Package: SeqGSEA

Version: 1.24.0

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SeqGSEA.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings SeqGSEA_1.24.0.tar.gz

StartedAt: 2019-10-16 07:01:46 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 07:08:45 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 419.4 seconds

RetCode: 0

Status:  OK

CheckDir: SeqGSEA.Rcheck

Warnings: 0

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SeqGSEA.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings SeqGSEA_1.24.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/SeqGSEA.Rcheck'
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SeqGSEA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SeqGSEA' version '1.24.0'
* 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 whether package 'SeqGSEA' can be installed ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 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 : : 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 : : no visible global function definition
  for 'read.table'
plotES : : no visible global function definition for
  'density'
plotES: no visible global function definition for 'density'
plotES: no visible global function definition for 'plot'
plotES : : 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 : : 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 : : 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 ... 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
scoreNormalization 11.46   0.02   11.48
DSresultExonTable  11.40   0.00   11.54
DSresultGeneTable  11.37   0.00   11.38
DSpermutePval      10.85   0.00   10.85
DSpermute4GSEA      9.92   0.01    9.93
normFactor          9.83   0.02    9.84
topDSExons          9.59   0.00    9.59
genpermuteMat       8.82   0.00    8.82
topDSGenes          8.55   0.00    8.55
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
scoreNormalization 12.32   0.00   12.31
topDSGenes         11.85   0.00   11.85
DSresultGeneTable  11.35   0.00   11.34
topDSExons         11.03   0.02   11.04
normFactor         10.81   0.02   10.83
DSresultExonTable  10.76   0.01   10.78
genpermuteMat      10.50   0.00   10.50
DSpermute4GSEA     10.10   0.00   10.11
DSpermutePval      10.10   0.00   10.09
* 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
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/SeqGSEA.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/SeqGSEA_1.24.0.tar.gz && rm -rf SeqGSEA.buildbin-libdir && mkdir SeqGSEA.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SeqGSEA.buildbin-libdir SeqGSEA_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL SeqGSEA_1.24.0.zip && rm SeqGSEA_1.24.0.tar.gz SeqGSEA_1.24.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

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100  878k  100  878k    0     0  12.0M      0 --:--:-- --:--:-- --:--:-- 13.4M

install for i386

* installing *source* package 'SeqGSEA' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'SeqGSEA'
    finding HTML links ... done
    DENBStat4GSEA                           html  
    DENBStatPermut4GSEA                     html  
    DENBTest                                html  
    DEpermutePval                           html  
    DEscore                                 html  
    DSpermute4GSEA                          html  
    DSpermutePval                           html  
    DSresultExonTable                       html  
    DSresultGeneTable                       html  
    GSEAresultTable                         html  
    GSEnrichAnalyze                         html  
    GS_example                              html  
    RCS_example                             html  
    ReadCountSet-class                      html  
    finding level-2 HTML links ... done

    SeqGSEA-package                         html  
    SeqGeneSet-class                        html  
    calES                                   html  
    calES.perm                              html  
    convertEnsembl2Symbol                   html  
    convertSymbol2Ensembl                   html  
    counts-methods                          html  
    estiExonNBstat                          html  
    estiGeneNBstat                          html  
    exonID                                  html  
    exonTestability                         html  
    geneID                                  html  
    geneList                                html  
    genePermuteScore                        html  
    geneScore                               html  
    geneSetDescs                            html  
    geneSetNames                            html  
    geneSetSize                             html  
    geneTestability                         html  
    genpermuteMat                           html  
    getGeneCount                            html  
    label                                   html  
    loadExonCountData                       html  
    loadGenesets                            html  
    newGeneSets                             html  
    newReadCountSet                         html  
    normES                                  html  
    normFactor                              html  
    plotES                                  html  
    plotGeneScore                           html  
    plotSig                                 html  
    plotSigGeneSet                          html  
    rankCombine                             html  
    runDESeq                                html  
    runSeqGSEA                              html  
    scoreNormalization                      html  
    signifES                                html  
    size                                    html  
    subsetByGenes                           html  
    topDEGenes                              html  
    topDSExons                              html  
    topDSGenes                              html  
    topGeneSets                             html  
    writeScores                             html  
    writeSigGeneSet                         html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'SeqGSEA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SeqGSEA' as SeqGSEA_1.24.0.zip
* DONE (SeqGSEA)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'SeqGSEA' successfully unpacked and MD5 sums checked