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INSTALL report for transcriptR on tokay2

This page was generated on 2019-10-16 12:34:35 -0400 (Wed, 16 Oct 2019).

Package 1666/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
transcriptR 1.12.0
Armen R. Karapetyan
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/transcriptR
Branch: RELEASE_3_9
Last Commit: 627ab11
Last Changed Date: 2019-05-02 11:53:59 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64 [ OK ] OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: transcriptR
Version: 1.12.0
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/transcriptR_1.12.0.tar.gz && rm -rf transcriptR.buildbin-libdir && mkdir transcriptR.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=transcriptR.buildbin-libdir transcriptR_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL transcriptR_1.12.0.zip && rm transcriptR_1.12.0.tar.gz transcriptR_1.12.0.zip
StartedAt: 2019-10-15 20:44:42 -0400 (Tue, 15 Oct 2019)
EndedAt: 2019-10-15 20:46:15 -0400 (Tue, 15 Oct 2019)
EllapsedTime: 93.0 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/transcriptR_1.12.0.tar.gz && rm -rf transcriptR.buildbin-libdir && mkdir transcriptR.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=transcriptR.buildbin-libdir transcriptR_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL transcriptR_1.12.0.zip && rm transcriptR_1.12.0.tar.gz transcriptR_1.12.0.zip
###
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100 2472k  100 2472k    0     0  27.7M      0 --:--:-- --:--:-- --:--:-- 30.1M

install for i386

* installing *source* package 'transcriptR' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'transcriptR'
    finding HTML links ... done
    ChipDataSet-class                       html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqqfsZu/R.INSTALL27a4144e700e/transcriptR/man/ChipDataSet-class.Rd:15: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqqfsZu/R.INSTALL27a4144e700e/transcriptR/man/ChipDataSet-class.Rd:17: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    TranscriptionDataSet-class              html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqqfsZu/R.INSTALL27a4144e700e/transcriptR/man/TranscriptionDataSet-class.Rd:18: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqqfsZu/R.INSTALL27a4144e700e/transcriptR/man/TranscriptionDataSet-class.Rd:23: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqqfsZu/R.INSTALL27a4144e700e/transcriptR/man/TranscriptionDataSet-class.Rd:26: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqqfsZu/R.INSTALL27a4144e700e/transcriptR/man/TranscriptionDataSet-class.Rd:29: file link 'RleList' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqqfsZu/R.INSTALL27a4144e700e/transcriptR/man/TranscriptionDataSet-class.Rd:43: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    addFeature-methods                      html  
    annot                                   html  
    finding level-2 HTML links ... done

    annotateTranscripts-methods             html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqqfsZu/R.INSTALL27a4144e700e/transcriptR/man/annotateTranscripts-methods.Rd:17: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqqfsZu/R.INSTALL27a4144e700e/transcriptR/man/annotateTranscripts-methods.Rd:24: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    breakTranscriptsByPeaks-methods         html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqqfsZu/R.INSTALL27a4144e700e/transcriptR/man/breakTranscriptsByPeaks-methods.Rd:25: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    cds                                     html  
    constructCDS                            html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqqfsZu/R.INSTALL27a4144e700e/transcriptR/man/constructCDS.Rd:18: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqqfsZu/R.INSTALL27a4144e700e/transcriptR/man/constructCDS.Rd:22: file link 'TxDb' in package 'GenomicFeatures' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqqfsZu/R.INSTALL27a4144e700e/transcriptR/man/constructCDS.Rd:44: file link 'ScanBamParam' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqqfsZu/R.INSTALL27a4144e700e/transcriptR/man/constructCDS.Rd:65: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    constructTDS                            html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqqfsZu/R.INSTALL27a4144e700e/transcriptR/man/constructTDS.Rd:13: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqqfsZu/R.INSTALL27a4144e700e/transcriptR/man/constructTDS.Rd:29: file link 'ScanBamParam' in package 'Rsamtools' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqqfsZu/R.INSTALL27a4144e700e/transcriptR/man/constructTDS.Rd:49: file link 'coverage' in package 'IRanges' does not exist and so has been treated as a topic
    detectTranscripts-methods               html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqqfsZu/R.INSTALL27a4144e700e/transcriptR/man/detectTranscripts-methods.Rd:42: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqqfsZu/R.INSTALL27a4144e700e/transcriptR/man/detectTranscripts-methods.Rd:47: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    estimateBackground-methods              html  
    estimateGapDistance-methods             html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqqfsZu/R.INSTALL27a4144e700e/transcriptR/man/estimateGapDistance-methods.Rd:20: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    exportCoverage-methods                  html  
    getConfusionMatrix-methods              html  
    getGenomicAnnot-methods                 html  
    getPeaks-methods                        html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqqfsZu/R.INSTALL27a4144e700e/transcriptR/man/getPeaks-methods.Rd:17: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    getPredictorSignificance-methods        html  
    getProbTreshold-methods                 html  
    getQuadProb-methods                     html  
    getTestedGapDistances-methods           html  
    getTranscripts-methods                  html  
Rd warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/RtmpqqfsZu/R.INSTALL27a4144e700e/transcriptR/man/getTranscripts-methods.Rd:26: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    peaksToBed-methods                      html  
    plotErrorRate-methods                   html  
    plotFeatures-methods                    html  
    plotGenomicAnnot-methods                html  
    plotROC-methods                         html  
    predictStrand-methods                   html  
    predictTssOverlap-methods               html  
    show                                    html  
    tds                                     html  
    transcriptsToBed-methods                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 'transcriptR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'transcriptR' as transcriptR_1.12.0.zip
* DONE (transcriptR)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'transcriptR' successfully unpacked and MD5 sums checked