BioC 2.13: CHECK report for SeqGSEA on moscato1

Package: SeqGSEA

Version: 1.2.1

Command: rm -rf SeqGSEA.buildbin-libdir && mkdir SeqGSEA.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SeqGSEA.buildbin-libdir SeqGSEA_1.2.1.tar.gz >SeqGSEA-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=SeqGSEA.buildbin-libdir --install="check:SeqGSEA-install.out" --force-multiarch --no-vignettes --timings SeqGSEA_1.2.1.tar.gz && mv SeqGSEA.buildbin-libdir/* SeqGSEA.Rcheck/ && rmdir SeqGSEA.buildbin-libdir

StartedAt: 2014-04-05 06:41:50 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 06:55:53 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 842.9 seconds

RetCode: 0

Status:  OK

CheckDir: SeqGSEA.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/SeqGSEA.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 'SeqGSEA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SeqGSEA' version '1.2.1'
* 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
* 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 ... 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 for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
  'SeqGSEA.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [311s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
runSeqGSEA         37.36   0.07   46.93
DSresultGeneTable  25.88   0.00   25.88
topDSGenes         25.07   0.00   25.07
topDSExons         24.08   0.00   24.09
DSresultExonTable  23.30   0.00   23.29
DSpermutePval      22.05   0.00   22.06
scoreNormalization 22.00   0.02   22.01
normFactor         21.34   0.00   21.34
genpermuteMat      21.23   0.00   21.24
DSpermute4GSEA     20.02   0.00   20.01
loadGenesets        2.20   0.01    5.20
** running examples for arch 'x64' ... [346s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
runSeqGSEA         39.07   0.08   48.36
topDSGenes         28.07   0.00   28.06
topDSExons         27.62   0.00   27.61
DSresultGeneTable  27.60   0.00   27.59
DSpermutePval      27.19   0.00   27.19
DSresultExonTable  26.72   0.00   26.72
scoreNormalization 26.00   0.00   26.00
DSpermute4GSEA     24.92   0.00   24.92
normFactor         24.06   0.00   24.05
genpermuteMat      22.99   0.00   22.99
loadGenesets        2.31   0.02    5.35
* 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 3 notes.
See
  'D:/biocbld/bbs-2.13-bioc/meat/SeqGSEA.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'SeqGSEA' ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import by 'DESeq::plotDispEsts' when loading 'SeqGSEA'
Warning: replacing previous import by 'DESeq::plotMA' when loading 'SeqGSEA'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import by 'DESeq::plotDispEsts' when loading 'SeqGSEA'
Warning: replacing previous import by 'DESeq::plotMA' when loading 'SeqGSEA'

install for x64

* installing *source* package 'SeqGSEA' ...
** testing if installed package can be loaded
Warning: replacing previous import by 'DESeq::plotDispEsts' when loading 'SeqGSEA'
Warning: replacing previous import by 'DESeq::plotMA' when loading 'SeqGSEA'
* MD5 sums
packaged installation of 'SeqGSEA' as SeqGSEA_1.2.1.zip
* DONE (SeqGSEA)

