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BioC 2.14: CHECK report for categoryCompare on moscato2

This page was generated on 2014-10-08 08:54:42 -0700 (Wed, 08 Oct 2014).

Package 122/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
categoryCompare 1.8.0
Robert M. Flight
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/categoryCompare
Last Changed Rev: 88838 / Revision: 95116
Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  ERROR  skipped 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ OK ] OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: categoryCompare
Version: 1.8.0
Command: rm -rf categoryCompare.buildbin-libdir && mkdir categoryCompare.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=categoryCompare.buildbin-libdir categoryCompare_1.8.0.tar.gz >categoryCompare-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=categoryCompare.buildbin-libdir --install="check:categoryCompare-install.out" --force-multiarch --no-vignettes --timings categoryCompare_1.8.0.tar.gz
StartedAt: 2014-10-07 23:26:36 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 23:32:10 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 333.9 seconds
RetCode: 0
Status:  OK  
CheckDir: categoryCompare.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf categoryCompare.buildbin-libdir && mkdir categoryCompare.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=categoryCompare.buildbin-libdir categoryCompare_1.8.0.tar.gz >categoryCompare-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=categoryCompare.buildbin-libdir --install="check:categoryCompare-install.out" --force-multiarch --no-vignettes --timings categoryCompare_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-2.14-bioc/meat/categoryCompare.Rcheck'
* using R version 3.1.1 (2014-07-10)
* 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 '1.8.0'
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [31s] OK
** running examples for arch 'x64' ... [33s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
ccEnrichResult-class 5.36   0.07    5.45
* 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 was 1 note.
See
  'E:/biocbld/bbs-2.14-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_1.8.0.zip
* DONE (categoryCompare)

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

nameusersystemelapsed
GENccEnrichResult-class0.730.010.75
HyperGParamsCC-class000
HyperGResultCC-class000
breakEdges-methods1.430.021.45
breakEdges000
ccCompare1.060.001.06
ccCompareCollection-class000
ccCompareResult-class000
ccData0.750.000.75
ccEnrich0.760.000.76
ccEnrichCollection-class2.700.012.72
ccEnrichResult-class4.620.074.68
ccGeneList-class0.810.010.83
ccOptions-class0.030.000.03
ccOutCyt-methods000
ccSigList-class000
cytOutData-methods0.020.000.01
cytOutNodes-methods000
hyperGTestCC1.040.001.05
mergeLists-methods1.000.031.03
mergedData-class0.890.000.89
minCount3.310.003.33
minNodes000
pvalueType2.890.052.94
show-methods000

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

nameusersystemelapsed
GENccEnrichResult-class0.890.000.88
HyperGParamsCC-class000
HyperGResultCC-class000
breakEdges-methods0.940.040.98
breakEdges000
ccCompare0.890.000.89
ccCompareCollection-class000
ccCompareResult-class000
ccData0.590.050.64
ccEnrich0.640.000.64
ccEnrichCollection-class3.330.053.37
ccEnrichResult-class5.360.075.45
ccGeneList-class1.450.031.48
ccOptions-class0.030.000.03
ccOutCyt-methods000
ccSigList-class000
cytOutData-methods000
cytOutNodes-methods000
hyperGTestCC0.890.060.96
mergeLists-methods0.800.020.82
mergedData-class0.810.000.81
minCount3.630.013.65
minNodes000
pvalueType2.610.022.62
show-methods000