BioC 3.6: CHECK report for SeqGSEA on veracruz1

Package: SeqGSEA

Version: 1.17.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SeqGSEA_1.17.0.tar.gz

StartedAt: 2017-08-16 08:26:44 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 08:31:19 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 275.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: SeqGSEA.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SeqGSEA_1.17.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/SeqGSEA.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (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 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            14.617  0.212  28.433
normFactor             8.478  0.102   8.874
DSresultGeneTable      8.383  0.099   8.789
DSresultExonTable      8.271  0.120   8.642
DSpermutePval          8.290  0.088   8.609
scoreNormalization     8.014  0.143   8.447
topDSExons             8.019  0.110   8.383
genpermuteMat          7.809  0.086   8.135
DSpermute4GSEA         7.372  0.133   7.733
topDSGenes             6.614  0.157   6.977
loadGenesets           1.073  0.010   5.080
convertSymbol2Ensembl  0.546  0.007   5.155
* 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
  ‘/Users/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	0.693	0.024	0.732
DENBStatPermut4GSEA	1.399	0.019	1.456
DENBTest	0.771	0.022	0.801
DEpermutePval	0.868	0.019	0.908
DSpermute4GSEA	7.372	0.133	7.733
DSpermutePval	8.290	0.088	8.609
DSresultExonTable	8.271	0.120	8.642
DSresultGeneTable	8.383	0.099	8.789
GSEAresultTable	2.133	0.004	2.213
GSEnrichAnalyze	2.258	0.004	2.348
ReadCountSet-class	0.002	0.000	0.002
SeqGeneSet-class	0.002	0.001	0.002
calES	0.007	0.001	0.008
calES.perm	2.102	0.004	2.167
convertEnsembl2Symbol	0.306	0.007	4.538
convertSymbol2Ensembl	0.546	0.007	5.155
counts-methods	0.015	0.001	0.016
estiExonNBstat	0.750	0.015	0.777
estiGeneNBstat	0.726	0.023	0.778
exonID	0.109	0.039	0.151
exonTestability	0.018	0.001	0.020
geneID	0.157	0.041	0.206
geneList	0.004	0.000	0.005
genePermuteScore	0.006	0.001	0.007
geneScore	0.004	0.001	0.005
geneSetDescs	0.003	0.001	0.004
geneSetNames	0.003	0.000	0.004
geneSetSize	0.002	0.001	0.003
geneTestability	0.025	0.001	0.035
genpermuteMat	7.809	0.086	8.135
getGeneCount	0.024	0.000	0.025
label	0.015	0.001	0.016
loadExonCountData	0.505	0.006	0.517
loadGenesets	1.073	0.010	5.080
newGeneSets	0.037	0.000	0.038
newReadCountSet	0.161	0.000	0.165
normFactor	8.478	0.102	8.874
plotES	2.247	0.010	2.337
plotGeneScore	0.149	0.003	0.154
plotSig	2.122	0.004	2.218
plotSigGeneSet	2.189	0.005	2.251
rankCombine	0.010	0.002	0.016
runDESeq	0.107	0.001	0.109
runSeqGSEA	14.617	0.212	28.433
scoreNormalization	8.014	0.143	8.447
size	0.002	0.000	0.003
subsetByGenes	0.067	0.000	0.077
topDEGenes	1.415	0.023	1.465
topDSExons	8.019	0.110	8.383
topDSGenes	6.614	0.157	6.977
topGeneSets	2.067	0.006	2.159
writeScores	0.008	0.001	0.008
writeSigGeneSet	1.768	0.004	1.804