BioC 2.14: CHECK report for SeqGSEA on moscato2

Package: SeqGSEA

Version: 1.4.2

Command: rm -rf SeqGSEA.buildbin-libdir && mkdir SeqGSEA.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SeqGSEA.buildbin-libdir SeqGSEA_1.4.2.tar.gz >SeqGSEA-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=SeqGSEA.buildbin-libdir --install="check:SeqGSEA-install.out" --force-multiarch --no-vignettes --timings SeqGSEA_1.4.2.tar.gz

StartedAt: 2014-10-08 05:03:22 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 05:16:47 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 805.3 seconds

RetCode: 0

Status: OK

CheckDir: SeqGSEA.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf SeqGSEA.buildbin-libdir && mkdir SeqGSEA.buildbin-libdir && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SeqGSEA.buildbin-libdir SeqGSEA_1.4.2.tar.gz >SeqGSEA-install.out 2>&1 && E:\biocbld\bbs-2.14-bioc\R\bin\R.exe CMD check --library=SeqGSEA.buildbin-libdir --install="check:SeqGSEA-install.out" --force-multiarch --no-vignettes --timings SeqGSEA_1.4.2.tar.gz
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* using log directory 'E:/biocbld/bbs-2.14-bioc/meat/SeqGSEA.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 'SeqGSEA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SeqGSEA' version '1.4.2'
* 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 'SeqGSEA' 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 ... NOTE
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'estiExonProbVar'
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
DENBStatPermut4GSEA: no visible binding for global variable 'i'
DSpermute4GSEA : <anonymous>: no visible binding for global variable
  'i'
calES.perm: no visible binding for global variable 'i'
calES.perm: no visible binding for global variable 'j'
* 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' ... [187s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
runSeqGSEA         21.39   0.14   28.54
DSresultGeneTable  13.30   0.00   13.29
scoreNormalization 13.28   0.00   13.27
DSpermutePval      12.74   0.00   12.74
normFactor         12.65   0.00   12.65
topDSGenes         12.56   0.00   12.56
DSresultExonTable  12.54   0.00   12.55
topDSExons         12.49   0.00   12.49
DSpermute4GSEA     11.58   0.00   11.58
genpermuteMat      11.07   0.00   11.08
** running examples for arch 'x64' ... [439s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
runSeqGSEA         23.57   0.05  265.35
normFactor         15.61   0.00   15.61
scoreNormalization 14.07   0.00   14.07
topDSGenes         13.87   0.00   13.87
topDSExons         13.62   0.00   13.62
genpermuteMat      13.54   0.00   13.55
DSpermutePval      13.27   0.00   13.28
DSresultExonTable  13.22   0.00   13.21
DSresultGeneTable  13.20   0.00   13.20
DSpermute4GSEA     11.70   0.00   11.70
* 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
  'E:/biocbld/bbs-2.14-bioc/meat/SeqGSEA.Rcheck/00check.log'
for details.


install for i386

* installing *source* package 'SeqGSEA' ...
** 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 'SeqGSEA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SeqGSEA' as SeqGSEA_1.4.2.zip
* DONE (SeqGSEA)

