BioC 3.2: CHECK report for SeqGSEA on zin1

Package: SeqGSEA

Version: 1.9.1

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings SeqGSEA_1.9.1.tar.gz

StartedAt: 2015-08-24 03:41:36 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 03:45:38 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 241.3 seconds

RetCode: 0

Status:  OK

CheckDir: SeqGSEA.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings SeqGSEA_1.9.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/SeqGSEA.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.9.1’
* 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 ... [8s/8s] 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’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [143s/158s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
runSeqGSEA         16.830  0.036  24.013
topDSExons         11.440  0.048  11.611
topDSGenes         11.239  0.004  11.255
DSresultGeneTable  11.194  0.000  11.202
scoreNormalization 11.144  0.008  11.156
normFactor         11.082  0.000  11.079
DSresultExonTable  10.872  0.012  10.901
DSpermutePval      10.863  0.004  10.861
genpermuteMat      10.079  0.004  10.103
DSpermute4GSEA     10.030  0.008  10.065
* 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-3.2-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	0.344	0.008	0.352
DENBStatPermut4GSEA	0.761	0.000	0.762
DENBTest	1.394	0.004	1.398
DEpermutePval	0.711	0.000	0.711
DSpermute4GSEA	10.030	0.008	10.065
DSpermutePval	10.863	0.004	10.861
DSresultExonTable	10.872	0.012	10.901
DSresultGeneTable	11.194	0.000	11.202
GSEAresultTable	1.931	0.012	1.942
GSEnrichAnalyze	1.936	0.000	1.938
ReadCountSet-class	0.002	0.000	0.001
SeqGeneSet-class	0.001	0.000	0.001
calES	0.006	0.004	0.007
calES.perm	1.854	0.000	1.857
convertEnsembl2Symbol	0.104	0.000	2.337
convertSymbol2Ensembl	0.093	0.004	2.362
counts-methods	0.014	0.000	0.013
estiExonNBstat	0.999	0.004	1.020
estiGeneNBstat	0.973	0.000	0.972
exonID	0.051	0.028	0.080
exonTestability	0.020	0.000	0.021
geneID	0.086	0.016	0.107
geneList	0.004	0.000	0.004
genePermuteScore	0.007	0.000	0.007
geneScore	0.004	0.000	0.004
geneSetDescs	0.003	0.000	0.003
geneSetNames	0.002	0.000	0.002
geneSetSize	0.003	0.000	0.003
geneTestability	0.024	0.000	0.024
genpermuteMat	10.079	0.004	10.103
getGeneCount	0.021	0.000	0.021
label	0.005	0.008	0.013
loadExonCountData	0.358	0.000	0.383
loadGenesets	1.074	0.004	3.440
newGeneSets	0.003	0.000	0.003
newReadCountSet	0.080	0.000	0.079
normFactor	11.082	0.000	11.079
plotES	2.059	0.000	2.071
plotGeneScore	0.107	0.000	0.109
plotSig	1.916	0.000	1.915
plotSigGeneSet	1.896	0.000	1.894
rankCombine	0.009	0.000	0.010
runDESeq	0.115	0.000	0.114
runSeqGSEA	16.830	0.036	24.013
scoreNormalization	11.144	0.008	11.156
size	0.003	0.000	0.003
subsetByGenes	0.03	0.00	0.03
topDEGenes	2.114	0.004	2.151
topDSExons	11.440	0.048	11.611
topDSGenes	11.239	0.004	11.255
topGeneSets	1.893	0.000	1.901
writeScores	0.01	0.00	0.01
writeSigGeneSet	1.913	0.000	1.916