BioC 3.3: CHECK report for SeqGSEA on oaxaca

Package: SeqGSEA

Version: 1.12.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SeqGSEA_1.12.0.tar.gz

StartedAt: 2016-10-13 06:13:22 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 06:18:16 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 294.0 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_1.12.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-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 ‘1.12.0’
* 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         17.264  0.230  28.066
DSresultExonTable  10.641  0.056  10.702
normFactor         10.551  0.134  10.693
DSresultGeneTable  10.385  0.081  10.475
scoreNormalization 10.263  0.181  10.452
DSpermutePval      10.220  0.045  10.271
DSpermute4GSEA      9.633  0.102   9.742
genpermuteMat       9.309  0.198   9.513
topDSExons          9.007  0.203   9.220
topDSGenes          8.127  0.316   8.447
* 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-3.3-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	0.482	0.010	0.493
DENBStatPermut4GSEA	0.915	0.016	0.932
DENBTest	0.863	0.012	0.876
DEpermutePval	0.953	0.007	0.961
DSpermute4GSEA	9.633	0.102	9.742
DSpermutePval	10.220	0.045	10.271
DSresultExonTable	10.641	0.056	10.702
DSresultGeneTable	10.385	0.081	10.475
GSEAresultTable	2.488	0.022	2.514
GSEnrichAnalyze	2.502	0.007	2.512
ReadCountSet-class	0.002	0.000	0.002
SeqGeneSet-class	0.002	0.000	0.002
calES	0.009	0.002	0.010
calES.perm	2.430	0.012	2.444
convertEnsembl2Symbol	0.252	0.010	3.834
convertSymbol2Ensembl	0.105	0.008	3.693
counts-methods	0.016	0.001	0.017
estiExonNBstat	0.988	0.027	1.016
estiGeneNBstat	0.962	0.024	0.987
exonID	0.124	0.039	0.164
exonTestability	0.025	0.002	0.026
geneID	0.156	0.035	0.192
geneList	0.006	0.000	0.006
genePermuteScore	0.007	0.001	0.007
geneScore	0.005	0.001	0.005
geneSetDescs	0.004	0.001	0.005
geneSetNames	0.004	0.001	0.004
geneSetSize	0.002	0.000	0.003
geneTestability	0.026	0.000	0.026
genpermuteMat	9.309	0.198	9.513
getGeneCount	0.019	0.001	0.019
label	0.013	0.000	0.013
loadExonCountData	0.681	0.009	0.691
loadGenesets	1.225	0.014	4.872
newGeneSets	0.003	0.001	0.004
newReadCountSet	0.100	0.000	0.101
normFactor	10.551	0.134	10.693
plotES	2.470	0.014	2.486
plotGeneScore	0.106	0.005	0.119
plotSig	2.364	0.005	2.371
plotSigGeneSet	2.420	0.007	2.429
rankCombine	0.011	0.001	0.013
runDESeq	0.126	0.001	0.128
runSeqGSEA	17.264	0.230	28.066
scoreNormalization	10.263	0.181	10.452
size	0.003	0.000	0.003
subsetByGenes	0.040	0.001	0.041
topDEGenes	1.572	0.024	1.599
topDSExons	9.007	0.203	9.220
topDSGenes	8.127	0.316	8.447
topGeneSets	2.250	0.007	2.258
writeScores	0.006	0.000	0.006
writeSigGeneSet	2.252	0.006	2.259