BioC 3.3: CHECK report for SeqGSEA on zin2

Package: SeqGSEA

Version: 1.12.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings SeqGSEA_1.12.0.tar.gz

StartedAt: 2016-10-13 06:42:22 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 06:46:46 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 263.7 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: SeqGSEA.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings SeqGSEA_1.12.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-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 ‘1.12.0’
* 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         16.108  0.048  26.493
DSpermutePval      11.341  0.004  11.340
DSresultExonTable  11.283  0.000  11.285
DSresultGeneTable  11.090  0.008  11.116
scoreNormalization 11.075  0.004  11.083
topDSExons         11.008  0.004  11.030
normFactor         10.865  0.008  10.866
topDSGenes         10.559  0.004  10.568
DSpermute4GSEA     10.185  0.000  10.204
genpermuteMat       9.849  0.000   9.848
* 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-3.3-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	0.373	0.004	0.376
DENBStatPermut4GSEA	0.658	0.000	0.658
DENBTest	1.458	0.004	1.462
DEpermutePval	0.650	0.000	0.651
DSpermute4GSEA	10.185	0.000	10.204
DSpermutePval	11.341	0.004	11.340
DSresultExonTable	11.283	0.000	11.285
DSresultGeneTable	11.090	0.008	11.116
GSEAresultTable	1.877	0.016	1.892
GSEnrichAnalyze	1.852	0.000	1.854
ReadCountSet-class	0.002	0.000	0.002
SeqGeneSet-class	0.001	0.000	0.002
calES	0.004	0.000	0.007
calES.perm	1.966	0.000	1.965
convertEnsembl2Symbol	0.086	0.008	3.483
convertSymbol2Ensembl	0.078	0.005	3.405
counts-methods	0.017	0.000	0.018
estiExonNBstat	1.179	0.000	1.178
estiGeneNBstat	0.994	0.000	0.994
exonID	0.060	0.012	0.072
exonTestability	0.019	0.000	0.018
geneID	0.066	0.024	0.089
geneList	0.003	0.000	0.004
genePermuteScore	0.009	0.000	0.009
geneScore	0.004	0.000	0.003
geneSetDescs	0.002	0.000	0.003
geneSetNames	0.003	0.000	0.003
geneSetSize	0.003	0.000	0.003
geneTestability	0.024	0.000	0.024
genpermuteMat	9.849	0.000	9.848
getGeneCount	0.018	0.000	0.018
label	0.013	0.000	0.013
loadExonCountData	0.341	0.004	0.345
loadGenesets	1.057	0.012	4.579
newGeneSets	0.000	0.000	0.002
newReadCountSet	0.066	0.000	0.065
normFactor	10.865	0.008	10.866
plotES	1.939	0.004	1.946
plotGeneScore	0.095	0.000	0.095
plotSig	1.842	0.004	1.844
plotSigGeneSet	1.902	0.004	1.905
rankCombine	0.011	0.000	0.010
runDESeq	0.112	0.000	0.112
runSeqGSEA	16.108	0.048	26.493
scoreNormalization	11.075	0.004	11.083
size	0.003	0.000	0.003
subsetByGenes	0.029	0.000	0.028
topDEGenes	1.897	0.000	1.910
topDSExons	11.008	0.004	11.030
topDSGenes	10.559	0.004	10.568
topGeneSets	1.847	0.004	1.852
writeScores	0.006	0.000	0.006
writeSigGeneSet	1.815	0.000	1.816