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BioC 3.2: CHECK report for affycoretools on moscato1

This page was generated on 2016-04-23 10:15:50 -0700 (Sat, 23 Apr 2016).

Package 20/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
affycoretools 1.42.0
James W. MacDonald
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/affycoretools
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: affycoretools
Version: 1.42.0
Command: rm -rf affycoretools.buildbin-libdir affycoretools.Rcheck && mkdir affycoretools.buildbin-libdir affycoretools.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=affycoretools.buildbin-libdir affycoretools_1.42.0.tar.gz >affycoretools.Rcheck\00install.out 2>&1 && cp affycoretools.Rcheck\00install.out affycoretools-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=affycoretools.buildbin-libdir --install="check:affycoretools-install.out" --force-multiarch --no-vignettes --timings affycoretools_1.42.0.tar.gz
StartedAt: 2016-04-22 23:21:02 -0700 (Fri, 22 Apr 2016)
EndedAt: 2016-04-22 23:32:10 -0700 (Fri, 22 Apr 2016)
EllapsedTime: 668.4 seconds
RetCode: 0
Status:  OK  
CheckDir: affycoretools.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf affycoretools.buildbin-libdir affycoretools.Rcheck && mkdir affycoretools.buildbin-libdir affycoretools.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=affycoretools.buildbin-libdir affycoretools_1.42.0.tar.gz >affycoretools.Rcheck\00install.out 2>&1 && cp affycoretools.Rcheck\00install.out affycoretools-install.out  && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=affycoretools.buildbin-libdir --install="check:affycoretools-install.out" --force-multiarch --no-vignettes --timings affycoretools_1.42.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/affycoretools.Rcheck'
* using R version 3.2.4 (2016-03-10)
* 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 '1.42.0'
* 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' ... [28s] OK
Examples with CPU or elapsed time > 5s
        user system elapsed
plotDeg 6.37   0.03     6.4
** running examples for arch 'x64' ... [28s] OK
Examples with CPU or elapsed time > 5s
        user system elapsed
plotDeg 7.65   0.04   11.48
* 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
  'D:/biocbld/bbs-3.2-bioc/meat/affycoretools.Rcheck/00check.log'
for details.


affycoretools.Rcheck/00install.out:


install for i386

* installing *source* package 'affycoretools' ...
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'ggbio'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'ggbio'

install for x64

* installing *source* package 'affycoretools' ...
** testing if installed package can be loaded
Warning: replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'ggbio'
* MD5 sums
packaged installation of 'affycoretools' as affycoretools_1.42.0.zip
* DONE (affycoretools)

affycoretools.Rcheck/examples_i386/affycoretools-Ex.timings:

nameusersystemelapsed
entrezLinks000
makeVenn000
plotDeg6.370.036.40
plotPCA0.050.001.53
vennCounts20.050.001.81
vennPage000

affycoretools.Rcheck/examples_x64/affycoretools-Ex.timings:

nameusersystemelapsed
entrezLinks000
makeVenn000
plotDeg 7.65 0.0411.48
plotPCA0.070.020.08
vennCounts20.040.000.04
vennPage000