BioC 2.14: CHECK report for SeqGSEA on zin2

Package: SeqGSEA

Version: 1.4.2

Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings SeqGSEA_1.4.2.tar.gz

StartedAt: 2014-10-08 02:45:05 -0700 (Wed, 08 Oct 2014)

EndedAt: 2014-10-08 02:50:17 -0700 (Wed, 08 Oct 2014)

EllapsedTime: 311.5 seconds

RetCode: 0

Status:  OK

CheckDir: SeqGSEA.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings SeqGSEA_1.4.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/SeqGSEA.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-unknown-linux-gnu (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 ‘1.4.2’
* 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’
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 binding for global variable ‘i’
DSpermute4GSEA : <anonymous>: no visible binding for global variable
  ‘i’
calES.perm: no visible binding for global variable ‘i’
calES.perm: no visible binding for global variable ‘j’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [166s/187s] OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
runSeqGSEA            18.861  0.052  25.804
DSpermutePval         12.949  0.016  13.174
DSresultExonTable     12.732  0.020  12.894
topDSExons            12.621  0.004  12.731
scoreNormalization    12.537  0.008  12.654
DSresultGeneTable     12.253  0.012  12.366
topDSGenes            12.165  0.016  12.201
normFactor            12.164  0.016  12.272
DSpermute4GSEA        11.573  0.028  11.658
genpermuteMat         11.192  0.024  11.370
convertEnsembl2Symbol  0.120  0.004   8.215
* 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

NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-2.14-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	0.432	0.000	0.434
DENBStatPermut4GSEA	1.216	0.004	1.284
DENBTest	1.444	0.004	1.475
DEpermutePval	1.212	0.004	1.219
DSpermute4GSEA	11.573	0.028	11.658
DSpermutePval	12.949	0.016	13.174
DSresultExonTable	12.732	0.020	12.894
DSresultGeneTable	12.253	0.012	12.366
GSEAresultTable	2.384	0.012	2.400
GSEnrichAnalyze	2.492	0.020	2.523
ReadCountSet-class	0.000	0.000	0.002
SeqGeneSet-class	0.000	0.000	0.002
calES	0.012	0.004	0.014
calES.perm	2.597	0.000	2.625
convertEnsembl2Symbol	0.120	0.004	8.215
convertSymbol2Ensembl	0.120	0.004	2.286
counts-methods	0.016	0.000	0.015
estiExonNBstat	1.060	0.004	1.071
estiGeneNBstat	1.204	0.004	1.236
exonID	0.060	0.028	0.087
exonTestability	0.028	0.000	0.025
geneID	0.076	0.036	0.113
geneList	0.004	0.000	0.005
genePermuteScore	0.012	0.000	0.012
geneScore	0.008	0.000	0.008
geneSetDescs	0.000	0.004	0.005
geneSetNames	0.004	0.000	0.004
geneSetSize	0.000	0.004	0.004
geneTestability	0.036	0.000	0.039
genpermuteMat	11.192	0.024	11.370
getGeneCount	0.024	0.000	0.026
label	0.012	0.000	0.014
loadExonCountData	0.461	0.008	0.466
loadGenesets	0.968	0.004	3.274
newGeneSets	0.004	0.000	0.003
newReadCountSet	0.108	0.000	0.109
normFactor	12.164	0.016	12.272
plotES	2.905	0.012	2.919
plotGeneScore	0.112	0.008	0.120
plotSig	2.460	0.004	2.493
plotSigGeneSet	2.548	0.004	2.604
rankCombine	0.020	0.000	0.022
runDESeq	0.160	0.000	0.164
runSeqGSEA	18.861	0.052	25.804
scoreNormalization	12.537	0.008	12.654
size	0.008	0.000	0.005
subsetByGenes	0.044	0.000	0.043
topDEGenes	2.244	0.000	2.248
topDSExons	12.621	0.004	12.731
topDSGenes	12.165	0.016	12.201
topGeneSets	2.528	0.000	2.575
writeScores	0.012	0.000	0.011
writeSigGeneSet	2.436	0.004	2.443