BioC 3.3: CHECK report for SeqGSEA on linux2.bioconductor.org

Package: SeqGSEA

Version: 1.11.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings SeqGSEA_1.11.0.tar.gz

StartedAt: 2015-10-27 07:58:39 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 08:02:10 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 210.6 seconds

RetCode: 0

Status:  OK

CheckDir: SeqGSEA.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings SeqGSEA_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/SeqGSEA.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-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 ‘1.11.0’
* 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 ... [7s/7s] 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’
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’
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’
runSeqGSEA: no visible global function definition for ‘makeCluster’
Undefined global functions or variables:
  %do% %dopar% foreach i j makeCluster
* 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 ... [133s/135s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
runSeqGSEA         18.468  0.044  19.887
topDSExons         12.304  0.008  12.312
scoreNormalization 11.314  0.012  11.329
normFactor         11.144  0.028  11.189
topDSGenes         11.077  0.000  11.078
genpermuteMat       9.456  0.016   9.489
DSresultExonTable   8.618  0.040   8.658
DSpermutePval       8.562  0.048   8.610
DSresultGeneTable   8.552  0.031   8.591
DSpermute4GSEA      7.625  0.056   7.681
* 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: 2 NOTEs
See
  ‘/home/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	0.323	0.000	0.323
DENBStatPermut4GSEA	0.583	0.004	0.587
DENBTest	1.177	0.012	1.190
DEpermutePval	0.548	0.004	0.552
DSpermute4GSEA	7.625	0.056	7.681
DSpermutePval	8.562	0.048	8.610
DSresultExonTable	8.618	0.040	8.658
DSresultGeneTable	8.552	0.031	8.591
GSEAresultTable	1.584	0.028	1.615
GSEnrichAnalyze	1.473	0.008	1.482
ReadCountSet-class	0.001	0.000	0.001
SeqGeneSet-class	0.001	0.000	0.001
calES	0.005	0.000	0.005
calES.perm	1.987	0.004	1.993
convertEnsembl2Symbol	0.102	0.000	0.463
convertSymbol2Ensembl	0.126	0.000	0.483
counts-methods	0.020	0.000	0.019
estiExonNBstat	1.297	0.012	1.317
estiGeneNBstat	0.841	0.000	0.841
exonID	0.048	0.008	0.056
exonTestability	0.016	0.000	0.016
geneID	0.068	0.004	0.072
geneList	0.004	0.000	0.004
genePermuteScore	0.005	0.000	0.006
geneScore	0.002	0.000	0.003
geneSetDescs	0.002	0.000	0.002
geneSetNames	0.002	0.000	0.001
geneSetSize	0.002	0.000	0.002
geneTestability	0.014	0.004	0.018
genpermuteMat	9.456	0.016	9.489
getGeneCount	0.015	0.000	0.015
label	0.011	0.000	0.010
loadExonCountData	0.286	0.000	0.287
loadGenesets	0.905	0.004	1.308
newGeneSets	0.002	0.000	0.002
newReadCountSet	0.059	0.000	0.060
normFactor	11.144	0.028	11.189
plotES	2.338	0.000	2.339
plotGeneScore	0.11	0.00	0.11
plotSig	1.507	0.004	1.515
plotSigGeneSet	1.505	0.004	1.509
rankCombine	0.008	0.000	0.008
runDESeq	0.089	0.000	0.089
runSeqGSEA	18.468	0.044	19.887
scoreNormalization	11.314	0.012	11.329
size	0.002	0.000	0.002
subsetByGenes	0.023	0.000	0.023
topDEGenes	1.65	0.00	1.65
topDSExons	12.304	0.008	12.312
topDSGenes	11.077	0.000	11.078
topGeneSets	2.011	0.000	2.011
writeScores	0.005	0.000	0.005
writeSigGeneSet	1.822	0.000	1.822