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INSTALL report for AneuFinder on tokay1

This page was generated on 2020-08-09 12:08:46 -0400 (Sun, 09 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE AneuFinder PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 52/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
AneuFinder 1.17.0
Aaron Taudt
Snapshot Date: 2020-08-08 14:51:01 -0400 (Sat, 08 Aug 2020)
URL: https://git.bioconductor.org/packages/AneuFinder
Branch: master
Last Commit: e64f35e
Last Changed Date: 2020-04-27 14:55:57 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64 [ OK ] OK  OK  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: AneuFinder
Version: 1.17.0
Command: C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/AneuFinder_1.17.0.tar.gz && rm -rf AneuFinder.buildbin-libdir && mkdir AneuFinder.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=AneuFinder.buildbin-libdir AneuFinder_1.17.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL AneuFinder_1.17.0.zip && rm AneuFinder_1.17.0.tar.gz AneuFinder_1.17.0.zip
StartedAt: 2020-08-08 18:11:10 -0400 (Sat, 08 Aug 2020)
EndedAt: 2020-08-08 18:12:30 -0400 (Sat, 08 Aug 2020)
EllapsedTime: 80.6 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/AneuFinder_1.17.0.tar.gz && rm -rf AneuFinder.buildbin-libdir && mkdir AneuFinder.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=AneuFinder.buildbin-libdir AneuFinder_1.17.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL AneuFinder_1.17.0.zip && rm AneuFinder_1.17.0.tar.gz AneuFinder_1.17.0.zip
###
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100  187k  100  187k    0     0  2811k      0 --:--:-- --:--:-- --:--:-- 2979k

install for i386

* installing *source* package 'AneuFinder' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c R_interface.cpp -o R_interface.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c densities.cpp -o densities.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c init.cpp -o init.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c loghmm.cpp -o loghmm.o
loghmm.cpp:320: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  #pragma omp parallel for
 
loghmm.cpp:480: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  #pragma omp parallel for
 
loghmm.cpp:518: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
   #pragma omp parallel for
 
loghmm.cpp:583: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  #pragma omp parallel for
 
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c scalehmm.cpp -o scalehmm.o
scalehmm.cpp:384: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  #pragma omp parallel for
 
scalehmm.cpp:400: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  #pragma omp parallel for
 
scalehmm.cpp:694: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  #pragma omp parallel for
 
scalehmm.cpp:732: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
   #pragma omp parallel for
 
scalehmm.cpp:791: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  #pragma omp parallel for
 
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c utility.cpp -o utility.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o AneuFinder.dll tmp.def R_interface.o densities.o init.o loghmm.o scalehmm.o utility.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/AneuFinder.buildbin-libdir/00LOCK-AneuFinder/00new/AneuFinder/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'AneuFinder'
    finding HTML links ... done
    AneuFinder-package                      html  
    Aneufinder                              html  
    finding level-2 HTML links ... done

    DNAcopy.findCNVs                        html  
    HMM.findCNVs                            html  
    aneuBiHMM                               html  
    aneuHMM                                 html  
    annotateBreakpoints                     html  
    bam2GRanges                             html  
    bed2GRanges                             html  
    bi.edivisive.findCNVs                   html  
    biDNAcopy.findCNVs                      html  
    biHMM.findCNVs                          html  
    binReads                                html  
    binned.data                             html  
    binning                                 html  
    blacklist                               html  
    clusterByQuality                        html  
    clusterHMMs                             html  
    collapseBins                            html  
    colors                                  html  
    compareMethods                          html  
    compareModels                           html  
    consensusSegments                       html  
    correctGC                               html  
    edivisive.findCNVs                      html  
    estimateComplexity                      html  
    export                                  html  
    filterSegments                          html  
    findCNVs                                html  
    findCNVs.strandseq                      html  
    findHotspots                            html  
    fixedWidthBins                          html  
    getBreakpoints                          html  
    getDistinctColors                       html  
    getQC                                   html  
    getSCEcoordinates                       html  
    heatmapAneuploidies                     html  
    heatmapGenomewide                       html  
    heatmapGenomewideClusters               html  
    hotspotter                              html  
    hotspotter.variable                     html  
    importBed                               html  
    initializeStates                        html  
    karyotypeMeasures                       html  
    loadFromFiles                           html  
    mergeStrandseqFiles                     html  
    plot.GRanges                            html  
    plot.GRangesList                        html  
    plot.aneuBiHMM                          html  
    plot.aneuHMM                            html  
    plot.character                          html  
    plotHeterogeneity                       html  
    plotHistogram                           html  
    plotKaryogram                           html  
    plotProfile                             html  
    plot_pca                                html  
    print.aneuBiHMM                         html  
    print.aneuHMM                           html  
    qualityControl                          html  
    readConfig                              html  
    refineBreakpoints                       html  
    simulateReads                           html  
    subsetByCNVprofile                      html  
    transCoord                              html  
    variableWidthBins                       html  
    writeConfig                             html  
    zinbinom                                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 'AneuFinder' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c R_interface.cpp -o R_interface.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c densities.cpp -o densities.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c init.cpp -o init.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c loghmm.cpp -o loghmm.o
loghmm.cpp:320: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  #pragma omp parallel for
 
loghmm.cpp:480: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  #pragma omp parallel for
 
loghmm.cpp:518: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
   #pragma omp parallel for
 
loghmm.cpp:583: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  #pragma omp parallel for
 
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c scalehmm.cpp -o scalehmm.o
scalehmm.cpp:384: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  #pragma omp parallel for
 
scalehmm.cpp:400: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  #pragma omp parallel for
 
scalehmm.cpp:694: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  #pragma omp parallel for
 
scalehmm.cpp:732: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
   #pragma omp parallel for
 
scalehmm.cpp:791: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  #pragma omp parallel for
 
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c utility.cpp -o utility.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o AneuFinder.dll tmp.def R_interface.o densities.o init.o loghmm.o scalehmm.o utility.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/AneuFinder.buildbin-libdir/AneuFinder/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'AneuFinder' as AneuFinder_1.17.0.zip
* DONE (AneuFinder)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'AneuFinder' successfully unpacked and MD5 sums checked