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).
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
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Version: 1.6.0
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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
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StartedAt: 2014-04-05 02:47:38 -0700 (Sat, 05 Apr 2014)
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EndedAt: 2014-04-05 02:54:00 -0700 (Sat, 05 Apr 2014)
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EllapsedTime: 381.6 seconds
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RetCode: 0
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Status: OK
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CheckDir: categoryCompare.Rcheck
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Warnings: 0
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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:
name | user | system | elapsed
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GENccEnrichResult-class | 0.98 | 0.02 | 1.00 |
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HyperGParamsCC-class | 0 | 0 | 0 |
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HyperGResultCC-class | 0.02 | 0.00 | 0.02 |
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breakEdges-methods | 1.01 | 0.01 | 1.02 |
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breakEdges | 0 | 0 | 0 |
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ccCompare | 1.62 | 0.02 | 1.64 |
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ccCompareCollection-class | 0 | 0 | 0 |
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ccCompareResult-class | 0 | 0 | 0 |
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ccData | 1.12 | 0.01 | 1.14 |
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ccEnrich | 1.12 | 0.00 | 1.12 |
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ccEnrichCollection-class | 2.20 | 0.01 | 2.22 |
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ccEnrichResult-class | 5.87 | 0.04 | 5.89 |
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ccGeneList-class | 0.92 | 0.00 | 0.92 |
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ccOptions-class | 0.05 | 0.00 | 0.04 |
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ccOutCyt-methods | 0 | 0 | 0 |
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ccSigList-class | 0 | 0 | 0 |
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cytOutData-methods | 0.02 | 0.00 | 0.01 |
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cytOutNodes-methods | 0.01 | 0.00 | 0.02 |
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hyperGTestCC | 1.06 | 0.00 | 1.06 |
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mergeLists-methods | 1.01 | 0.00 | 1.02 |
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mergedData-class | 0.88 | 0.01 | 0.89 |
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minCount | 3.45 | 0.02 | 3.47 |
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minNodes | 0.01 | 0.00 | 0.01 |
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pvalueType | 4.65 | 0.01 | 4.67 |
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show-methods | 0.02 | 0.00 | 0.01 |
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categoryCompare.Rcheck/examples_x64/categoryCompare-Ex.timings:
name | user | system | elapsed
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GENccEnrichResult-class | 0.92 | 0.00 | 0.92 |
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HyperGParamsCC-class | 0 | 0 | 0 |
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HyperGResultCC-class | 0 | 0 | 0 |
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breakEdges-methods | 1.41 | 0.00 | 1.40 |
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breakEdges | 0 | 0 | 0 |
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ccCompare | 2.70 | 0.02 | 2.71 |
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ccCompareCollection-class | 0.01 | 0.00 | 0.01 |
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ccCompareResult-class | 0 | 0 | 0 |
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ccData | 0.64 | 0.00 | 0.64 |
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ccEnrich | 0.66 | 0.00 | 0.66 |
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ccEnrichCollection-class | 1.87 | 0.00 | 1.87 |
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ccEnrichResult-class | 5.76 | 0.05 | 5.80 |
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ccGeneList-class | 0.70 | 0.01 | 0.72 |
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ccOptions-class | 0.05 | 0.00 | 0.05 |
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ccOutCyt-methods | 0.01 | 0.00 | 0.01 |
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ccSigList-class | 0.02 | 0.00 | 0.02 |
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cytOutData-methods | 0.01 | 0.00 | 0.01 |
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cytOutNodes-methods | 0 | 0 | 0 |
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hyperGTestCC | 0.87 | 0.00 | 0.87 |
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mergeLists-methods | 0.84 | 0.00 | 0.84 |
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mergedData-class | 0.69 | 0.00 | 0.69 |
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minCount | 3.41 | 0.06 | 3.48 |
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minNodes | 0.05 | 0.00 | 0.04 |
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pvalueType | 3.85 | 0.04 | 3.89 |
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show-methods | 0 | 0 | 0 |
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