BioC 3.3: CHECK report for SeqGSEA on moscato2

Package: SeqGSEA

Version: 1.12.0

Command: rm -rf SeqGSEA.buildbin-libdir SeqGSEA.Rcheck && mkdir SeqGSEA.buildbin-libdir SeqGSEA.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SeqGSEA.buildbin-libdir SeqGSEA_1.12.0.tar.gz >SeqGSEA.Rcheck\00install.out 2>&1 && cp SeqGSEA.Rcheck\00install.out SeqGSEA-install.out && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=SeqGSEA.buildbin-libdir --install="check:SeqGSEA-install.out" --force-multiarch --no-vignettes --timings SeqGSEA_1.12.0.tar.gz

StartedAt: 2016-10-13 08:48:39 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 08:59:46 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 667.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: SeqGSEA.Rcheck

Warnings: 1

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### Running command:
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###   rm -rf SeqGSEA.buildbin-libdir SeqGSEA.Rcheck && mkdir SeqGSEA.buildbin-libdir SeqGSEA.Rcheck && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=SeqGSEA.buildbin-libdir SeqGSEA_1.12.0.tar.gz >SeqGSEA.Rcheck\00install.out 2>&1 && cp SeqGSEA.Rcheck\00install.out SeqGSEA-install.out  && E:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=SeqGSEA.buildbin-libdir --install="check:SeqGSEA-install.out" --force-multiarch --no-vignettes --timings SeqGSEA_1.12.0.tar.gz
###
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* using log directory 'E:/biocbld/bbs-3.3-bioc/meat/SeqGSEA.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-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 '1.12.0'
* 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 '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'
* 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 global function definition for
  '%dopar%'
DENBStatPermut4GSEA: no visible global function definition for
  'foreach'
DENBStatPermut4GSEA: no visible binding for global variable 'i'
DENBTest: no visible global function definition for 'p.adjust'
DEpermutePval: no visible global function definition for 'p.adjust'
DSpermute4GSEA: no visible global function definition for '%dopar%'
DSpermute4GSEA: no visible global function definition for 'foreach'
DSpermute4GSEA : <anonymous>: no visible binding for global variable
  'i'
DSpermutePval: no visible global function definition for 'p.adjust'
calES.perm: no visible global function definition for '%dopar%'
calES.perm: no visible global function definition for 'foreach'
calES.perm: no visible binding for global variable 'i'
calES.perm: no visible global function definition for '%do%'
calES.perm: no visible binding for global variable 'j'
loadExonCountData : <anonymous>: no visible global function definition
  for 'read.table'
plotES : <anonymous>: no visible global function definition for
  'density'
plotES: no visible global function definition for 'density'
plotES: no visible global function definition for 'plot'
plotES : <anonymous>: no visible global function definition for
  'points'
plotES: no visible global function definition for 'points'
plotES: no visible global function definition for 'colors'
plotES: no visible global function definition for 'lines'
plotES: no visible global function definition for 'legend'
plotES: no visible global function definition for 'dev.off'
plotGeneScore: no visible global function definition for 'plot'
plotGeneScore: no visible global function definition for 'lines'
plotGeneScore: no visible global function definition for 'colors'
plotGeneScore: no visible global function definition for 'points'
plotGeneScore: no visible global function definition for 'matlines'
plotGeneScore: no visible global function definition for 'legend'
plotGeneScore: no visible global function definition for 'dev.off'
plotSig: no visible global function definition for 'plot'
plotSig: no visible global function definition for 'points'
plotSig: no visible global function definition for 'colors'
plotSig: no visible global function definition for 'legend'
plotSig: no visible global function definition for 'dev.off'
plotSigGeneSet: no visible global function definition for 'par'
plotSigGeneSet: no visible global function definition for 'layout'
plotSigGeneSet: no visible global function definition for 'plot'
plotSigGeneSet: no visible global function definition for 'lines'
plotSigGeneSet : <anonymous>: no visible global function definition for
  'lines'
plotSigGeneSet: no visible global function definition for 'colors'
plotSigGeneSet: no visible global function definition for 'text'
plotSigGeneSet: no visible global function definition for 'density'
plotSigGeneSet: no visible global function definition for 'legend'
plotSigGeneSet: no visible global function definition for 'dev.off'
runSeqGSEA: no visible global function definition for 'makeCluster'
runSeqGSEA: no visible global function definition for 'write.table'
signifES : <anonymous>: no visible global function definition for
  'median'
writeScores: no visible global function definition for 'write.table'
writeSigGeneSet: no visible global function definition for
  'write.table'
Undefined global functions or variables:
  %do% %dopar% colors density dev.off foreach i j layout legend lines
  makeCluster matlines median p.adjust par plot points read.table text
  write.table
Consider adding
  importFrom("grDevices", "colors", "dev.off")
  importFrom("graphics", "layout", "legend", "lines", "matlines", "par",
             "plot", "points", "text")
  importFrom("stats", "density", "median", "p.adjust")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'SeqGeneSet,numeric,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
runSeqGSEA         19.22   0.07   31.09
topDSGenes         16.55   0.00   16.56
scoreNormalization 16.08   0.00   16.08
topDSExons         15.24   0.00   15.24
DSresultGeneTable  15.16   0.00   15.16
DSpermute4GSEA     14.50   0.00   14.51
normFactor         14.32   0.00   14.32
DSpermutePval      14.12   0.00   14.13
genpermuteMat      13.45   0.02   13.47
DSresultExonTable  13.06   0.00   13.06
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
runSeqGSEA         23.11   0.12   35.59
scoreNormalization 16.50   0.00   16.50
DSresultGeneTable  15.64   0.00   15.64
topDSExons         15.19   0.02   15.21
DSresultExonTable  15.17   0.00   15.18
normFactor         15.08   0.00   15.08
topDSGenes         14.74   0.00   14.74
DSpermutePval      14.44   0.01   14.46
DSpermute4GSEA     14.14   0.02   14.15
genpermuteMat      12.99   0.00   13.00
* 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
* DONE

