BioC 3.6: CHECK report for SeqGSEA on malbec1

Package: SeqGSEA

Version: 1.17.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings SeqGSEA_1.17.0.tar.gz

StartedAt: 2017-08-16 02:21:05 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 02:24:57 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 232.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: SeqGSEA.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings SeqGSEA_1.17.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-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 ‘1.17.0’
* 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         12.172  0.028  21.730
normFactor          7.608  0.004   7.617
scoreNormalization  7.480  0.004   7.488
DSresultGeneTable   7.368  0.008   7.381
DSresultExonTable   7.288  0.004   7.293
DSpermutePval       7.284  0.000   7.289
topDSGenes          7.188  0.012   7.203
topDSExons          7.080  0.008   7.093
genpermuteMat       6.852  0.000   6.855
DSpermute4GSEA      6.480  0.004   6.487
* 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-3.6-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	0.652	0.020	0.669
DENBStatPermut4GSEA	1.212	0.000	1.214
DENBTest	0.780	0.000	0.782
DEpermutePval	1.036	0.008	1.043
DSpermute4GSEA	6.480	0.004	6.487
DSpermutePval	7.284	0.000	7.289
DSresultExonTable	7.288	0.004	7.293
DSresultGeneTable	7.368	0.008	7.381
GSEAresultTable	1.624	0.004	1.627
GSEnrichAnalyze	1.744	0.000	1.743
ReadCountSet-class	0.000	0.000	0.002
SeqGeneSet-class	0.004	0.000	0.001
calES	0.004	0.000	0.006
calES.perm	1.616	0.004	1.619
convertEnsembl2Symbol	0.332	0.004	3.948
convertSymbol2Ensembl	0.520	0.000	3.698
counts-methods	0.012	0.000	0.012
estiExonNBstat	0.632	0.008	0.642
estiGeneNBstat	0.660	0.004	0.665
exonID	0.036	0.020	0.057
exonTestability	0.016	0.000	0.016
geneID	0.068	0.004	0.075
geneList	0.004	0.000	0.004
genePermuteScore	0.004	0.000	0.006
geneScore	0.000	0.000	0.003
geneSetDescs	0.000	0.000	0.002
geneSetNames	0.004	0.000	0.002
geneSetSize	0.004	0.000	0.002
geneTestability	0.020	0.000	0.019
genpermuteMat	6.852	0.000	6.855
getGeneCount	0.016	0.000	0.017
label	0.012	0.000	0.012
loadExonCountData	0.332	0.004	0.339
loadGenesets	0.964	0.000	4.651
newGeneSets	0.032	0.000	0.029
newReadCountSet	0.124	0.000	0.124
normFactor	7.608	0.004	7.617
plotES	1.772	0.000	1.772
plotGeneScore	0.124	0.000	0.124
plotSig	1.632	0.000	1.633
plotSigGeneSet	1.652	0.000	1.653
rankCombine	0.008	0.000	0.008
runDESeq	0.084	0.000	0.081
runSeqGSEA	12.172	0.028	21.730
scoreNormalization	7.480	0.004	7.488
size	0.000	0.000	0.002
subsetByGenes	0.060	0.000	0.063
topDEGenes	1.172	0.012	1.186
topDSExons	7.080	0.008	7.093
topDSGenes	7.188	0.012	7.203
topGeneSets	1.620	0.000	1.622
writeScores	0.008	0.000	0.005
writeSigGeneSet	1.648	0.000	1.649