name	user	system	elapsed
DENBStat4GSEA	0.43	0.02	0.46
DENBStatPermut4GSEA	1.32	0.00	1.31
DENBTest	1.74	0.01	1.76
DEpermutePval	1.12	0.00	1.12
DSpermute4GSEA	20.02	0.00	20.01
DSpermutePval	22.05	0.00	22.06
DSresultExonTable	23.30	0.00	23.29
DSresultGeneTable	25.88	0.00	25.88
GSEAresultTable	2.85	0.02	2.87
GSEnrichAnalyze	3.46	0.01	3.48
ReadCountSet-class	0	0	0
SeqGeneSet-class	0	0	0
calES	0.04	0.00	0.03
calES.perm	2.89	0.00	2.89
convertEnsembl2Symbol	0.47	0.05	3.50
convertSymbol2Ensembl	0.37	0.00	3.29
counts-methods	0.01	0.00	0.02
estiExonNBstat	2.23	0.00	2.23
estiGeneNBstat	2.45	0.00	2.45
exonID	0.09	0.00	0.09
exonTestability	0.16	0.00	0.16
geneID	0.04	0.03	0.08
geneList	0	0	0
genePermuteScore	0.01	0.02	0.04
geneScore	0.00	0.01	0.01
geneSetDescs	0	0	0
geneSetNames	0	0	0
geneSetSize	0.02	0.00	0.01
geneTestability	0.03	0.02	0.05
genpermuteMat	21.23	0.00	21.24
getGeneCount	0.05	0.00	0.04
label	0.01	0.00	0.01
loadExonCountData	0.52	0.00	0.52
loadGenesets	2.20	0.01	5.20
newGeneSets	0.02	0.00	0.01
newReadCountSet	0.11	0.00	0.11
normFactor	21.34	0.00	21.34
plotES	3.57	0.04	3.61
plotGeneScore	0.14	0.01	0.15
plotSig	3.01	0.00	3.01
plotSigGeneSet	3.04	0.00	3.04
rankCombine	0.03	0.02	0.05
runDESeq	0.3	0.0	0.3
runSeqGSEA	37.36	0.07	46.93
scoreNormalization	22.00	0.02	22.01
size	0	0	0
subsetByGenes	0.06	0.00	0.06
topDEGenes	2.80	0.00	2.79
topDSExons	24.08	0.00	24.09
topDSGenes	25.07	0.00	25.07
topGeneSets	4.9	0.0	4.9
writeScores	0.04	0.00	0.05
writeSigGeneSet	3.36	0.03	3.38

name	user	system	elapsed
DENBStat4GSEA	0.47	0.01	0.48
DENBStatPermut4GSEA	1.48	0.02	1.50
DENBTest	2.04	0.01	2.06
DEpermutePval	1.17	0.00	1.17
DSpermute4GSEA	24.92	0.00	24.92
DSpermutePval	27.19	0.00	27.19
DSresultExonTable	26.72	0.00	26.72
DSresultGeneTable	27.60	0.00	27.59
GSEAresultTable	3.33	0.00	3.34
GSEnrichAnalyze	3.42	0.00	3.42
ReadCountSet-class	0	0	0
SeqGeneSet-class	0.01	0.00	0.02
calES	0.02	0.02	0.03
calES.perm	4.02	0.00	4.03
convertEnsembl2Symbol	0.46	0.08	3.55
convertSymbol2Ensembl	0.21	0.00	3.37
counts-methods	0.01	0.00	0.02
estiExonNBstat	2.28	0.00	2.28
estiGeneNBstat	2.57	0.00	2.58
exonID	0.06	0.02	0.07
exonTestability	0.05	0.00	0.05
geneID	0.06	0.01	0.08
geneList	0	0	0
genePermuteScore	0.02	0.00	0.02
geneScore	0.19	0.00	0.18
geneSetDescs	0	0	0
geneSetNames	0.02	0.00	0.01
geneSetSize	0.00	0.02	0.02
geneTestability	0.05	0.00	0.05
genpermuteMat	22.99	0.00	22.99
getGeneCount	0.03	0.01	0.05
label	0.02	0.00	0.01
loadExonCountData	0.61	0.02	0.62
loadGenesets	2.31	0.02	5.35
newGeneSets	0	0	0
newReadCountSet	0.13	0.00	0.12
normFactor	24.06	0.00	24.05
plotES	3.80	0.01	3.82
plotGeneScore	0.18	0.00	0.18
plotSig	3.82	0.00	3.82
plotSigGeneSet	3.61	0.00	3.61
rankCombine	0.02	0.03	0.05
runDESeq	0.29	0.00	0.30
runSeqGSEA	39.07	0.08	48.36
scoreNormalization	26	0	26
size	0.01	0.00	0.01
subsetByGenes	0.1	0.0	0.1
topDEGenes	3.01	0.00	3.01
topDSExons	27.62	0.00	27.61
topDSGenes	28.07	0.00	28.06
topGeneSets	3.41	0.02	3.44
writeScores	0.01	0.00	0.02
writeSigGeneSet	3.73	0.00	3.73