BioC 3.4: CHECK report for SeqGSEA on malbec1

Package: SeqGSEA

Version: 1.14.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings SeqGSEA_1.14.0.tar.gz

StartedAt: 2017-04-15 01:12:51 -0400 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 01:16:51 -0400 (Sat, 15 Apr 2017)

EllapsedTime: 239.8 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: SeqGSEA.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings SeqGSEA_1.14.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/SeqGSEA.Rcheck’
* using R version 3.3.3 (2017-03-06)
* 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 ‘1.14.0’
* 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         13.272  0.012  24.633
DSresultExonTable   9.044  0.000   9.061
DSpermutePval       9.020  0.004   9.036
DSresultGeneTable   8.364  0.004   8.380
normFactor          8.220  0.000   8.226
scoreNormalization  8.104  0.000   8.109
topDSExons          7.940  0.000   7.944
topDSGenes          7.788  0.008   7.802
DSpermute4GSEA      7.440  0.000   7.446
genpermuteMat       6.952  0.012   6.972
loadGenesets        1.192  0.004   5.345
* 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-3.4-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	0.172	0.008	0.181
DENBStatPermut4GSEA	0.820	0.012	0.833
DENBTest	0.756	0.000	0.756
DEpermutePval	0.568	0.000	0.566
DSpermute4GSEA	7.440	0.000	7.446
DSpermutePval	9.020	0.004	9.036
DSresultExonTable	9.044	0.000	9.061
DSresultGeneTable	8.364	0.004	8.380
GSEAresultTable	1.576	0.012	1.589
GSEnrichAnalyze	1.780	0.012	1.792
ReadCountSet-class	0.004	0.000	0.001
SeqGeneSet-class	0.000	0.000	0.001
calES	0.008	0.000	0.006
calES.perm	1.504	0.000	1.506
convertEnsembl2Symbol	0.108	0.000	3.197
convertSymbol2Ensembl	0.092	0.004	3.001
counts-methods	0.012	0.000	0.014
estiExonNBstat	0.680	0.000	0.681
estiGeneNBstat	0.704	0.004	0.709
exonID	0.036	0.020	0.054
exonTestability	0.016	0.000	0.016
geneID	0.056	0.016	0.072
geneList	0.004	0.000	0.004
genePermuteScore	0.004	0.000	0.005
geneScore	0.004	0.000	0.004
geneSetDescs	0.004	0.000	0.002
geneSetNames	0.000	0.004	0.002
geneSetSize	0.000	0.000	0.002
geneTestability	0.02	0.00	0.02
genpermuteMat	6.952	0.012	6.972
getGeneCount	0.016	0.000	0.015
label	0.008	0.000	0.011
loadExonCountData	0.308	0.000	0.309
loadGenesets	1.192	0.004	5.345
newGeneSets	0.000	0.000	0.002
newReadCountSet	0.06	0.00	0.06
normFactor	8.220	0.000	8.226
plotES	1.684	0.008	1.695
plotGeneScore	0.08	0.00	0.08
plotSig	1.604	0.000	1.606
plotSigGeneSet	1.556	0.000	1.558
rankCombine	0.004	0.004	0.008
runDESeq	0.080	0.000	0.083
runSeqGSEA	13.272	0.012	24.633
scoreNormalization	8.104	0.000	8.109
size	0.004	0.000	0.002
subsetByGenes	0.028	0.000	0.027
topDEGenes	1.160	0.004	1.165
topDSExons	7.940	0.000	7.944
topDSGenes	7.788	0.008	7.802
topGeneSets	1.696	0.000	1.698
writeScores	0.008	0.000	0.006
writeSigGeneSet	1.688	0.000	1.690