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BioC 2.12: CHECK report for cummeRbund on moscato2

This page was generated on 2013-10-09 09:39:01 -0700 (Wed, 09 Oct 2013).

Package 160/671HostnameOS / ArchBUILDCHECKBUILD BIN
cummeRbund 2.2.0
Loyal A. Goff
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/cummeRbund
Last Changed Rev: 75263 / Revision: 81334
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ OK ] OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: cummeRbund
Version: 2.2.0
Command: rm -rf cummeRbund.buildbin-libdir && mkdir cummeRbund.buildbin-libdir && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=cummeRbund.buildbin-libdir cummeRbund_2.2.0.tar.gz >cummeRbund-install.out 2>&1 && E:\biocbld\bbs-2.12-bioc\R\bin\R.exe CMD check --library=cummeRbund.buildbin-libdir --install="check:cummeRbund-install.out" --force-multiarch --no-vignettes --timings cummeRbund_2.2.0.tar.gz && mv cummeRbund.buildbin-libdir/* cummeRbund.Rcheck/ && rmdir cummeRbund.buildbin-libdir
StartedAt: 2013-10-09 01:45:00 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 01:52:08 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 427.4 seconds
RetCode: 0
Status:  OK  
CheckDir: cummeRbund.Rcheck
Warnings: 0

Command output

* using log directory 'E:/biocbld/bbs-2.12-bioc/meat/cummeRbund.Rcheck'
* using R version 3.0.1 (2013-05-16)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'cummeRbund/DESCRIPTION' ... OK
* this is package 'cummeRbund' version '2.2.0'
* 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 ... NOTE
Found the following hidden files and directories:
  inst/extdata/.RData
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'cummeRbund' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc       2.5Mb
    extdata   5.6Mb
* checking package 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 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 ... NOTE
.CVdensity: no visible binding for global variable 'CV'
.CVdensity: no visible binding for global variable 'sample_name'
.MAplot: no visible binding for global variable 'A'
.MAplot: no visible binding for global variable 'M'
.MDSplot: no visible binding for global variable 'M1'
.MDSplot: no visible binding for global variable 'M2'
.PCAplot: no visible binding for global variable 'obsnames'
.PCAplot: no visible binding for global variable 'v1'
.PCAplot: no visible binding for global variable 'v2'
.PCAplot: no visible binding for global variable 'varnames'
.barplot: no visible binding for global variable 'sample_name'
.barplot: no visible binding for global variable 'conf_lo'
.barplot: no visible binding for global variable 'conf_hi'
.barplot: no visible binding for global variable 'quant_status'
.boxplot: no visible binding for global variable 'condition'
.confidencePlot: no visible binding for global variable 'CV'
.confidencePlot: no visible binding for global variable 'sample_name'
.density: no visible binding for global variable 'condition'
.dispersionPlot: no visible binding for global variable 'dispersion'
.dispersionPlot: no visible binding for global variable 'sample_name'
.distheat: no visible binding for global variable 'X1'
.distheat: no visible binding for global variable 'X2'
.distheat: no visible binding for global variable 'value'
.expressionPlot: no visible binding for global variable 'sample_name'
.expressionPlot: no visible binding for global variable 'tracking_id'
.expressionPlot: no visible binding for global variable 'conf_lo'
.expressionPlot: no visible binding for global variable 'conf_hi'
.expressionPlot: no visible binding for global variable 'quant_status'
.fpkmSCVPlot: no visible binding for global variable 'stdev'
.fpkmSCVPlot: no visible binding for global variable 'sample_name'
.ggheat: no visible binding for global variable 'colInd'
.ggheat: no visible binding for global variable 'rowInd'
.ggheat: no visible binding for global variable 'value'
.heatmap: no visible binding for global variable 'tracking_id'
.heatmap: no visible binding for global variable 'sample_name'
.plotmatrix: no visible binding for global variable 'x'
.plotmatrix: no visible binding for global variable 'y'
.plotmatrix: no visible binding for global variable '..scaled..'
.sigMatrix: no visible binding for global variable 'sample_1'
.sigMatrix: no visible binding for global variable 'sample_2'
.sigMatrix: no visible binding for global variable '..n..'
.volcano: no visible binding for global variable 'log2_fold_change'
.volcano: no visible binding for global variable 'p_value'
.volcano: no visible binding for global variable 'significant'
.volcanoMatrix: no visible binding for global variable 'label'
csClusterPlot: no visible binding for global variable 'variable'
csClusterPlot: no visible binding for global variable 'value'
csClusterPlot: no visible binding for global variable 'cluster'
csClusterPlot: no visible binding for global variable 'ids'
PCAplot,CuffData: no visible binding for global variable 'obsnames'
PCAplot,CuffData: no visible binding for global variable 'v1'
PCAplot,CuffData: no visible binding for global variable 'v2'
PCAplot,CuffData: no visible binding for global variable 'varnames'
csDistHeat,CuffData: no visible binding for global variable 'X1'
csDistHeat,CuffData: no visible binding for global variable 'X2'
csDistHeat,CuffData: no visible binding for global variable 'value'
csDistHeat,CuffFeatureSet: no visible binding for global variable 'X1'
csDistHeat,CuffFeatureSet: no visible binding for global variable 'X2'
csDistHeat,CuffFeatureSet: no visible binding for global variable
  'value'
dispersionPlot,CuffData: no visible binding for global variable
  'dispersion'
dispersionPlot,CuffData: no visible binding for global variable
  'sample_name'
sigMatrix,CuffSet: no visible binding for global variable 'sample_1'
sigMatrix,CuffSet: no visible binding for global variable 'sample_2'
sigMatrix,CuffSet: no visible binding for global variable '..n..'
* 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 examples ...
** running examples for arch 'i386' ... [36s] OK
** running examples for arch 'x64' ... [32s] 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 3 notes.
See
  'E:/biocbld/bbs-2.12-bioc/meat/cummeRbund.Rcheck/00check.log'
for details.

cummeRbund.Rcheck/00install.out:


install for i386

* installing *source* package 'cummeRbund' ...
** 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 'cummeRbund' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'cummeRbund' as cummeRbund_2.2.0.zip
* DONE (cummeRbund)