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INSTALL report for CoGAPS on tokay2

This page was generated on 2018-10-17 08:34:51 -0400 (Wed, 17 Oct 2018).

Package 287/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CoGAPS 3.0.2
Elana J. Fertig
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/CoGAPS
Branch: RELEASE_3_7
Last Commit: 9d82c1f
Last Changed Date: 2018-07-26 15:59:34 -0400 (Thu, 26 Jul 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  OK  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: CoGAPS
Version: 3.0.2
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/CoGAPS_3.0.2.tar.gz && rm -rf CoGAPS.buildbin-libdir && mkdir CoGAPS.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CoGAPS.buildbin-libdir CoGAPS_3.0.2.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL CoGAPS_3.0.2.zip && rm CoGAPS_3.0.2.tar.gz CoGAPS_3.0.2.zip
StartedAt: 2018-10-16 19:15:44 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 19:19:40 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 235.7 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/CoGAPS_3.0.2.tar.gz && rm -rf CoGAPS.buildbin-libdir && mkdir CoGAPS.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CoGAPS.buildbin-libdir CoGAPS_3.0.2.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL CoGAPS_3.0.2.zip && rm CoGAPS_3.0.2.tar.gz CoGAPS_3.0.2.zip
###
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install for i386

* installing *source* package 'CoGAPS' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c Algorithms.cpp -o Algorithms.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c AtomicSupport.cpp -o AtomicSupport.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c Cogaps.cpp -o Cogaps.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c GibbsSampler.cpp -o GibbsSampler.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c Matrix.cpp -o Matrix.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c Random.cpp -o Random.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/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˜1.7-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c test-runner.cpp -o test-runner.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c cpp_tests/testAlgorithms.cpp -o cpp_tests/testAlgorithms.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c cpp_tests/testAtomicSupport.cpp -o cpp_tests/testAtomicSupport.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c cpp_tests/testGibbsSampler.cpp -o cpp_tests/testGibbsSampler.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c cpp_tests/testMatrix.cpp -o cpp_tests/testMatrix.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c cpp_tests/testRandom.cpp -o cpp_tests/testRandom.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c cpp_tests/testSerialization.cpp -o cpp_tests/testSerialization.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o CoGAPS.dll tmp.def Algorithms.o AtomicSupport.o Cogaps.o GibbsSampler.o Matrix.o Random.o RcppExports.o test-runner.o cpp_tests/testAlgorithms.o cpp_tests/testAtomicSupport.o cpp_tests/testGibbsSampler.o cpp_tests/testMatrix.o cpp_tests/testRandom.o cpp_tests/testSerialization.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/CoGAPS.buildbin-libdir/CoGAPS/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'CoGAPS'
    finding HTML links ... done
    CoGAPS-package                          html  
    CoGAPS                                  html  
    CoGapsFromCheckpoint                    html  
    GIST.D                                  html  
    GIST.S                                  html  
    GSets                                   html  
    GWCoGAPS                                html  
    GWCoGapsFromCheckpoint                  html  
    SimpSim.A                               html  
    SimpSim.D                               html  
    SimpSim.P                               html  
    SimpSim.S                               html  
    SimpSim.result                          html  
    binaryA                                 html  
    calcCoGAPSStat                          html  
    calcGeneGSStat                          html  
    calcZ                                   html  
    cellMatchR                              html  
    computeGeneGSProb                       html  
    createGWCoGAPSSets                      html  
    createscCoGAPSSets                      html  
    displayBuildReport                      html  
    gapsMapRun                              html  
    gapsRun                                 html  
    generateSeeds                           html  
    patternMarkers                          html  
    patternMatch4Parallel                   html  
    patternMatcher                          html  
    plotAtoms                               html  
    plotDiag                                html  
    plotGAPS                                html  
    plotP                                   html  
    plotPatternMarkers                      html  
    finding level-2 HTML links ... done

    plotSmoothPatterns                      html  
    postFixed4Parallel                      html  
    postFixed4SC                            html  
    reOrderBySet                            html  
    reconstructGene                         html  
    reorderByPatternMatch                   html  
    residuals                               html  
    scCoGAPS                                html  
    scCoGapsFromCheckpoint                  html  
    tf2ugFC                                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'CoGAPS' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c Algorithms.cpp -o Algorithms.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c AtomicSupport.cpp -o AtomicSupport.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c Cogaps.cpp -o Cogaps.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c GibbsSampler.cpp -o GibbsSampler.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c Matrix.cpp -o Matrix.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c Random.cpp -o Random.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/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˜1.7-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c test-runner.cpp -o test-runner.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c cpp_tests/testAlgorithms.cpp -o cpp_tests/testAlgorithms.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c cpp_tests/testAtomicSupport.cpp -o cpp_tests/testAtomicSupport.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c cpp_tests/testGibbsSampler.cpp -o cpp_tests/testGibbsSampler.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c cpp_tests/testMatrix.cpp -o cpp_tests/testMatrix.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c cpp_tests/testRandom.cpp -o cpp_tests/testRandom.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c cpp_tests/testSerialization.cpp -o cpp_tests/testSerialization.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o CoGAPS.dll tmp.def Algorithms.o AtomicSupport.o Cogaps.o GibbsSampler.o Matrix.o Random.o RcppExports.o test-runner.o cpp_tests/testAlgorithms.o cpp_tests/testAtomicSupport.o cpp_tests/testGibbsSampler.o cpp_tests/testMatrix.o cpp_tests/testRandom.o cpp_tests/testSerialization.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/CoGAPS.buildbin-libdir/CoGAPS/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CoGAPS' as CoGAPS_3.0.2.zip
* DONE (CoGAPS)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'CoGAPS' successfully unpacked and MD5 sums checked
In R CMD INSTALL