BioC 3.4: CHECK report for SeqGSEA on morelia

Package: SeqGSEA

Version: 1.13.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SeqGSEA_1.13.0.tar.gz

StartedAt: 2016-09-20 12:57:41 -0700 (Tue, 20 Sep 2016)

EndedAt: 2016-09-20 13:01:12 -0700 (Tue, 20 Sep 2016)

EllapsedTime: 211.5 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_1.13.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/SeqGSEA.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.13.0’
* 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         13.149  0.226  16.501
scoreNormalization  7.892  0.211   8.105
DSresultGeneTable   7.915  0.097   8.015
normFactor          7.674  0.336   8.012
DSpermutePval       7.618  0.086   7.707
topDSGenes          7.299  0.228   7.531
DSresultExonTable   7.374  0.116   7.494
genpermuteMat       6.769  0.227   7.000
topDSExons          6.518  0.252   6.772
DSpermute4GSEA      6.585  0.103   6.693
* 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	0.329	0.005	0.334
DENBStatPermut4GSEA	0.680	0.015	0.696
DENBTest	0.683	0.010	0.694
DEpermutePval	0.659	0.007	0.665
DSpermute4GSEA	6.585	0.103	6.693
DSpermutePval	7.618	0.086	7.707
DSresultExonTable	7.374	0.116	7.494
DSresultGeneTable	7.915	0.097	8.015
GSEAresultTable	1.725	0.024	1.750
GSEnrichAnalyze	1.587	0.003	1.592
ReadCountSet-class	0.001	0.000	0.001
SeqGeneSet-class	0.001	0.000	0.001
calES	0.005	0.001	0.007
calES.perm	1.809	0.004	1.812
convertEnsembl2Symbol	0.093	0.009	1.119
convertSymbol2Ensembl	0.092	0.008	1.078
counts-methods	0.017	0.001	0.018
estiExonNBstat	0.923	0.005	0.928
estiGeneNBstat	0.595	0.028	0.622
exonID	0.071	0.024	0.095
exonTestability	0.016	0.001	0.017
geneID	0.102	0.024	0.126
geneList	0.004	0.001	0.004
genePermuteScore	0.004	0.000	0.005
geneScore	0.005	0.001	0.005
geneSetDescs	0.003	0.000	0.003
geneSetNames	0.004	0.000	0.004
geneSetSize	0.003	0.001	0.003
geneTestability	0.036	0.001	0.037
genpermuteMat	6.769	0.227	7.000
getGeneCount	0.014	0.001	0.015
label	0.01	0.00	0.01
loadExonCountData	0.417	0.005	0.423
loadGenesets	1.035	0.019	2.073
newGeneSets	0.003	0.000	0.003
newReadCountSet	0.057	0.000	0.058
normFactor	7.674	0.336	8.012
plotES	1.879	0.010	1.889
plotGeneScore	0.093	0.002	0.099
plotSig	1.958	0.006	1.966
plotSigGeneSet	2.111	0.007	2.119
rankCombine	0.011	0.001	0.012
runDESeq	0.151	0.002	0.153
runSeqGSEA	13.149	0.226	16.501
scoreNormalization	7.892	0.211	8.105
size	0.002	0.000	0.002
subsetByGenes	0.022	0.000	0.023
topDEGenes	1.423	0.013	1.437
topDSExons	6.518	0.252	6.772
topDSGenes	7.299	0.228	7.531
topGeneSets	1.865	0.006	1.873
writeScores	0.008	0.000	0.009
writeSigGeneSet	1.814	0.005	1.820