BioC 3.1: CHECK report for affycoretools on moscato2

Package: affycoretools

Version: 1.40.5

Command: rm -rf affycoretools.buildbin-libdir affycoretools.Rcheck && mkdir affycoretools.buildbin-libdir affycoretools.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=affycoretools.buildbin-libdir affycoretools_1.40.5.tar.gz >affycoretools.Rcheck\00install.out 2>&1 && cp affycoretools.Rcheck\00install.out affycoretools-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=affycoretools.buildbin-libdir --install="check:affycoretools-install.out" --force-multiarch --no-vignettes --timings affycoretools_1.40.5.tar.gz

StartedAt: 2015-10-08 23:08:47 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-08 23:16:43 -0700 (Thu, 08 Oct 2015)

EllapsedTime: 475.4 seconds

RetCode: 0

Status:  OK

CheckDir: affycoretools.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf affycoretools.buildbin-libdir affycoretools.Rcheck && mkdir affycoretools.buildbin-libdir affycoretools.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=affycoretools.buildbin-libdir affycoretools_1.40.5.tar.gz >affycoretools.Rcheck\00install.out 2>&1 && cp affycoretools.Rcheck\00install.out affycoretools-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=affycoretools.buildbin-libdir --install="check:affycoretools-install.out" --force-multiarch --no-vignettes --timings affycoretools_1.40.5.tar.gz
###
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* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/affycoretools.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'affycoretools/DESCRIPTION' ... OK
* this is package 'affycoretools' version '1.40.5'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'affycoretools' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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 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 ... NOTE
makeGenePlots: no visible global function definition for 'cpm'
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [20s] OK
Examples with CPU or elapsed time > 5s
        user system elapsed
plotDeg 5.37   0.02    5.38
** running examples for arch 'x64' ... [24s] OK
Examples with CPU or elapsed time > 5s
        user system elapsed
plotDeg 6.88   0.08    6.96
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  'E:/biocbld/bbs-3.1-bioc/meat/affycoretools.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'affycoretools' ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'

install for x64

* installing *source* package 'affycoretools' ...
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* MD5 sums
packaged installation of 'affycoretools' as affycoretools_1.40.5.zip
* DONE (affycoretools)

name	user	system	elapsed
entrezLinks	0	0	0
makeVenn	0	0	0
plotDeg	5.37	0.02	5.38
plotPCA	0.03	0.00	0.14
vennCounts2	0.08	0.00	0.08
vennPage	0	0	0

name	user	system	elapsed
entrezLinks	0	0	0
makeVenn	0	0	0
plotDeg	6.88	0.08	6.96
plotPCA	0.02	0.01	0.04
vennCounts2	0.06	0.00	0.06
vennPage	0	0	0