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INSTALL report for OncoSimulR on tokay2

This page was generated on 2019-10-16 12:30:36 -0400 (Wed, 16 Oct 2019).

Package 1139/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OncoSimulR 2.14.0
Ramon Diaz-Uriarte
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/OncoSimulR
Branch: RELEASE_3_9
Last Commit: 2a871d8
Last Changed Date: 2019-05-02 11:53:48 -0400 (Thu, 02 May 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: OncoSimulR
Version: 2.14.0
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/OncoSimulR_2.14.0.tar.gz && rm -rf OncoSimulR.buildbin-libdir && mkdir OncoSimulR.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=OncoSimulR.buildbin-libdir OncoSimulR_2.14.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL OncoSimulR_2.14.0.zip && rm OncoSimulR_2.14.0.tar.gz OncoSimulR_2.14.0.zip
StartedAt: 2019-10-15 20:03:06 -0400 (Tue, 15 Oct 2019)
EndedAt: 2019-10-15 20:05:14 -0400 (Tue, 15 Oct 2019)
EllapsedTime: 128.4 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/OncoSimulR_2.14.0.tar.gz && rm -rf OncoSimulR.buildbin-libdir && mkdir OncoSimulR.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=OncoSimulR.buildbin-libdir OncoSimulR_2.14.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL OncoSimulR_2.14.0.zip && rm OncoSimulR_2.14.0.tar.gz OncoSimulR_2.14.0.zip
###
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install for i386

* installing *source* package 'OncoSimulR' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -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 BNB_nr.cpp -o BNB_nr.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -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 BNB_v1.cpp -o BNB_v1.o
C:/Rtools/mingw_32/bin/gcc  -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"     -O3 -Wall  -std=gnu99 -mtune=generic -c OncoSimulR_init.c -o OncoSimulR_init.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -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++  -std=gnu++11 -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 accessible_genotypes.cpp -o accessible_genotypes.o
accessible_genotypes.cpp: In function 'Rcpp::IntegerVector accessibleGenotypesPeaksLandscape(Rcpp::IntegerMatrix, Rcpp::NumericVector, Rcpp::IntegerVector, double, bool)':
accessible_genotypes.cpp:224:7: warning: unused variable 'numMutdiff' [-Wunused-variable]
   int numMutdiff = 0;
       ^
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -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 bnb_common.cpp -o bnb_common.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -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 new_restrict.cpp -o new_restrict.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -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 new_restrict_former_print_utils.cpp -o new_restrict_former_print_utils.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o OncoSimulR.dll tmp.def BNB_nr.o BNB_v1.o OncoSimulR_init.o RcppExports.o accessible_genotypes.o bnb_common.o new_restrict.o new_restrict_former_print_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/OncoSimulR.buildbin-libdir/00LOCK-OncoSimulR/00new/OncoSimulR/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'OncoSimulR'
    finding HTML links ... done
    OncoSimulWide2Long                      html  
    POM                                     html  
    allFitnessEffects                       html  
    benchmarks                              html  
    evalAllGenotypes                        html  
    example-missing-drivers                 html  
    examplePosets                           html  
    examplesFitnessEffects                  html  
    mcfLs                                   html  
    oncoSimulIndiv                          html  
    plot.fitnessEffects                     html  
    plot.oncosimul                          html  
    finding level-2 HTML links ... done

    plotClonePhylog                         html  
    plotFitnessLandscape                    html  
    plotPoset                               html  
    poset                                   html  
    rfitness                                html  
    samplePop                               html  
    simOGraph                               html  
    to_Magellan                             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 'OncoSimulR' ...
** libs
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -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 BNB_nr.cpp -o BNB_nr.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -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 BNB_v1.cpp -o BNB_v1.o
C:/Rtools/mingw_64/bin/gcc  -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  -std=gnu99 -mtune=generic -c OncoSimulR_init.c -o OncoSimulR_init.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -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++  -std=gnu++11 -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 accessible_genotypes.cpp -o accessible_genotypes.o
accessible_genotypes.cpp: In function 'Rcpp::IntegerVector accessibleGenotypesPeaksLandscape(Rcpp::IntegerMatrix, Rcpp::NumericVector, Rcpp::IntegerVector, double, bool)':
accessible_genotypes.cpp:224:7: warning: unused variable 'numMutdiff' [-Wunused-variable]
   int numMutdiff = 0;
       ^
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -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 bnb_common.cpp -o bnb_common.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -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 new_restrict.cpp -o new_restrict.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -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 new_restrict_former_print_utils.cpp -o new_restrict_former_print_utils.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o OncoSimulR.dll tmp.def BNB_nr.o BNB_v1.o OncoSimulR_init.o RcppExports.o accessible_genotypes.o bnb_common.o new_restrict.o new_restrict_former_print_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/OncoSimulR.buildbin-libdir/OncoSimulR/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'OncoSimulR' as OncoSimulR_2.14.0.zip
* DONE (OncoSimulR)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'OncoSimulR' successfully unpacked and MD5 sums checked