BioC 3.5: CHECK report for SeqGSEA on toluca2

Package: SeqGSEA

Version: 1.15.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SeqGSEA_1.15.0.tar.gz

StartedAt: 2017-04-23 09:46:01 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 09:51:20 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 319.2 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_1.15.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/SeqGSEA.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* 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 ‘1.15.0’
* 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         17.460  0.276  25.343
scoreNormalization 10.203  0.202  10.518
DSresultExonTable  10.041  0.217  10.435
topDSExons          9.961  0.268  10.296
DSpermutePval       9.911  0.199  10.181
topDSGenes          9.625  0.385  10.050
DSresultGeneTable   9.503  0.254   9.838
normFactor          9.527  0.186   9.749
DSpermute4GSEA      9.062  0.276   9.451
genpermuteMat       9.074  0.247   9.377
* 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	0.887	0.037	0.926
DENBStatPermut4GSEA	1.668	0.022	1.699
DENBTest	0.863	0.028	0.897
DEpermutePval	1.092	0.029	1.123
DSpermute4GSEA	9.062	0.276	9.451
DSpermutePval	9.911	0.199	10.181
DSresultExonTable	10.041	0.217	10.435
DSresultGeneTable	9.503	0.254	9.838
GSEAresultTable	2.808	0.011	2.835
GSEnrichAnalyze	2.779	0.012	2.811
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	2.571	0.005	2.588
convertEnsembl2Symbol	0.897	0.008	3.367
convertSymbol2Ensembl	0.802	0.007	3.354
counts-methods	0.016	0.001	0.017
estiExonNBstat	0.841	0.027	0.873
estiGeneNBstat	0.887	0.021	0.910
exonID	0.118	0.034	0.152
exonTestability	0.023	0.001	0.024
geneID	0.164	0.043	0.207
geneList	0.004	0.000	0.005
genePermuteScore	0.005	0.001	0.006
geneScore	0.003	0.000	0.005
geneSetDescs	0.004	0.000	0.003
geneSetNames	0.003	0.000	0.003
geneSetSize	0.003	0.001	0.003
geneTestability	0.026	0.001	0.026
genpermuteMat	9.074	0.247	9.377
getGeneCount	0.022	0.000	0.023
label	0.015	0.000	0.016
loadExonCountData	0.737	0.008	0.750
loadGenesets	1.317	0.011	3.905
newGeneSets	0.043	0.000	0.043
newReadCountSet	0.180	0.000	0.181
normFactor	9.527	0.186	9.749
plotES	3.063	0.018	3.167
plotGeneScore	0.184	0.003	0.200
plotSig	2.659	0.007	2.680
plotSigGeneSet	2.683	0.007	2.710
rankCombine	0.010	0.001	0.011
runDESeq	0.113	0.000	0.115
runSeqGSEA	17.460	0.276	25.343
scoreNormalization	10.203	0.202	10.518
size	0.003	0.000	0.003
subsetByGenes	0.107	0.000	0.107
topDEGenes	1.694	0.041	1.744
topDSExons	9.961	0.268	10.296
topDSGenes	9.625	0.385	10.050
topGeneSets	2.686	0.009	2.701
writeScores	0.008	0.001	0.008
writeSigGeneSet	2.676	0.007	2.700