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INSTALL report for CAGEr on tokay1

This page was generated on 2020-08-07 12:01:50 -0400 (Fri, 07 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE CAGEr PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 214/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CAGEr 1.31.4
Vanja Haberle , Charles Plessy , Damir Baranasic , Sarvesh Nikumbh
Snapshot Date: 2020-08-06 14:50:46 -0400 (Thu, 06 Aug 2020)
URL: https://git.bioconductor.org/packages/CAGEr
Branch: master
Last Commit: f845b5c
Last Changed Date: 2020-07-14 02:01:55 -0400 (Tue, 14 Jul 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64 [ OK ] OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CAGEr
Version: 1.31.4
Command: C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/CAGEr_1.31.4.tar.gz && rm -rf CAGEr.buildbin-libdir && mkdir CAGEr.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CAGEr.buildbin-libdir CAGEr_1.31.4.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL CAGEr_1.31.4.zip && rm CAGEr_1.31.4.tar.gz CAGEr_1.31.4.zip
StartedAt: 2020-08-06 18:15:00 -0400 (Thu, 06 Aug 2020)
EndedAt: 2020-08-06 18:17:04 -0400 (Thu, 06 Aug 2020)
EllapsedTime: 123.9 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/CAGEr_1.31.4.tar.gz && rm -rf CAGEr.buildbin-libdir && mkdir CAGEr.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CAGEr.buildbin-libdir CAGEr_1.31.4.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL CAGEr_1.31.4.zip && rm CAGEr_1.31.4.tar.gz CAGEr_1.31.4.zip
###
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100  767k  100  767k    0     0  18.8M      0 --:--:-- --:--:-- --:--:-- 21.4M

install for i386

* installing *source* package 'CAGEr' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'CAGEr'
    finding HTML links ... done
    CAGEexp-class                           html  
    finding level-2 HTML links ... done

    CAGEr-class                             html  
    CAGEr-package                           html  
    CAGEr_Multicore                         html  
    CAGEset-class                           html  
    CTSS-class                              html  
    CTSSclusteringMethod                    html  
    CTSScoordinates                         html  
    CTSScumulativesTagClusters              html  
    CTSSnormalizedTpm                       html  
    CTSStagCount                            html  
    CTSStagCountTable                       html  
    CTSStoGenes                             html  
    CustomConsensusClusters                 html  
    FANTOM5humanSamples                     html  
    FANTOM5mouseSamples                     html  
    GeneExpDESeq2                           html  
    GeneExpSE                               html  
    QuantileWidthFunctions                  html  
    aggregateTagClusters                    html  
    annotateCTSS                            html  
    bam2CTSS                                html  
    byCtss                                  html  
    clusterAggregateAndSum                  html  
    clusterCTSS                             html  
    coerceInBSgenome                        html  
    consensusClusterConvertors              html  
    consensusClusters-set                   html  
    consensusClusters                       html  
    consensusClustersDESeq2                 html  
    consensusClustersQuantile               html  
    consensusClustersTpm                    html  
    coverage-functions                      html  
    cumulativeCTSSdistribution              html  
    distclu-functions                       html  
    exampleCAGEexp                          html  
    exampleCAGEset                          html  
    exampleZv9_annot                        html  
    exportCTSStoBedGraph                    html  
    exportToBed                             html  
    expressionClasses                       html  
    extractExpressionClass                  html  
    genomeName                              html  
    getCTSS                                 html  
    getExpressionProfiles                   html  
    getShiftingPromoters                    html  
    hanabi-class                            html  
    hanabi                                  html  
    hanabiPlot                              html  
    import.CAGEscanMolecule                 html  
    import.CTSS                             html  
    import.bam                              html  
    import.bam.ctss                         html  
    import.bedCTSS                          html  
    import.bedScore                         html  
    import.bedmolecule                      html  
    importPublicData                        html  
    inputFiles                              html  
    inputFilesType                          html  
    librarySizes                            html  
    loadFileIntoGPos                        html  
    mapStats                                html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpScYjdb/R.INSTALL23b8777c14d4/CAGEr/man/mapStats.Rd:29: file link 'mixedorder' in package 'gtools' does not exist and so has been treated as a topic
    mapStatsScopes                          html  
    mergeCAGEsets                           html  
    mergeSamples                            html  
    moleculesGR2CTSS                        html  
    normalizeTagCount                       html  
    parseCAGEscanBlocksToGrangeTSS          html  
    plot.hanabi                             html  
    plotAnnot                               html  
    plotCorrelation                         html  
    plotExpressionProfiles                  html  
    plotInterquantileWidth                  html  
    plotReverseCumulatives                  html  
    powerLaw                                html  
    quantilePositions                       html  
    ranges2annot                            html  
    ranges2genes                            html  
    ranges2names                            html  
    sampleLabels                            html  
    scoreShift                              html  
    seqNameTotalsSE                         html  
    setColors                               html  
    show-methods                            html  
    strandInvaders                          html  
    summariseChrExpr                        html  
    tagClusterConvertors                    html  
    tagClusters                             html  
    tagClustersQuantile                     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 'CAGEr' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CAGEr' as CAGEr_1.31.4.zip
* DONE (CAGEr)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'CAGEr' successfully unpacked and MD5 sums checked