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BioC 2.13: CHECK report for categoryCompare on moscato1

This page was generated on 2014-04-05 09:50:50 -0700 (Sat, 05 Apr 2014).

Package 113/750HostnameOS / ArchBUILDCHECKBUILD BIN
categoryCompare 1.6.0
Robert M. Flight
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/categoryCompare
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: categoryCompare
Version: 1.6.0
Command: rm -rf categoryCompare.buildbin-libdir && mkdir categoryCompare.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=categoryCompare.buildbin-libdir categoryCompare_1.6.0.tar.gz >categoryCompare-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=categoryCompare.buildbin-libdir --install="check:categoryCompare-install.out" --force-multiarch --no-vignettes --timings categoryCompare_1.6.0.tar.gz && mv categoryCompare.buildbin-libdir/* categoryCompare.Rcheck/ && rmdir categoryCompare.buildbin-libdir
StartedAt: 2014-04-05 02:47:38 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 02:54:00 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 381.6 seconds
RetCode: 0
Status:  OK  
CheckDir: categoryCompare.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/categoryCompare.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'categoryCompare/DESCRIPTION' ... OK
* this is package 'categoryCompare' version '1.6.0'
* 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 'categoryCompare' 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 ... OK
* 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 ... NOTE
  Note: the specification for S3 class "AsIs" in package 'XMLRPC' seems equivalent to one from package 'BiocGenerics': not turning on duplicate class definitions for this class.
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
  'categoryCompare_vignette.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [37s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
ccEnrichResult-class 5.87   0.04    5.89
** running examples for arch 'x64' ... [37s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
ccEnrichResult-class 5.76   0.05     5.8
* 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

NOTE: There were 2 notes.
See
  'D:/biocbld/bbs-2.13-bioc/meat/categoryCompare.Rcheck/00check.log'
for details.

categoryCompare.Rcheck/00install.out:


install for i386

* installing *source* package 'categoryCompare' ...
** R
** data
** inst
** preparing package for lazy loading
Note: the specification for S3 class "AsIs" in package 'XMLRPC' seems equivalent to one from package 'BiocGenerics': not turning on duplicate class definitions for this class.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Note: the specification for S3 class "AsIs" in package 'XMLRPC' seems equivalent to one from package 'BiocGenerics': not turning on duplicate class definitions for this class.

install for x64

* installing *source* package 'categoryCompare' ...
** testing if installed package can be loaded
Note: the specification for S3 class "AsIs" in package 'XMLRPC' seems equivalent to one from package 'BiocGenerics': not turning on duplicate class definitions for this class.
* MD5 sums
packaged installation of 'categoryCompare' as categoryCompare_1.6.0.zip
* DONE (categoryCompare)

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

nameusersystemelapsed
GENccEnrichResult-class0.980.021.00
HyperGParamsCC-class000
HyperGResultCC-class0.020.000.02
breakEdges-methods1.010.011.02
breakEdges000
ccCompare1.620.021.64
ccCompareCollection-class000
ccCompareResult-class000
ccData1.120.011.14
ccEnrich1.120.001.12
ccEnrichCollection-class2.200.012.22
ccEnrichResult-class5.870.045.89
ccGeneList-class0.920.000.92
ccOptions-class0.050.000.04
ccOutCyt-methods000
ccSigList-class000
cytOutData-methods0.020.000.01
cytOutNodes-methods0.010.000.02
hyperGTestCC1.060.001.06
mergeLists-methods1.010.001.02
mergedData-class0.880.010.89
minCount3.450.023.47
minNodes0.010.000.01
pvalueType4.650.014.67
show-methods0.020.000.01

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

nameusersystemelapsed
GENccEnrichResult-class0.920.000.92
HyperGParamsCC-class000
HyperGResultCC-class000
breakEdges-methods1.410.001.40
breakEdges000
ccCompare2.700.022.71
ccCompareCollection-class0.010.000.01
ccCompareResult-class000
ccData0.640.000.64
ccEnrich0.660.000.66
ccEnrichCollection-class1.870.001.87
ccEnrichResult-class5.760.055.80
ccGeneList-class0.700.010.72
ccOptions-class0.050.000.05
ccOutCyt-methods0.010.000.01
ccSigList-class0.020.000.02
cytOutData-methods0.010.000.01
cytOutNodes-methods000
hyperGTestCC0.870.000.87
mergeLists-methods0.840.000.84
mergedData-class0.690.000.69
minCount3.410.063.48
minNodes0.050.000.04
pvalueType3.850.043.89
show-methods000