BioC 3.5: CHECK report for SeqGSEA on malbec2

Package: SeqGSEA

Version: 1.16.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings SeqGSEA_1.16.0.tar.gz

StartedAt: 2017-08-16 02:12:46 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 02:16:52 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 246.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: SeqGSEA.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings SeqGSEA_1.16.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/SeqGSEA.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (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 ‘1.16.0’
* 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 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            12.464  0.020  22.366
DSpermutePval          8.596  0.000   8.604
normFactor             7.948  0.004   7.962
DSresultExonTable      7.908  0.000   7.910
scoreNormalization     7.680  0.000   7.681
DSpermute4GSEA         7.348  0.000   7.349
topDSGenes             7.248  0.008   7.261
DSresultGeneTable      7.036  0.004   7.044
topDSExons             7.008  0.000   7.011
genpermuteMat          6.812  0.000   6.812
convertSymbol2Ensembl  0.500  0.008  14.019
* 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
  ‘/home/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	0.796	0.024	0.821
DENBStatPermut4GSEA	1.188	0.000	1.193
DENBTest	0.832	0.000	0.833
DEpermutePval	0.928	0.008	0.937
DSpermute4GSEA	7.348	0.000	7.349
DSpermutePval	8.596	0.000	8.604
DSresultExonTable	7.908	0.000	7.910
DSresultGeneTable	7.036	0.004	7.044
GSEAresultTable	1.840	0.012	1.849
GSEnrichAnalyze	1.956	0.000	1.956
ReadCountSet-class	0.000	0.000	0.003
SeqGeneSet-class	0.000	0.000	0.002
calES	0.008	0.000	0.009
calES.perm	1.776	0.000	1.780
convertEnsembl2Symbol	0.324	0.016	4.685
convertSymbol2Ensembl	0.500	0.008	14.019
counts-methods	0.012	0.000	0.012
estiExonNBstat	0.916	0.008	0.924
estiGeneNBstat	0.652	0.004	0.655
exonID	0.040	0.016	0.056
exonTestability	0.020	0.000	0.021
geneID	0.060	0.008	0.070
geneList	0.000	0.000	0.004
genePermuteScore	0.004	0.000	0.005
geneScore	0.004	0.000	0.003
geneSetDescs	0.004	0.000	0.002
geneSetNames	0.004	0.000	0.002
geneSetSize	0.000	0.000	0.002
geneTestability	0.020	0.000	0.019
genpermuteMat	6.812	0.000	6.812
getGeneCount	0.016	0.000	0.015
label	0.012	0.000	0.012
loadExonCountData	0.316	0.004	0.322
loadGenesets	1.232	0.008	4.530
newGeneSets	0.048	0.000	0.051
newReadCountSet	0.212	0.000	0.213
normFactor	7.948	0.004	7.962
plotES	1.820	0.000	1.822
plotGeneScore	0.124	0.000	0.124
plotSig	1.716	0.000	1.717
plotSigGeneSet	1.660	0.000	1.661
rankCombine	0.008	0.000	0.007
runDESeq	0.088	0.004	0.093
runSeqGSEA	12.464	0.020	22.366
scoreNormalization	7.680	0.000	7.681
size	0.000	0.000	0.002
subsetByGenes	0.064	0.000	0.066
topDEGenes	1.260	0.004	1.262
topDSExons	7.008	0.000	7.011
topDSGenes	7.248	0.008	7.261
topGeneSets	1.644	0.000	1.644
writeScores	0.000	0.004	0.005
writeSigGeneSet	1.672	0.000	1.675