BioC 3.5: CHECK report for SeqGSEA on veracruz2

Package: SeqGSEA

Version: 1.16.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SeqGSEA_1.16.0.tar.gz

StartedAt: 2017-10-18 08:56:40 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 09:01:30 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 289.4 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_1.16.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/SeqGSEA.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.16.0’
* 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 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         15.227  0.167  26.677
DSpermute4GSEA      9.252  0.143   9.649
scoreNormalization  8.847  0.070   9.187
DSresultExonTable   8.692  0.063   9.013
normFactor          8.609  0.061   8.926
DSpermutePval       8.479  0.054   8.765
topDSGenes          8.276  0.051   8.581
DSresultGeneTable   8.201  0.051   8.496
topDSExons          8.072  0.067   8.376
genpermuteMat       7.743  0.045   8.002
* 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-3.5-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	0.844	0.040	0.915
DENBStatPermut4GSEA	1.227	0.019	1.278
DENBTest	0.842	0.019	0.880
DEpermutePval	0.922	0.008	0.953
DSpermute4GSEA	9.252	0.143	9.649
DSpermutePval	8.479	0.054	8.765
DSresultExonTable	8.692	0.063	9.013
DSresultGeneTable	8.201	0.051	8.496
GSEAresultTable	1.971	0.016	2.064
GSEnrichAnalyze	2.337	0.013	2.410
ReadCountSet-class	0.002	0.000	0.002
SeqGeneSet-class	0.001	0.001	0.002
calES	0.006	0.001	0.008
calES.perm	2.154	0.010	2.223
convertEnsembl2Symbol	0.312	0.007	3.688
convertSymbol2Ensembl	0.620	0.008	3.453
counts-methods	0.012	0.001	0.013
estiExonNBstat	0.758	0.014	0.780
estiGeneNBstat	0.731	0.006	0.755
exonID	0.112	0.042	0.157
exonTestability	0.021	0.001	0.022
geneID	0.154	0.038	0.201
geneList	0.003	0.000	0.004
genePermuteScore	0.004	0.001	0.005
geneScore	0.004	0.001	0.005
geneSetDescs	0.003	0.000	0.004
geneSetNames	0.002	0.001	0.002
geneSetSize	0.003	0.000	0.003
geneTestability	0.024	0.001	0.025
genpermuteMat	7.743	0.045	8.002
getGeneCount	0.023	0.001	0.024
label	0.014	0.001	0.016
loadExonCountData	0.508	0.007	0.528
loadGenesets	1.104	0.010	4.014
newGeneSets	0.031	0.001	0.032
newReadCountSet	0.177	0.001	0.181
normFactor	8.609	0.061	8.926
plotES	2.382	0.018	2.479
plotGeneScore	0.155	0.003	0.168
plotSig	2.239	0.013	2.321
plotSigGeneSet	2.162	0.014	2.238
rankCombine	0.008	0.001	0.010
runDESeq	0.100	0.002	0.106
runSeqGSEA	15.227	0.167	26.677
scoreNormalization	8.847	0.070	9.187
size	0.003	0.000	0.003
subsetByGenes	0.081	0.001	0.083
topDEGenes	1.477	0.027	1.547
topDSExons	8.072	0.067	8.376
topDSGenes	8.276	0.051	8.581
topGeneSets	2.256	0.014	2.352
writeScores	0.007	0.001	0.009
writeSigGeneSet	2.230	0.012	2.307