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INSTALL report for genoset on tokay2

This page was generated on 2019-10-16 12:25:00 -0400 (Wed, 16 Oct 2019).

Package 663/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
genoset 1.40.0
Peter M. Haverty
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/genoset
Branch: RELEASE_3_9
Last Commit: 102035f
Last Changed Date: 2019-05-02 11:53:24 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  WARNINGS 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  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: genoset
Version: 1.40.0
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/genoset_1.40.0.tar.gz && rm -rf genoset.buildbin-libdir && mkdir genoset.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=genoset.buildbin-libdir genoset_1.40.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL genoset_1.40.0.zip && rm genoset_1.40.0.tar.gz genoset_1.40.0.zip
StartedAt: 2019-10-15 20:04:47 -0400 (Tue, 15 Oct 2019)
EndedAt: 2019-10-15 20:06:12 -0400 (Tue, 15 Oct 2019)
EllapsedTime: 85.1 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/genoset_1.40.0.tar.gz && rm -rf genoset.buildbin-libdir && mkdir genoset.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=genoset.buildbin-libdir genoset_1.40.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL genoset_1.40.0.zip && rm genoset_1.40.0.tar.gz genoset_1.40.0.zip
###
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install for i386

* installing *source* package 'genoset' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c bounds.c -o bounds.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c init.c -o init.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c rangeSummaries.c -o rangeSummaries.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c utils.c -o utils.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o genoset.dll tmp.def bounds.o init.o rangeSummaries.o utils.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/genoset.buildbin-libdir/00LOCK-genoset/00new/genoset/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
From .checkSubclasses(): subclass "GenomicPos" of class "GenomicRanges" is not local and is not updated for new inheritance information currently; 
[where=, where2=]
** help
*** installing help indices
  converting help for package 'genoset'
    finding HTML links ... done
    GenoSet-class                           html  
    finding level-2 HTML links ... done

    RleDataFrame-class                      html  
    RleDataFrame-views                      html  
    baf2mbaf                                html  
    boundingIndices                         html  
    boundingIndicesByChr                    html  
    bounds2Rle                              html  
    calcGC                                  html  
    calcGC2                                 html  
    chr-methods                             html  
    chrIndices-methods                      html  
    chrInfo-methods                         html  
    chrNames-methods                        html  
    chrOrder                                html  
    chrPartitioning                         html  
    cn2lr-methods                           html  
    do_rledf_range_summary                  html  
    do_rledf_views                          html  
    fixSegNAs                               html  
    gcCorrect                               html  
    genoPlot-methods                        html  
    genoPos-methods                         html  
    genome                                  html  
    genomeAxis                              html  
    genomicranges-methods                   html  
    genoset-dataset                         html  
    genoset-methods                         html  
    genoset-package                         html  
    genoset-subset                          html  
    isGenomeOrder                           html  
    lr2cn                                   html  
    modeCenter                              html  
    numCallable                             html  
    pos-methods                             html  
    rangeSampleMeans                        html  
    rangeSegMeanLength-methods              html  
    rbindDataframe                          html  
    readGenoSet                             html  
    runCBS                                  html  
    segPairTable-methods                    html  
    segTable-methods                        html  
    segs2Granges                            html  
    segs2Rle                                html  
    segs2RleDataFrame                       html  
    toGenomeOrder                           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 'genoset' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c bounds.c -o bounds.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c init.c -o init.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c rangeSummaries.c -o rangeSummaries.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c utils.c -o utils.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o genoset.dll tmp.def bounds.o init.o rangeSummaries.o utils.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/genoset.buildbin-libdir/genoset/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'genoset' as genoset_1.40.0.zip
* DONE (genoset)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'genoset' successfully unpacked and MD5 sums checked