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: 2017-08-16 08:07:40 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 08:12:31 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 291.3 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 3.4.1 (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 ‘1.16.0’
* 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            13.939  0.164  31.186
DSpermutePval          8.618  0.056   8.902
scoreNormalization     8.559  0.099   8.958
DSresultExonTable      8.393  0.078   8.709
topDSGenes             8.162  0.144   8.559
normFactor             8.195  0.093   8.521
topDSExons             8.046  0.111   8.415
DSresultGeneTable      7.811  0.087   8.092
DSpermute4GSEA         7.776  0.085   8.138
genpermuteMat          7.759  0.077   8.069
loadGenesets           1.090  0.009   6.004
convertEnsembl2Symbol  0.296  0.007   6.653
* 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	0.749	0.033	0.803
DENBStatPermut4GSEA	1.460	0.022	1.505
DENBTest	0.757	0.021	0.800
DEpermutePval	0.889	0.014	0.939
DSpermute4GSEA	7.776	0.085	8.138
DSpermutePval	8.618	0.056	8.902
DSresultExonTable	8.393	0.078	8.709
DSresultGeneTable	7.811	0.087	8.092
GSEAresultTable	2.276	0.007	2.345
GSEnrichAnalyze	2.232	0.004	2.334
ReadCountSet-class	0.002	0.000	0.003
SeqGeneSet-class	0.002	0.000	0.002
calES	0.007	0.001	0.010
calES.perm	2.144	0.005	2.188
convertEnsembl2Symbol	0.296	0.007	6.653
convertSymbol2Ensembl	0.626	0.012	4.917
counts-methods	0.016	0.001	0.017
estiExonNBstat	0.757	0.013	0.797
estiGeneNBstat	0.793	0.015	0.815
exonID	0.116	0.038	0.160
exonTestability	0.022	0.001	0.023
geneID	0.146	0.034	0.186
geneList	0.003	0.000	0.004
genePermuteScore	0.006	0.001	0.007
geneScore	0.004	0.000	0.005
geneSetDescs	0.003	0.000	0.004
geneSetNames	0.003	0.001	0.004
geneSetSize	0.001	0.000	0.002
geneTestability	0.026	0.001	0.028
genpermuteMat	7.759	0.077	8.069
getGeneCount	0.023	0.000	0.024
label	0.011	0.001	0.011
loadExonCountData	0.518	0.006	0.535
loadGenesets	1.090	0.009	6.004
newGeneSets	0.033	0.000	0.033
newReadCountSet	0.155	0.001	0.169
normFactor	8.195	0.093	8.521
plotES	2.078	0.010	2.138
plotGeneScore	0.149	0.002	0.165
plotSig	2.023	0.005	2.097
plotSigGeneSet	1.847	0.005	1.908
rankCombine	0.007	0.001	0.009
runDESeq	0.090	0.001	0.101
runSeqGSEA	13.939	0.164	31.186
scoreNormalization	8.559	0.099	8.958
size	0.002	0.001	0.003
subsetByGenes	0.092	0.001	0.093
topDEGenes	1.442	0.029	1.486
topDSExons	8.046	0.111	8.415
topDSGenes	8.162	0.144	8.559
topGeneSets	2.134	0.008	2.210
writeScores	0.006	0.000	0.007
writeSigGeneSet	2.190	0.006	2.270