BioC 3.4: CHECK report for SeqGSEA on zin1

Package: SeqGSEA

Version: 1.13.0

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings SeqGSEA_1.13.0.tar.gz

StartedAt: 2016-09-20 12:26:59 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 12:31:41 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 282.2 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_1.13.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/SeqGSEA.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.13.0’
* 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         20.300  0.040  24.449
DSpermutePval      15.372  0.000  15.372
normFactor         15.312  0.008  15.322
DSresultExonTable  15.216  0.020  15.237
scoreNormalization 15.076  0.000  15.074
DSresultGeneTable  14.928  0.000  14.929
topDSExons         14.924  0.004  14.929
topDSGenes         14.676  0.004  14.688
DSpermute4GSEA     13.920  0.012  13.930
genpermuteMat      13.536  0.008  13.543
* 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	0.364	0.000	0.366
DENBStatPermut4GSEA	0.632	0.000	0.635
DENBTest	1.836	0.000	1.838
DEpermutePval	0.664	0.000	0.662
DSpermute4GSEA	13.920	0.012	13.930
DSpermutePval	15.372	0.000	15.372
DSresultExonTable	15.216	0.020	15.237
DSresultGeneTable	14.928	0.000	14.929
GSEAresultTable	1.720	0.016	1.736
GSEnrichAnalyze	1.708	0.000	1.707
ReadCountSet-class	0.004	0.000	0.001
SeqGeneSet-class	0.000	0.000	0.001
calES	0.008	0.000	0.007
calES.perm	1.700	0.000	1.697
convertEnsembl2Symbol	0.084	0.004	1.393
convertSymbol2Ensembl	0.072	0.008	1.178
counts-methods	0.012	0.000	0.012
estiExonNBstat	1.532	0.000	1.529
estiGeneNBstat	1.348	0.000	1.348
exonID	0.048	0.020	0.069
exonTestability	0.016	0.000	0.018
geneID	0.064	0.024	0.087
geneList	0.004	0.000	0.003
genePermuteScore	0.008	0.000	0.008
geneScore	0.000	0.000	0.003
geneSetDescs	0.000	0.000	0.003
geneSetNames	0.004	0.000	0.002
geneSetSize	0.004	0.000	0.002
geneTestability	0.020	0.000	0.021
genpermuteMat	13.536	0.008	13.543
getGeneCount	0.020	0.000	0.018
label	0.012	0.000	0.012
loadExonCountData	0.324	0.000	0.324
loadGenesets	0.856	0.000	2.191
newGeneSets	0.000	0.000	0.002
newReadCountSet	0.080	0.000	0.076
normFactor	15.312	0.008	15.322
plotES	1.812	0.004	1.816
plotGeneScore	0.088	0.000	0.089
plotSig	1.684	0.000	1.682
plotSigGeneSet	1.712	0.004	1.717
rankCombine	0.008	0.000	0.009
runDESeq	0.104	0.000	0.106
runSeqGSEA	20.300	0.040	24.449
scoreNormalization	15.076	0.000	15.074
size	0.004	0.000	0.002
subsetByGenes	0.028	0.000	0.030
topDEGenes	2.344	0.000	2.346
topDSExons	14.924	0.004	14.929
topDSGenes	14.676	0.004	14.688
topGeneSets	1.632	0.000	1.630
writeScores	0.008	0.000	0.007
writeSigGeneSet	1.616	0.004	1.620