BioC 3.4: CHECK report for SeqGSEA on morelia

Package: SeqGSEA

Version: 1.14.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SeqGSEA_1.14.0.tar.gz

StartedAt: 2017-04-15 07:57:56 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 08:02:48 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 292.4 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_1.14.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/SeqGSEA.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.14.0’
* 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         16.323  0.363  29.081
DSpermutePval       9.617  0.126   9.754
normFactor          9.391  0.171   9.573
topDSExons          9.341  0.208   9.559
DSresultExonTable   9.213  0.082   9.304
DSresultGeneTable   9.058  0.095   9.170
genpermuteMat       8.711  0.212   8.931
scoreNormalization  8.697  0.221   8.927
DSpermute4GSEA      8.479  0.181   8.666
topDSGenes          7.812  0.167   7.982
loadGenesets        1.370  0.013   5.240
* 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-3.4-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	0.203	0.005	0.208
DENBStatPermut4GSEA	1.062	0.021	1.083
DENBTest	0.807	0.023	0.831
DEpermutePval	0.879	0.014	0.893
DSpermute4GSEA	8.479	0.181	8.666
DSpermutePval	9.617	0.126	9.754
DSresultExonTable	9.213	0.082	9.304
DSresultGeneTable	9.058	0.095	9.170
GSEAresultTable	2.042	0.011	2.055
GSEnrichAnalyze	2.429	0.005	2.436
ReadCountSet-class	0.002	0.000	0.002
SeqGeneSet-class	0.001	0.001	0.002
calES	0.008	0.001	0.010
calES.perm	2.052	0.004	2.058
convertEnsembl2Symbol	0.643	0.010	4.523
convertSymbol2Ensembl	0.104	0.009	4.625
counts-methods	0.013	0.001	0.013
estiExonNBstat	0.868	0.006	0.873
estiGeneNBstat	0.819	0.012	0.833
exonID	0.127	0.038	0.166
exonTestability	0.032	0.001	0.033
geneID	0.166	0.036	0.203
geneList	0.006	0.000	0.007
genePermuteScore	0.007	0.000	0.008
geneScore	0.004	0.000	0.004
geneSetDescs	0.003	0.001	0.004
geneSetNames	0.003	0.001	0.004
geneSetSize	0.004	0.000	0.005
geneTestability	0.029	0.000	0.029
genpermuteMat	8.711	0.212	8.931
getGeneCount	0.019	0.001	0.020
label	0.015	0.000	0.015
loadExonCountData	0.552	0.012	0.564
loadGenesets	1.370	0.013	5.240
newGeneSets	0.003	0.000	0.003
newReadCountSet	0.082	0.001	0.083
normFactor	9.391	0.171	9.573
plotES	2.429	0.011	2.442
plotGeneScore	0.114	0.003	0.126
plotSig	2.445	0.006	2.456
plotSigGeneSet	2.606	0.007	2.618
rankCombine	0.011	0.001	0.013
runDESeq	0.122	0.000	0.124
runSeqGSEA	16.323	0.363	29.081
scoreNormalization	8.697	0.221	8.927
size	0.003	0.000	0.004
subsetByGenes	0.032	0.000	0.033
topDEGenes	1.331	0.016	1.349
topDSExons	9.341	0.208	9.559
topDSGenes	7.812	0.167	7.982
topGeneSets	1.544	0.002	1.546
writeScores	0.006	0.001	0.007
writeSigGeneSet	1.544	0.003	1.712