Package: IsoformSwitchAnalyzeR

Version: 1.0.0

Command: rm -rf IsoformSwitchAnalyzeR.buildbin-libdir IsoformSwitchAnalyzeR.Rcheck && mkdir IsoformSwitchAnalyzeR.buildbin-libdir IsoformSwitchAnalyzeR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=IsoformSwitchAnalyzeR.buildbin-libdir IsoformSwitchAnalyzeR_1.0.0.tar.gz >IsoformSwitchAnalyzeR.Rcheck\00install.out 2>&1 && cp IsoformSwitchAnalyzeR.Rcheck\00install.out IsoformSwitchAnalyzeR-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=IsoformSwitchAnalyzeR.buildbin-libdir --install="check:IsoformSwitchAnalyzeR-install.out" --force-multiarch --no-vignettes --timings IsoformSwitchAnalyzeR_1.0.0.tar.gz

StartedAt: 2018-04-12 00:53:48 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 01:04:28 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 639.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: IsoformSwitchAnalyzeR.Rcheck

Warnings: 1

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### Running command:
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###   rm -rf IsoformSwitchAnalyzeR.buildbin-libdir IsoformSwitchAnalyzeR.Rcheck && mkdir IsoformSwitchAnalyzeR.buildbin-libdir IsoformSwitchAnalyzeR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=IsoformSwitchAnalyzeR.buildbin-libdir IsoformSwitchAnalyzeR_1.0.0.tar.gz >IsoformSwitchAnalyzeR.Rcheck\00install.out 2>&1 && cp IsoformSwitchAnalyzeR.Rcheck\00install.out IsoformSwitchAnalyzeR-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=IsoformSwitchAnalyzeR.buildbin-libdir --install="check:IsoformSwitchAnalyzeR-install.out" --force-multiarch --no-vignettes --timings IsoformSwitchAnalyzeR_1.0.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/IsoformSwitchAnalyzeR.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'IsoformSwitchAnalyzeR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'IsoformSwitchAnalyzeR' version '1.0.0'
* 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 'IsoformSwitchAnalyzeR' can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'plyr::desc' by 'IRanges::desc' when loading 'IsoformSwitchAnalyzeR'
  Warning: replacing previous import 'GenomicRanges::promoters' by 'cummeRbund::promoters' when loading 'IsoformSwitchAnalyzeR'
  Warning: replacing previous import 'plyr::count' by 'cummeRbund::count' when loading 'IsoformSwitchAnalyzeR'
  Warning: replacing previous import 'cummeRbund::samples' by 'DRIMSeq::samples' when loading 'IsoformSwitchAnalyzeR'
  Warning: replacing previous import 'cummeRbund::conditions' by 'spliceR::conditions' when loading 'IsoformSwitchAnalyzeR'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/IsoformSwitchAnalyzeR.Rcheck/00install.out' for details.
* 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
createSwitchAnalyzeRlist: no visible global function definition for
  'Rle'
expressionAnalysisPlot: no visible binding for global variable
  'Condition'
expressionAnalysisPlot: no visible binding for global variable
  'gene_expression'
expressionAnalysisPlot: no visible binding for global variable 'CI_up'
expressionAnalysisPlot: no visible binding for global variable
  'CI_down'
expressionAnalysisPlot: no visible binding for global variable
  'sigLevelPos'
expressionAnalysisPlot: no visible binding for global variable
  'sigLevel'
expressionAnalysisPlot: no visible binding for global variable 'CI_hi'
expressionAnalysisPlot: no visible binding for global variable 'CI_low'
expressionAnalysisPlot: no visible binding for global variable 'ymax'
expressionAnalysisPlot: no visible binding for global variable
  'sigEval'
expressionAnalysisPlot: no visible binding for global variable 'idNr'
expressionAnalysisPlot: no visible binding for global variable 'IF'
extractConsequenceSummary: no visible binding for global variable
  'switchConsequence'
extractConsequenceSummary: no visible binding for global variable
  'geneFraction'
extractConsequenceSummary: no visible binding for global variable
  'nrGenesWithConsequences'
extractConsequenceSummary: no visible binding for global variable
  'isoFraction'
extractConsequenceSummary: no visible binding for global variable
  'nrIsoWithConsequences'
extractGenomeWideAnalysis: no visible binding for global variable
  'isoform_feature'
extractGenomeWideAnalysis: no visible binding for global variable
  'value'
extractGenomeWideAnalysis: no visible binding for global variable
  'variable'
extractGenomeWideAnalysis: no visible binding for global variable
  'ymax'
extractGenomeWideAnalysis: no visible binding for global variable
  'significance'
extractGenomeWideAnalysis: no visible binding for global variable
  'idNr'
switchPlotTranscript: no visible global function definition for
  'queryHits'
switchPlotTranscript: no visible binding for global variable 'y'
switchPlotTranscript: no visible binding for global variable 'yend'
switchPlotTranscript: no visible binding for global variable 'x'
switchPlotTranscript: no visible binding for global variable 'ymin'
switchPlotTranscript: no visible binding for global variable 'xmin'
switchPlotTranscript: no visible binding for global variable 'ymax'
switchPlotTranscript: no visible binding for global variable 'xmax'
switchPlotTranscript: no visible binding for global variable 'Domain'
Undefined global functions or variables:
  CI_down CI_hi CI_low CI_up Condition Domain IF Rle geneFraction
  gene_expression idNr isoFraction isoform_feature
  nrGenesWithConsequences nrIsoWithConsequences queryHits sigEval
  sigLevel sigLevelPos significance switchConsequence value variable x
  xmax xmin y yend ymax ymin
* 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
isoformSwitchAnalysisCombined 14.67   0.17   14.84
IsoformSwitchTestDRIMSeq      13.80   0.22   18.37
isoformSwitchAnalysisPart1     9.09   0.00    9.09
extractGenomeWideAnalysis      5.91   0.04    5.93
analyzeIntronRetention         5.30   0.03    5.33
switchAnalyzeRlist             4.95   0.11    5.08
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                               user system elapsed
isoformSwitchAnalysisCombined 20.80   0.07   20.89
IsoformSwitchTestDRIMSeq      13.85   0.14   14.00
isoformSwitchAnalysisPart1    11.96   0.03   12.00
analyzeIntronRetention         6.72   0.00    6.71
isoformSwitchAnalysisPart2     5.99   0.04    6.02
extractGenomeWideAnalysis      5.86   0.11    5.97
importCufflinksData            5.30   0.12    5.42
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: 'pheatmap'
* 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: 1 WARNING, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/IsoformSwitchAnalyzeR.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'IsoformSwitchAnalyzeR' ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import 'plyr::desc' by 'IRanges::desc' when loading 'IsoformSwitchAnalyzeR'
Warning: replacing previous import 'GenomicRanges::promoters' by 'cummeRbund::promoters' when loading 'IsoformSwitchAnalyzeR'
Warning: replacing previous import 'plyr::count' by 'cummeRbund::count' when loading 'IsoformSwitchAnalyzeR'
Warning: replacing previous import 'cummeRbund::samples' by 'DRIMSeq::samples' when loading 'IsoformSwitchAnalyzeR'
Warning: replacing previous import 'cummeRbund::conditions' by 'spliceR::conditions' when loading 'IsoformSwitchAnalyzeR'
** help
*** installing help indices
  converting help for package 'IsoformSwitchAnalyzeR'
    finding HTML links ... done
    IsoformSwitchTestDRIMSeq                html  
    finding level-2 HTML links ... done

