BioC 3.1: CHECK report for SeqGSEA on zin2

Package: SeqGSEA

Version: 1.8.1

Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings SeqGSEA_1.8.1.tar.gz

StartedAt: 2015-10-09 05:25:32 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 05:29:18 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 226.2 seconds

RetCode: 0

Status:  OK

CheckDir: SeqGSEA.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings SeqGSEA_1.8.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-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 ‘1.8.1’
* 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 ... [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’
* 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 ... [130s/144s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
runSeqGSEA         15.151  0.040  22.235
normFactor         10.370  0.004  10.377
DSresultGeneTable  10.294  0.004  10.296
DSresultExonTable  10.205  0.000  10.203
DSpermutePval      10.133  0.000  10.147
topDSExons          9.926  0.012   9.947
scoreNormalization  9.849  0.004   9.851
topDSGenes          9.815  0.000   9.822
DSpermute4GSEA      9.294  0.011   9.317
genpermuteMat       9.196  0.012   9.215
* 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
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.1-bioc/meat/SeqGSEA.Rcheck/00check.log’
for details.

* installing *source* package ‘SeqGSEA’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (SeqGSEA)

name	user	system	elapsed
DENBStat4GSEA	0.203	0.005	0.206
DENBStatPermut4GSEA	0.867	0.000	0.867
DENBTest	1.218	0.000	1.217
DEpermutePval	0.824	0.000	0.825
DSpermute4GSEA	9.294	0.011	9.317
DSpermutePval	10.133	0.000	10.147
DSresultExonTable	10.205	0.000	10.203
DSresultGeneTable	10.294	0.004	10.296
GSEAresultTable	1.660	0.008	1.666
GSEnrichAnalyze	1.674	0.000	1.673
ReadCountSet-class	0.001	0.000	0.001
SeqGeneSet-class	0.001	0.000	0.001
calES	0.006	0.000	0.007
calES.perm	1.676	0.000	1.674
convertEnsembl2Symbol	0.096	0.009	2.282
convertSymbol2Ensembl	0.095	0.000	2.347
counts-methods	0.016	0.000	0.016
estiExonNBstat	0.953	0.000	0.956
estiGeneNBstat	1.045	0.000	1.044
exonID	0.044	0.024	0.067
exonTestability	0.019	0.000	0.020
geneID	0.072	0.012	0.084
geneList	0.004	0.000	0.003
genePermuteScore	0.005	0.000	0.006
geneScore	0.003	0.000	0.003
geneSetDescs	0.003	0.000	0.002
geneSetNames	0.002	0.000	0.002
geneSetSize	0.002	0.000	0.002
geneTestability	0.021	0.000	0.020
genpermuteMat	9.196	0.012	9.215
getGeneCount	0.013	0.008	0.021
label	0.012	0.000	0.012
loadExonCountData	0.331	0.004	0.335
loadGenesets	0.977	0.000	3.279
newGeneSets	0.003	0.000	0.003
newReadCountSet	0.068	0.000	0.068
normFactor	10.370	0.004	10.377
plotES	1.785	0.004	1.790
plotGeneScore	0.081	0.004	0.085
plotSig	1.650	0.004	1.654
plotSigGeneSet	1.666	0.008	1.679
rankCombine	0.009	0.000	0.009
runDESeq	0.100	0.000	0.099
runSeqGSEA	15.151	0.040	22.235
scoreNormalization	9.849	0.004	9.851
size	0.002	0.000	0.002
subsetByGenes	0.028	0.000	0.027
topDEGenes	1.737	0.000	1.740
topDSExons	9.926	0.012	9.947
topDSGenes	9.815	0.000	9.822
topGeneSets	1.633	0.000	1.634
writeScores	0.006	0.000	0.006
writeSigGeneSet	1.644	0.000	1.645