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: 2017-10-18 02:25:34 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 02:29:40 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 246.0 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 3.4.2 (2017-09-28)
* 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         12.388  0.016  23.764
topDSGenes          8.752  0.000   8.757
scoreNormalization  8.276  0.008   8.289
normFactor          8.204  0.008   8.218
DSpermutePval       8.096  0.004   8.104
DSresultExonTable   7.688  0.012   7.708
DSresultGeneTable   7.624  0.004   7.632
topDSExons          7.188  0.008   7.199
genpermuteMat       7.164  0.004   7.178
DSpermute4GSEA      6.876  0.008   6.891
* 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	0.688	0.016	0.704
DENBStatPermut4GSEA	0.884	0.012	0.895
DENBTest	0.788	0.000	0.786
DEpermutePval	1.016	0.004	1.020
DSpermute4GSEA	6.876	0.008	6.891
DSpermutePval	8.096	0.004	8.104
DSresultExonTable	7.688	0.012	7.708
DSresultGeneTable	7.624	0.004	7.632
GSEAresultTable	1.652	0.012	1.665
GSEnrichAnalyze	1.748	0.000	1.747
ReadCountSet-class	0.000	0.000	0.001
SeqGeneSet-class	0.004	0.000	0.001
calES	0.004	0.000	0.006
calES.perm	1.636	0.000	1.638
convertEnsembl2Symbol	0.384	0.012	3.659
convertSymbol2Ensembl	0.656	0.000	3.815
counts-methods	0.016	0.000	0.019
estiExonNBstat	0.748	0.000	0.749
estiGeneNBstat	0.720	0.000	0.719
exonID	0.060	0.032	0.095
exonTestability	0.024	0.000	0.029
geneID	0.100	0.024	0.123
geneList	0.000	0.004	0.006
genePermuteScore	0.008	0.000	0.007
geneScore	0.004	0.000	0.004
geneSetDescs	0.004	0.000	0.003
geneSetNames	0.000	0.000	0.003
geneSetSize	0.004	0.000	0.003
geneTestability	0.032	0.000	0.033
genpermuteMat	7.164	0.004	7.178
getGeneCount	0.012	0.000	0.015
label	0.008	0.000	0.011
loadExonCountData	0.320	0.000	0.321
loadGenesets	1.272	0.004	4.812
newGeneSets	0.040	0.000	0.041
newReadCountSet	0.232	0.000	0.231
normFactor	8.204	0.008	8.218
plotES	1.800	0.000	1.801
plotGeneScore	0.144	0.000	0.146
plotSig	1.740	0.000	1.742
plotSigGeneSet	1.680	0.004	1.684
rankCombine	0.004	0.004	0.008
runDESeq	0.092	0.000	0.090
runSeqGSEA	12.388	0.016	23.764
scoreNormalization	8.276	0.008	8.289
size	0.004	0.000	0.003
subsetByGenes	0.068	0.000	0.070
topDEGenes	1.300	0.004	1.306
topDSExons	7.188	0.008	7.199
topDSGenes	8.752	0.000	8.757
topGeneSets	2.564	0.000	2.565
writeScores	0.004	0.000	0.006
writeSigGeneSet	1.776	0.000	1.780