3,] 0.5684211 0.5051546 NA 0.4456522 0.2987013 NA < [4,] NA 0.4591837 0.4313725 NA 0.6521739 0.7604167 < [5,] NA NA 0.2268908 0.5916667 NA 0.7801418 < [6,] NA NA NA 0.7641026 0.6923077 NA --- > [1,] NA 0.7050691 0.5497382 NA NA NA > [2,] 0.7522936 NA 0.5547445 0.6287879 NA NA > [3,] 0.5794393 0.5865385 NA 0.5308642 0.5476190 NA > [4,] NA 0.6666667 0.5505618 NA 0.8271605 0.6836735 > [5,] NA NA 0.5438596 0.8925620 NA 0.8373984 > [6,] NA NA NA 0.8390805 0.9022989 NA 75c75 < [1] 0.48000000 0.49538462 0.50153846 0.67538462 0.84153846 0.03384615 --- > [1] 0.54923077 0.40923077 0.39538462 0.09692308 0.12923077 0.60000000 77c77 < [1] 0.03234281 0.04760462 0.05262073 0.04796499 0.03539826 0.02378911 --- > [1] 0.03482043 0.04817350 0.05463694 0.02855536 0.02113093 0.05130821 88,93c88,93 < [1,] 0.5106796 0.01617462 < [2,] 0.4883495 0.02681146 < [3,] 0.5188350 0.03846681 < [4,] 0.5483495 0.04520497 < [5,] 0.3899029 0.04452159 < [6,] 0.6850485 0.04735145 --- > [1,] 0.5231068 0.01389634 > [2,] 0.5361165 0.02213288 > [3,] 0.4904854 0.03961204 > [4,] 0.5652427 0.04909165 > [5,] 0.4056311 0.05106757 > [6,] 0.2450485 0.05108284 Running 'temp-par.R' Comparing 'temp-par.Rout' to 'temp-par.Rout.save' ...19c19 < -2.0371 -0.6337 0.2394 0.6685 1.9599 --- > -2.0371 -0.6337 0.2394 0.6686 1.9599 32,34c32,34 < Null deviance: 134.602 on 99 degrees of freedom < Residual deviance: 86.439 on 96 degrees of freedom < AIC: 94.439 --- > Null deviance: 134.60 on 99 degrees of freedom > Residual deviance: 86.44 on 96 degrees of freedom > AIC: 94.44 Running 'temp-ser-witch.R' Comparing 'temp-ser-witch.Rout' to 'temp-ser-witch.Rout.save' ...51c51 < [1] 0.6012526 0.4306220 0.4153005 0.4578005 0.5673981 0.6214286 --- > [1] 0.6388889 0.4385246 0.3631714 0.4885246 0.4709677 0.4735516 55,60c55,60 < [1,] NA 0.4600760 0.2480315 NA NA NA < [2,] 0.6965517 NA 0.5673759 0.5538462 NA NA < [3,] 0.7592593 0.6976744 NA 0.5752212 0.6145833 NA < [4,] NA 0.8202247 0.7848101 NA 0.7816092 0.7567568 < [5,] NA NA 0.6853933 0.6034483 NA 0.8878505 < [6,] NA NA NA 0.5839416 0.6780822 NA --- > [1,] NA 0.5071770 0.2727273 NA NA NA > [2,] 0.7070064 NA 0.4355828 0.4186047 NA NA > [3,] 0.5816327 0.8039216 NA 0.5888889 0.5662651 NA > [4,] NA 0.7415730 0.8571429 NA 0.7857143 0.6626506 > [5,] NA NA 0.5204082 0.6516854 NA 0.8378378 > [6,] NA NA NA 0.3515152 0.5056818 NA 63c63 < [1] 0.2261538 0.1861538 0.1615385 0.1676923 0.1384615 0.1200000 --- > [1] 0.1830769 0.2153846 0.1630769 0.1369231 0.1353846 0.1661538 89c89 < [1] 0.07631068 0.06776699 0.07592233 0.07281553 0.13281553 0.14466019 --- > [1] 0.06660194 0.06388350 0.05766990 0.06563107 0.10368932 0.22912621 91c91 < [1] 0.1433010 0.1415534 0.1499029 0.1466019 0.2013592 0.2172816 --- > [1] 0.1365049 0.1258252 0.1293204 0.1370874 0.1716505 0.2996117 93c93 < [1] 0.5325203 0.4787380 0.5064767 0.4966887 0.6595950 0.6657730 --- > [1] 0.4879090 0.5077160 0.4459459 0.4787535 0.6040724 0.7647440 101c101 < [1] 0.03773086 0.05495142 0.09243929 0.11012287 0.08575721 0.11489579 --- > [1] 0.05010927 0.07897321 0.09678339 0.12636113 0.11261781 0.07082685 107,112c107,112 < [1,] 0.5325203 0.02009245 < [2,] 0.4787380 0.02630733 < [3,] 0.5064767 0.04681835 < [4,] 0.4966887 0.05469679 < [5,] 0.6595950 0.05656503 < [6,] 0.6657730 0.07649451 --- > [1,] 0.4879090 0.02444876 > [2,] 0.5077160 0.04009596 > [3,] 0.4459459 0.04316016 > [4,] 0.4787535 0.06049584 > [5,] 0.6040724 0.06802931 > [6,] 0.7647440 0.05416441 Running 'temp-ser.R' Comparing 'temp-ser.Rout' to 'temp-ser.Rout.save' ...19c19 < -2.0371 -0.6337 0.2394 0.6685 1.9599 --- > -2.0371 -0.6337 0.2394 0.6686 1.9599 32,34c32,34 < Null deviance: 134.602 on 99 degrees of freedom < Residual deviance: 86.439 on 96 degrees of freedom < AIC: 94.439 --- > Null deviance: 134.60 on 99 degrees of freedom > Residual deviance: 86.44 on 96 degrees of freedom > AIC: 94.44 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignettes ... SKIPPED * checking PDF version of manual ... OK * using check arguments '--no-vignettes'