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INSTALL report for amplican on tokay2

This page was generated on 2019-10-16 12:39:19 -0400 (Wed, 16 Oct 2019).

Package 49/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
amplican 1.6.2
Eivind Valen
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/amplican
Branch: RELEASE_3_9
Last Commit: 3b63746
Last Changed Date: 2019-06-06 14:33:47 -0400 (Thu, 06 Jun 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  OK  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: amplican
Version: 1.6.2
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/amplican_1.6.2.tar.gz && rm -rf amplican.buildbin-libdir && mkdir amplican.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=amplican.buildbin-libdir amplican_1.6.2.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL amplican_1.6.2.zip && rm amplican_1.6.2.tar.gz amplican_1.6.2.zip
StartedAt: 2019-10-15 20:16:19 -0400 (Tue, 15 Oct 2019)
EndedAt: 2019-10-15 20:18:28 -0400 (Tue, 15 Oct 2019)
EllapsedTime: 128.6 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/amplican_1.6.2.tar.gz && rm -rf amplican.buildbin-libdir && mkdir amplican.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=amplican.buildbin-libdir amplican_1.6.2.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL amplican_1.6.2.zip && rm amplican_1.6.2.tar.gz amplican_1.6.2.zip
###
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  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 2073k  100 2073k    0     0  23.6M      0 --:--:-- --:--:-- --:--:-- 25.6M

install for i386

* installing *source* package 'amplican' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c bezier.cpp -o bezier.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o amplican.dll tmp.def RcppExports.o bezier.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/amplican.buildbin-libdir/00LOCK-amplican/00new/amplican/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'amplican'
    finding HTML links ... done
    AlignmentsExperimentSet-class           html  
    finding level-2 HTML links ... done

    alphabetQuality                         html  
    amplican                                html  
    amplicanAlign                           html  
    amplicanConsensus                       html  
    amplicanFilter                          html  
    amplicanMap                             html  
    amplicanNormalize                       html  
    amplicanOverlap                         html  
    amplicanPipeline                        html  
    amplicanPipelineConservative            html  
    amplicanReport                          html  
    amplicanSummarize                       html  
    amplican_print_reads                    html  
    assignedCount                           html  
    barcodeData-set                         html  
    barcodeData                             html  
    checkConfigFile                         html  
    checkFileWriteAccess                    html  
    checkPrimers                            html  
    checkTarget                             html  
    cigarsToEvents                          html  
    comb_along                              html  
    cumsumw                                 html  
    decode                                  html  
    defGR                                   html  
    experimentData-set                      html  
    experimentData                          html  
    extractEvents                           html  
    findEOP                                 html  
    findLQR                                 html  
    findPD                                  html  
    flipRanges                              html  
    fwdReads-set                            html  
    fwdReads                                html  
    fwdReadsType-set                        html  
    fwdReadsType                            html  
    geom_bezier                             html  
    getEventInfo                            html  
    getEvents                               html  
    get_amplicon                            html  
    get_left_primer                         html  
    get_right_primer                        html  
    goodAvgQuality                          html  
    goodBaseQuality                         html  
    lookupAlignment                         html  
    makeAlignment                           html  
    metaplot_deletions                      html  
    metaplot_insertions                     html  
    metaplot_mismatches                     html  
    pairToEvents                            html  
    plot_amplicon                           html  
    plot_cuts                               html  
    plot_deletions                          html  
    plot_height                             html  
    plot_heterogeneity                      html  
    plot_insertions                         html  
    plot_mismatches                         html  
    plot_variants                           html  
    readCounts-set                          html  
    readCounts                              html  
    revComp                                 html  
    rveReads-set                            html  
    rveReads                                html  
    rveReadsType-set                        html  
    rveReadsType                            html  
    unassignedCount                         html  
    unassignedData-set                      html  
    unassignedData                          html  
    upperGroups                             html  
    writeAlignments                         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 'amplican' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c bezier.cpp -o bezier.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o amplican.dll tmp.def RcppExports.o bezier.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/amplican.buildbin-libdir/amplican/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'amplican' as amplican_1.6.2.zip
* DONE (amplican)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'amplican' successfully unpacked and MD5 sums checked