BioC 3.3: CHECK report for SeqGSEA on morelia

Package: SeqGSEA

Version: 1.11.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SeqGSEA_1.11.0.tar.gz

StartedAt: 2016-04-21 07:27:10 -0700 (Thu, 21 Apr 2016)

EndedAt: 2016-04-21 07:36:21 -0700 (Thu, 21 Apr 2016)

EllapsedTime: 551.1 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_1.11.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/SeqGSEA.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* 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 ‘1.11.0’
* 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 ... [11s/11s] 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 ... [133s/426s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
runSeqGSEA            16.551  0.427 180.762
DSresultExonTable      9.463  0.177   9.669
DSresultGeneTable      9.442  0.137   9.594
topDSExons             9.298  0.210   9.520
scoreNormalization     9.150  0.224   9.386
normFactor             8.851  0.306   9.163
DSpermutePval          8.888  0.133   9.029
topDSGenes             8.831  0.150   8.991
DSpermute4GSEA         8.797  0.154   8.962
genpermuteMat          6.591  0.147   6.744
loadGenesets           1.281  0.014  90.748
convertEnsembl2Symbol  0.104  0.009  19.156
convertSymbol2Ensembl  0.100  0.008  18.992
* 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	0.290	0.026	0.317
DENBStatPermut4GSEA	0.961	0.016	0.979
DENBTest	0.990	0.025	1.017
DEpermutePval	0.920	0.010	0.934
DSpermute4GSEA	8.797	0.154	8.962
DSpermutePval	8.888	0.133	9.029
DSresultExonTable	9.463	0.177	9.669
DSresultGeneTable	9.442	0.137	9.594
GSEAresultTable	2.270	0.010	2.282
GSEnrichAnalyze	2.327	0.006	2.338
ReadCountSet-class	0.002	0.000	0.001
SeqGeneSet-class	0.001	0.001	0.001
calES	0.005	0.001	0.006
calES.perm	2.482	0.005	2.492
convertEnsembl2Symbol	0.104	0.009	19.156
convertSymbol2Ensembl	0.100	0.008	18.992
counts-methods	0.017	0.001	0.018
estiExonNBstat	1.064	0.022	1.086
estiGeneNBstat	0.787	0.042	0.829
exonID	0.100	0.032	0.132
exonTestability	0.023	0.000	0.024
geneID	0.143	0.035	0.178
geneList	0.006	0.000	0.006
genePermuteScore	0.008	0.004	0.011
geneScore	0.004	0.000	0.003
geneSetDescs	0.003	0.001	0.002
geneSetNames	0.003	0.000	0.003
geneSetSize	0.003	0.000	0.003
geneTestability	0.024	0.001	0.025
genpermuteMat	6.591	0.147	6.744
getGeneCount	0.020	0.000	0.022
label	0.014	0.001	0.016
loadExonCountData	0.488	0.006	0.493
loadGenesets	1.281	0.014	90.748
newGeneSets	0.004	0.000	0.004
newReadCountSet	0.114	0.000	0.115
normFactor	8.851	0.306	9.163
plotES	2.761	0.018	2.785
plotGeneScore	0.110	0.004	0.123
plotSig	2.406	0.007	2.416
plotSigGeneSet	2.592	0.008	2.608
rankCombine	0.012	0.002	0.013
runDESeq	0.144	0.001	0.145
runSeqGSEA	16.551	0.427	180.762
scoreNormalization	9.150	0.224	9.386
size	0.003	0.001	0.002
subsetByGenes	0.040	0.001	0.040
topDEGenes	1.701	0.024	1.730
topDSExons	9.298	0.210	9.520
topDSGenes	8.831	0.150	8.991
topGeneSets	2.578	0.007	2.592
writeScores	0.009	0.001	0.009
writeSigGeneSet	2.584	0.009	2.597