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BioC 3.0: CHECK report for affycomp on moscato1

This page was generated on 2015-04-10 09:43:06 -0700 (Fri, 10 Apr 2015).

Package 15/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
affycomp 1.42.0
Rafael A. Irizarry
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/affycomp
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: affycomp
Version: 1.42.0
Command: rm -rf affycomp.buildbin-libdir affycomp.Rcheck && mkdir affycomp.buildbin-libdir affycomp.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=affycomp.buildbin-libdir affycomp_1.42.0.tar.gz >affycomp.Rcheck\00install.out 2>&1 && cp affycomp.Rcheck\00install.out affycomp-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=affycomp.buildbin-libdir --install="check:affycomp-install.out" --force-multiarch --no-vignettes --timings affycomp_1.42.0.tar.gz
StartedAt: 2015-04-09 22:20:30 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 22:21:47 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 77.1 seconds
RetCode: 0
Status:  OK  
CheckDir: affycomp.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf affycomp.buildbin-libdir affycomp.Rcheck && mkdir affycomp.buildbin-libdir affycomp.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=affycomp.buildbin-libdir affycomp_1.42.0.tar.gz >affycomp.Rcheck\00install.out 2>&1 && cp affycomp.Rcheck\00install.out affycomp-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=affycomp.buildbin-libdir --install="check:affycomp-install.out" --force-multiarch --no-vignettes --timings affycomp_1.42.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/affycomp.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'affycomp/DESCRIPTION' ... OK
* this is package 'affycomp' 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 'affycomp' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   7.0Mb
* 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 ... NOTE
'library' or 'require' call to 'splines' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'Biobase' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
affycomp.figure2b: warning in affycomp.compfig2b(list(l), method.name =
  l$method.name, add.legend = FALSE, main = main): partial argument
  match of 'method.name' to 'method.names'
affycompPlot: warning in vector(mode = "character", len = N): partial
  argument match of 'len' to 'length'
tableAll: warning in vector(mode = "character", len = N): partial
  argument match of 'len' to 'length'
tableOverallSNR: warning in vector(mode = "character", len = N):
  partial argument match of 'len' to 'length'
tableRanks: warning in vector(mode = "character", len = N): partial
  argument match of 'len' to 'length'
.onAttach: no visible global function definition for 'addVigs2WinMenu'
assessDilution: no visible global function definition for 'exprs'
assessDilution: no visible global function definition for 'pData'
assessFC: no visible global function definition for 'exprs'
assessFC: no visible global function definition for 'pData'
assessFC2: no visible global function definition for 'exprs'
assessFC2: no visible global function definition for 'pData'
assessLS: no visible global function definition for 'exprs'
assessLS: no visible global function definition for 'pData'
assessLS: no visible global function definition for 'featureNames'
assessMA: no visible global function definition for 'exprs'
assessMA: no visible global function definition for 'pData'
assessMA2: no visible global function definition for 'exprs'
assessMA2: no visible global function definition for 'pData'
assessMA2: no visible global function definition for 'featureNames'
assessSD: no visible global function definition for 'exprs'
assessSD: no visible global function definition for 'assayDataElement'
assessSD: no visible global function definition for 'pData'
assessSignal: no visible global function definition for 'exprs'
assessSignal: no visible global function definition for 'pData'
assessSignal: no visible global function definition for 'featureNames'
assessSpikeIn2: no visible global function definition for 'exprs'
assessSpikeInSD: no visible global function definition for 'pData'
assessSpikeInSD: no visible global function definition for
  'featureNames'
assessSpikeInSD: no visible global function definition for 'esApply'
exprset.log: no visible global function definition for 'exprs'
exprset.log: no visible global function definition for 'exprs<-'
read.dilution: no visible global function definition for 'sampleNames'
read.spikein: no visible global function definition for 'sampleNames'
remove.hgu133a.xhyb: no visible global function definition for
  'featureNames'
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [7s] OK
** running examples for arch 'x64' ... [5s] OK
* 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

NOTE: There were 3 notes.
See
  'D:/biocbld/bbs-3.0-bioc/meat/affycomp.Rcheck/00check.log'
for details.

affycomp.Rcheck/00install.out:


install for i386

* installing *source* package 'affycomp' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'affycomp' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'affycomp' as affycomp_1.42.0.zip
* DONE (affycomp)

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

nameusersystemelapsed
SD1.020.011.35
affycomp.compfigs.auxiliary0.750.021.85
affycomp.figures.auxiliary0.760.010.81
affycomp.table0.420.020.44
affycompPlot1.050.031.08

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

nameusersystemelapsed
SD0.790.000.80
affycomp.compfigs.auxiliary0.740.040.78
affycomp.figures.auxiliary0.610.030.76
affycomp.table0.430.000.44
affycompPlot1.230.051.28