BioC 3.5: CHECK report for SeqGSEA on oaxaca

Package: SeqGSEA

Version: 1.15.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SeqGSEA_1.15.0.tar.gz

StartedAt: 2017-03-04 08:58:08 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 09:02:57 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 288.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: SeqGSEA.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SeqGSEA_1.15.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/SeqGSEA.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SeqGSEA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SeqGSEA’ version ‘1.15.0’
* 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 for sufficient/correct file permissions ... 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
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
runSeqGSEA         16.322  0.377  27.024
scoreNormalization  9.493  0.269   9.766
normFactor          9.536  0.208   9.748
DSpermutePval       9.072  0.234   9.311
topDSGenes          8.914  0.271   9.189
DSresultExonTable   8.878  0.278   9.161
DSresultGeneTable   8.791  0.281   9.078
DSpermute4GSEA      8.679  0.271   8.957
genpermuteMat       8.459  0.258   8.720
topDSExons          8.076  0.272   8.350
loadGenesets        1.445  0.013   5.308
* 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
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/SeqGSEA.Rcheck/00check.log’
for details.

* 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
* DONE (SeqGSEA)

name	user	system	elapsed
DENBStat4GSEA	0.877	0.029	0.907
DENBStatPermut4GSEA	1.594	0.029	1.623
DENBTest	0.848	0.023	0.873
DEpermutePval	1.038	0.017	1.056
DSpermute4GSEA	8.679	0.271	8.957
DSpermutePval	9.072	0.234	9.311
DSresultExonTable	8.878	0.278	9.161
DSresultGeneTable	8.791	0.281	9.078
GSEAresultTable	2.997	0.015	3.015
GSEnrichAnalyze	2.708	0.009	2.720
ReadCountSet-class	0.002	0.000	0.002
SeqGeneSet-class	0.001	0.000	0.002
calES	0.008	0.001	0.010
calES.perm	2.489	0.007	2.498
convertEnsembl2Symbol	0.384	0.008	3.820
convertSymbol2Ensembl	0.774	0.007	4.205
counts-methods	0.018	0.001	0.018
estiExonNBstat	0.870	0.023	0.895
estiGeneNBstat	0.888	0.023	0.913
exonID	0.092	0.029	0.121
exonTestability	0.021	0.001	0.021
geneID	0.134	0.030	0.165
geneList	0.004	0.001	0.003
genePermuteScore	0.005	0.000	0.005
geneScore	0.003	0.001	0.003
geneSetDescs	0.003	0.000	0.003
geneSetNames	0.002	0.001	0.002
geneSetSize	0.002	0.000	0.002
geneTestability	0.017	0.001	0.018
genpermuteMat	8.459	0.258	8.720
getGeneCount	0.025	0.001	0.026
label	0.017	0.001	0.017
loadExonCountData	0.529	0.007	0.536
loadGenesets	1.445	0.013	5.308
newGeneSets	0.033	0.000	0.034
newReadCountSet	0.197	0.000	0.198
normFactor	9.536	0.208	9.748
plotES	2.145	0.010	2.157
plotGeneScore	0.180	0.003	0.187
plotSig	2.122	0.007	2.130
plotSigGeneSet	2.290	0.008	2.298
rankCombine	0.010	0.001	0.012
runDESeq	0.100	0.001	0.100
runSeqGSEA	16.322	0.377	27.024
scoreNormalization	9.493	0.269	9.766
size	0.002	0.000	0.003
subsetByGenes	0.070	0.001	0.070
topDEGenes	1.492	0.035	1.527
topDSExons	8.076	0.272	8.350
topDSGenes	8.914	0.271	9.189
topGeneSets	2.493	0.007	2.501
writeScores	0.009	0.001	0.009
writeSigGeneSet	2.512	0.011	2.525