Status: 1 WARNING, 2 NOTEs
See
  'E:/biocbld/bbs-3.3-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_1.12.0.zip
* DONE (SeqGSEA)

name	user	system	elapsed
DENBStat4GSEA	0.52	0.00	0.52
DENBStatPermut4GSEA	1.10	0.00	1.11
DENBTest	2.05	0.00	2.04
DEpermutePval	0.78	0.00	0.78
DSpermute4GSEA	14.50	0.00	14.51
DSpermutePval	14.12	0.00	14.13
DSresultExonTable	13.06	0.00	13.06
DSresultGeneTable	15.16	0.00	15.16
GSEAresultTable	2.05	0.04	2.08
GSEnrichAnalyze	3.15	0.00	3.15
ReadCountSet-class	0	0	0
SeqGeneSet-class	0	0	0
calES	0.00	0.01	0.01
calES.perm	3.01	0.00	3.02
convertEnsembl2Symbol	0.47	0.08	4.04
convertSymbol2Ensembl	0.20	0.00	3.85
counts-methods	0.03	0.00	0.03
estiExonNBstat	1.34	0.00	1.34
estiGeneNBstat	1.66	0.00	1.66
exonID	0.06	0.01	0.07
exonTestability	0.03	0.00	0.03
geneID	0.14	0.00	0.15
geneList	0.02	0.00	0.01
genePermuteScore	0.01	0.00	0.02
geneScore	0	0	0
geneSetDescs	0.02	0.00	0.01
geneSetNames	0	0	0
geneSetSize	0.01	0.00	0.02
geneTestability	0.05	0.00	0.04
genpermuteMat	13.45	0.02	13.47
getGeneCount	0.03	0.00	0.03
label	0.01	0.00	0.01
loadExonCountData	0.44	0.00	0.44
loadGenesets	1.37	0.00	4.95
newGeneSets	0	0	0
newReadCountSet	0.11	0.00	0.11
normFactor	14.32	0.00	14.32
plotES	2.48	0.00	2.48
plotGeneScore	0.20	0.00	0.21
plotSig	2.15	0.00	2.15
plotSigGeneSet	2.27	0.02	2.28
rankCombine	0.01	0.00	0.01
runDESeq	0.17	0.00	0.17
runSeqGSEA	19.22	0.07	31.09
scoreNormalization	16.08	0.00	16.08
size	0	0	0
subsetByGenes	0.06	0.00	0.06
topDEGenes	2.76	0.00	2.76
topDSExons	15.24	0.00	15.24
topDSGenes	16.55	0.00	16.56
topGeneSets	2.67	0.02	2.68
writeScores	0.02	0.00	0.01
writeSigGeneSet	2.82	0.00	2.83

name	user	system	elapsed
DENBStat4GSEA	0.46	0.00	0.45
DENBStatPermut4GSEA	0.84	0.00	0.84
DENBTest	1.53	0.00	1.53
DEpermutePval	1.21	0.00	1.22
DSpermute4GSEA	14.14	0.02	14.15
DSpermutePval	14.44	0.01	14.46
DSresultExonTable	15.17	0.00	15.18
DSresultGeneTable	15.64	0.00	15.64
GSEAresultTable	2.51	0.04	2.54
GSEnrichAnalyze	2.72	0.00	2.72
ReadCountSet-class	0.01	0.00	0.01
SeqGeneSet-class	0	0	0
calES	0.02	0.00	0.02
calES.perm	2.61	0.00	2.61
convertEnsembl2Symbol	0.59	0.07	4.41
convertSymbol2Ensembl	0.12	0.00	3.62
counts-methods	0.03	0.00	0.03
estiExonNBstat	1.69	0.00	1.69
estiGeneNBstat	1.42	0.00	1.42
exonID	0.05	0.03	0.07
exonTestability	0.00	0.02	0.02
geneID	0.07	0.00	0.08
geneList	0.02	0.00	0.01
genePermuteScore	0	0	0
geneScore	0.01	0.00	0.02
geneSetDescs	0	0	0
geneSetNames	0	0	0
geneSetSize	0	0	0
geneTestability	0.04	0.00	0.03
genpermuteMat	12.99	0.00	13.00
getGeneCount	0.01	0.00	0.02
label	0.02	0.00	0.01
loadExonCountData	0.59	0.02	0.61
loadGenesets	1.05	0.00	4.91
newGeneSets	0	0	0
newReadCountSet	0.09	0.00	0.10
normFactor	15.08	0.00	15.08
plotES	2.73	0.01	2.75
plotGeneScore	0.11	0.02	0.12
plotSig	2.56	0.00	2.56
plotSigGeneSet	3.35	0.00	3.35
rankCombine	0.02	0.00	0.02
runDESeq	0.12	0.00	0.12
runSeqGSEA	23.11	0.12	35.59
scoreNormalization	16.5	0.0	16.5
size	0	0	0
subsetByGenes	0.04	0.00	0.04
topDEGenes	2.86	0.00	2.86
topDSExons	15.19	0.02	15.21
topDSGenes	14.74	0.00	14.74
topGeneSets	3.97	0.01	3.98
writeScores	0.01	0.00	0.02
writeSigGeneSet	3.43	0.00	3.43