* checking for working latex ... OK * using log directory 'd:/Rcompile/CRANpkg/check/1.8/ape.Rcheck' * checking for file 'ape/DESCRIPTION' ... OK * checking if this is a source package ... OK ---------- Making package ape ------------ adding build stamp to DESCRIPTION making DLL ... making nprsfunc.d from nprsfunc.c making treefunc.d from treefunc.c gcc -Id:/Rcompile/recent/R-1.8.1/src/include -Wall -O2 -c nprsfunc.c -o nprsfunc.o gcc -Id:/Rcompile/recent/R-1.8.1/src/include -Wall -O2 -c treefunc.c -o treefunc.o ar cr ape.a *.o ranlib ape.a windres --include-dir d:/Rcompile/recent/R-1.8.1/src/include -i ape_res.rc -o ape_res.o gcc --shared -s -o ape.dll ape.def ape.a ape_res.o -Ld:/Rcompile/recent/R-1.8.1/src/gnuwin32 -lg2c -lR ... DLL made installing DLL installing R files installing data files installing man source files installing indices not zipping data installing help >>> Building/Updating help pages for package 'ape' Formats: text html latex example GC.content text html latex NPRS.criterion text html latex example add.scale.bar text html latex all.equal.phylo text html latex example ape-internal text html latex as.phylo text html latex example balance text html latex base.freq text html latex bind.tree text html latex example bird.families text html latex example bird.orders text html latex example birthdeath text html latex branching.times text html latex cherry text html latex chiroptera text html latex example chronogram text html latex example coalescent.intervals text html latex example collapsed.intervals text html latex example compar.gee text html latex example compar.lynch text html latex example dist.dna text html latex dist.gene text html latex dist.phylo text html latex diversi.gof text html latex diversi.time text html latex drop.tip text html latex example gammaStat text html latex heterozygosity text html latex hivtree text html latex example is.binary.tree text html latex example is.ultrametric text html latex klastorin text html latex example landplants text html latex example ltt.plot text html latex example mantel.test text html latex example mst text html latex example node.depth text html latex node.depth.edgelength text html latex opsin text html latex example pic text html latex example plot.phylo text html latex example ratogram text html latex example read.GenBank text html latex example read.dna text html latex example read.nexus text html latex read.tree text html latex example rtree text html latex example seg.sites text html latex example skyline text html latex example skylineplot text html latex example summary.phylo text html latex example theta.h text html latex theta.k text html latex theta.s text html latex example vcv.phylo text html latex woodmouse text html latex example write.dna text html latex write.nexus text html latex write.tree text html latex xenarthra text html latex example yule text html latex zoom text html latex example >>> Building/Updating help pages for package 'ape' Formats: chm GC.content chm NPRS.criterion chm add.scale.bar chm all.equal.phylo chm ape-internal chm as.phylo chm balance chm base.freq chm bind.tree chm bird.families chm bird.orders chm birthdeath chm branching.times chm cherry chm chiroptera chm chronogram chm coalescent.intervals chm collapsed.intervals chm compar.gee chm compar.lynch chm dist.dna chm dist.gene chm dist.phylo chm diversi.gof chm diversi.time chm drop.tip chm gammaStat chm heterozygosity chm hivtree chm is.binary.tree chm is.ultrametric chm klastorin chm landplants chm ltt.plot chm mantel.test chm mst chm node.depth chm node.depth.edgelength chm opsin chm pic chm plot.phylo chm ratogram chm read.GenBank chm read.dna chm read.nexus chm read.tree chm rtree chm seg.sites chm skyline chm skylineplot chm summary.phylo chm theta.h chm theta.k chm theta.s chm vcv.phylo chm woodmouse chm write.dna chm write.nexus chm write.tree chm xenarthra chm yule chm zoom chm Microsoft HTML Help Compiler 4.74.8702 Compiling d:\Rcompile\CRANpkg\check\1.8\ape\chm\ape.chm Compile time: 0 minutes, 3 seconds 63 Topics 273 Local links 27 Internet links 1 Graphic Created d:\Rcompile\CRANpkg\check\1.8\ape\chm\ape.chm, 118,557 bytes Compression decreased file by 132,335 bytes. adding MD5 sums installing R.css in d:/Rcompile/CRANpkg/check/1.8/ape.Rcheck * checking package directory ... OK * checking for portable file names ... OK * checking DESCRIPTION meta-information ... OK * checking package dependencies ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for syntax errors ... OK * checking R files for library.dynam ... OK * checking S3 generic/method consistency ... OK * checking for replacement functions with final arg not named 'value' ... OK * checking Rd files ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking for CRLF line endings in C sources/headers ... OK * creating ape-Ex.R ... OK * checking examples ... ERROR Running examples in ape-Ex.R failed.