name	user	system	elapsed
DENBStat4GSEA	0.39	0.00	0.39
DENBStatPermut4GSEA	1.1	0.0	1.1
DENBTest	1.78	0.00	1.78
DEpermutePval	0.9	0.0	0.9
DSpermute4GSEA	11.58	0.00	11.58
DSpermutePval	12.74	0.00	12.74
DSresultExonTable	12.54	0.00	12.55
DSresultGeneTable	13.30	0.00	13.29
GSEAresultTable	2.59	0.00	2.59
GSEnrichAnalyze	2.52	0.00	2.52
ReadCountSet-class	0	0	0
SeqGeneSet-class	0	0	0
calES	0.02	0.00	0.02
calES.perm	2.47	0.02	2.49
convertEnsembl2Symbol	0.25	0.01	2.48
convertSymbol2Ensembl	0.15	0.02	2.54
counts-methods	0.04	0.00	0.03
estiExonNBstat	1.2	0.0	1.2
estiGeneNBstat	1.23	0.00	1.23
exonID	0.08	0.00	0.08
exonTestability	0.03	0.00	0.03
geneID	0.09	0.00	0.10
geneList	0	0	0
genePermuteScore	0.02	0.00	0.01
geneScore	0.01	0.00	0.02
geneSetDescs	0	0	0
geneSetNames	0.02	0.00	0.01
geneSetSize	0	0	0
geneTestability	0.05	0.00	0.05
genpermuteMat	11.07	0.00	11.08
getGeneCount	0.03	0.00	0.03
label	0.02	0.00	0.01
loadExonCountData	0.56	0.01	0.58
loadGenesets	0.97	0.00	3.49
newGeneSets	0	0	0
newReadCountSet	0.11	0.00	0.11
normFactor	12.65	0.00	12.65
plotES	2.78	0.02	2.79
plotGeneScore	0.14	0.00	0.14
plotSig	2.54	0.00	2.55
plotSigGeneSet	2.64	0.00	2.63
rankCombine	0.03	0.00	0.03
runDESeq	0.14	0.00	0.14
runSeqGSEA	21.39	0.14	28.54
scoreNormalization	13.28	0.00	13.27
size	0	0	0
subsetByGenes	0.05	0.00	0.04
topDEGenes	2.81	0.02	2.83
topDSExons	12.49	0.00	12.49
topDSGenes	12.56	0.00	12.56
topGeneSets	2.57	0.03	2.61
writeScores	0.02	0.00	0.01
writeSigGeneSet	3.54	0.01	3.56

name	user	system	elapsed
DENBStat4GSEA	0.45	0.00	0.45
DENBStatPermut4GSEA	1.22	0.00	1.21
DENBTest	1.71	0.02	1.74
DEpermutePval	1.08	0.00	1.07
DSpermute4GSEA	11.7	0.0	11.7
DSpermutePval	13.27	0.00	13.28
DSresultExonTable	13.22	0.00	13.21
DSresultGeneTable	13.2	0.0	13.2
GSEAresultTable	2.93	0.01	2.95
GSEnrichAnalyze	2.96	0.04	2.99
ReadCountSet-class	0	0	0
SeqGeneSet-class	0	0	0
calES	0.02	0.00	0.02
calES.perm	2.9	0.0	2.9
convertEnsembl2Symbol	0.28	0.04	2.48
convertSymbol2Ensembl	0.14	0.00	2.26
counts-methods	0.03	0.00	0.03
estiExonNBstat	1.59	0.00	1.59
estiGeneNBstat	1.24	0.00	1.23
exonID	0.09	0.01	0.11
exonTestability	0.01	0.02	0.03
geneID	0.07	0.01	0.08
geneList	0	0	0
genePermuteScore	0.01	0.00	0.02
geneScore	0	0	0
geneSetDescs	0.01	0.00	0.02
geneSetNames	0	0	0
geneSetSize	0	0	0
geneTestability	0.05	0.00	0.04
genpermuteMat	13.54	0.00	13.55
getGeneCount	0.06	0.00	0.06
label	0.02	0.00	0.01
loadExonCountData	0.48	0.02	0.50
loadGenesets	1.62	0.02	3.82
newGeneSets	0.02	0.00	0.02
newReadCountSet	0.14	0.00	0.14
normFactor	15.61	0.00	15.61
plotES	3.56	0.01	3.57
plotGeneScore	0.16	0.00	0.16
plotSig	3.35	0.00	3.35
plotSigGeneSet	4.07	0.02	4.09
rankCombine	0.02	0.00	0.02
runDESeq	0.17	0.00	0.17
runSeqGSEA	23.57	0.05	265.35
scoreNormalization	14.07	0.00	14.07
size	0	0	0
subsetByGenes	0.04	0.00	0.05
topDEGenes	2.72	0.00	2.71
topDSExons	13.62	0.00	13.62
topDSGenes	13.87	0.00	13.87
topGeneSets	3.15	0.02	3.17
writeScores	0.02	0.00	0.02
writeSigGeneSet	3.09	0.00	3.09

BioC 2.14: CHECK report for SeqGSEA on moscato2

Summary

Command output