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INSTALL report for CrispRVariants on tokay2

This page was generated on 2018-10-17 08:41:29 -0400 (Wed, 17 Oct 2018).

Package 323/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CrispRVariants 1.8.0
Helen Lindsay
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/CrispRVariants
Branch: RELEASE_3_7
Last Commit: c9f0422
Last Changed Date: 2018-04-30 10:35:39 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: CrispRVariants
Version: 1.8.0
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/CrispRVariants_1.8.0.tar.gz && rm -rf CrispRVariants.buildbin-libdir && mkdir CrispRVariants.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CrispRVariants.buildbin-libdir CrispRVariants_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL CrispRVariants_1.8.0.zip && rm CrispRVariants_1.8.0.tar.gz CrispRVariants_1.8.0.zip
StartedAt: 2018-10-16 19:36:15 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 19:37:53 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 97.9 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/CrispRVariants_1.8.0.tar.gz && rm -rf CrispRVariants.buildbin-libdir && mkdir CrispRVariants.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CrispRVariants.buildbin-libdir CrispRVariants_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL CrispRVariants_1.8.0.zip && rm CrispRVariants_1.8.0.tar.gz CrispRVariants_1.8.0.zip
###
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100 1394k  100 1394k    0     0  22.4M      0 --:--:-- --:--:-- --:--:-- 23.8M

install for i386

* installing *source* package 'CrispRVariants' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'CrispRVariants'
    finding HTML links ... done
    CrisprRun-class                         html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpATTD36/R.INSTALL1dfc2db24932/CrispRVariants/man/CrisprRun-class.Rd:105: file link 'CrisprSet' in package 'CrispRVariants' does not exist and so has been treated as a topic
    CrisprSet-class                         html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpATTD36/R.INSTALL1dfc2db24932/CrispRVariants/man/CrisprSet-class.Rd:293: file link 'CrisprRun' in package 'CrispRVariants' does not exist and so has been treated as a topic
    abifToFastq                             html  
    addClipped                              html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpATTD36/R.INSTALL1dfc2db24932/CrispRVariants/man/addClipped.Rd:19: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    addCodonFrame                           html  
    alleleLabelsHelpers                     html  
    alleles                                 html  
    alns                                    html  
    annotateGenePlot                        html  
    arrangePlots                            html  
    barplotAlleleFreqs                      html  
    collapsePairs                           html  
    consensusSeqs                           html  
    dispatchDots                            html  
    excludeFromBam                          html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpATTD36/R.INSTALL1dfc2db24932/CrispRVariants/man/excludeFromBam.Rd:12: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
    explodeCigarOpCombs                     html  
    findChimeras                            html  
    findSNVs                                html  
    getAxisCoords                           html  
    getChimeras                             html  
    getInsertionsTable                      html  
    gol_clutch1                             html  
    indelCounts                             html  
    indelLabels                             html  
    intersperse                             html  
    makeAlignmentTilePlot                   html  
    mergeChimeras                           html  
    mergeCrisprSets                         html  
    mismatchLabels                          html  
    mutationEfficiency                      html  
    narrowAlignments                        html  
    plotAlignments                          html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpATTD36/R.INSTALL1dfc2db24932/CrispRVariants/man/plotAlignments.Rd:131: file link 'CrisprSet' in package 'CrispRVariants' does not exist and so has been treated as a topic
    plotChimeras                            html  
    plotFreqHeatmap                         html  
    plotVariants                            html  
    rcAlns                                  html  
    readTargetBam                           html  
    readsByPCRPrimer                        html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpATTD36/R.INSTALL1dfc2db24932/CrispRVariants/man/readsByPCRPrimer.Rd:32: file link 'findOverlaps' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpATTD36/R.INSTALL1dfc2db24932/CrispRVariants/man/readsByPCRPrimer.Rd:33: file link 'disjoin' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpATTD36/R.INSTALL1dfc2db24932/CrispRVariants/man/readsByPCRPrimer.Rd:43: file link 'Hits' in package 'S4Vectors' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpATTD36/R.INSTALL1dfc2db24932/CrispRVariants/man/readsByPCRPrimer.Rd:57: file link 'GRanges' in package 'GenomicRanges' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpATTD36/R.INSTALL1dfc2db24932/CrispRVariants/man/readsByPCRPrimer.Rd:57: file link 'GAlignments' in package 'GenomicAlignments' does not exist and so has been treated as a topic
    readsToTarget                           html  
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpATTD36/R.INSTALL1dfc2db24932/CrispRVariants/man/readsToTarget.Rd:111: file link 'findOverlaps' in package 'GenomicAlignments' does not exist and so has been treated as a topic
Rd warning: C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpATTD36/R.INSTALL1dfc2db24932/CrispRVariants/man/readsToTarget.Rd:114: file link 'bpparam' in package 'BiocParallel' does not exist and so has been treated as a topic
    refFromAlns                             html  
    reverseCigar                            html  
    rmMultiPCRChimera                       html  
    selectAlnRegionsHelpers                 html  
    selectOps                               html  
    seqsToAln                               html  
    setDNATileColours                       html  
    setMismatchTileColours                  html  
    transformAlnsToLong                     html  
    variantCounts                           html  
    writeFastq                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'CrispRVariants' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CrispRVariants' as CrispRVariants_1.8.0.zip
* DONE (CrispRVariants)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'CrispRVariants' successfully unpacked and MD5 sums checked
In R CMD INSTALL