    analyzeCPAT                             html  
    analyzeIntronRetention                  html  
    analyzeORF                              html  
    analyzePFAM                             html  
    analyzeSignalP                          html  
    analyzeSwitchConsequences               html  
    expressionAnalysisPlots                 html  
    extractCallibarionStatus                html  
    extractConsequenceSummary               html  
    extractExpressionMatrix                 html  
    extractGenomeWideAnalysis               html  
    extractSequence                         html  
    extractSwitchSummary                    html  
    extractTopSwitches                      html  
    importCufflinksData                     html  
    importCufflinksGalaxyData               html  
    importGTF                               html  
    importIsoformExpression                 html  
    importRdata                             html  
    isoformSwitchAnalysisCombined           html  
    isoformSwitchAnalysisPart1              html  
    isoformSwitchAnalysisPart2              html  
    isoformSwitchTest                       html  
    isoformToGeneExp                        html  
    preFilter                               html  
    prepareCuffExample                      html  
    subsetSwitchAnalyzeRlist                html  
    switchAnalyzeRlist                      html  
    switchPlot                              html  
    switchPlotTopSwitches                   html  
    switchPlotTranscript                    html  
    testData                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'plyr::desc' by 'IRanges::desc' when loading 'IsoformSwitchAnalyzeR'
Warning: replacing previous import 'GenomicRanges::promoters' by 'cummeRbund::promoters' when loading 'IsoformSwitchAnalyzeR'
Warning: replacing previous import 'plyr::count' by 'cummeRbund::count' when loading 'IsoformSwitchAnalyzeR'
Warning: replacing previous import 'cummeRbund::samples' by 'DRIMSeq::samples' when loading 'IsoformSwitchAnalyzeR'
Warning: replacing previous import 'cummeRbund::conditions' by 'spliceR::conditions' when loading 'IsoformSwitchAnalyzeR'
In R CMD INSTALL

install for x64

* installing *source* package 'IsoformSwitchAnalyzeR' ...
** testing if installed package can be loaded
Warning: replacing previous import 'plyr::desc' by 'IRanges::desc' when loading 'IsoformSwitchAnalyzeR'
Warning: replacing previous import 'plyr::count' by 'cummeRbund::count' when loading 'IsoformSwitchAnalyzeR'
Warning: replacing previous import 'GenomicRanges::promoters' by 'cummeRbund::promoters' when loading 'IsoformSwitchAnalyzeR'
Warning: replacing previous import 'cummeRbund::samples' by 'DRIMSeq::samples' when loading 'IsoformSwitchAnalyzeR'
Warning: replacing previous import 'cummeRbund::conditions' by 'spliceR::conditions' when loading 'IsoformSwitchAnalyzeR'
* MD5 sums
packaged installation of 'IsoformSwitchAnalyzeR' as IsoformSwitchAnalyzeR_1.0.0.zip
* DONE (IsoformSwitchAnalyzeR)
In R CMD INSTALL
In R CMD INSTALL