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INSTALL report for GenoGAM on tokay1

This page was generated on 2020-04-15 12:26:27 -0400 (Wed, 15 Apr 2020).

Package 673/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenoGAM 2.4.0
Georg Stricker
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/GenoGAM
Branch: RELEASE_3_10
Last Commit: 6753a93
Last Changed Date: 2019-10-29 13:09:36 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64 [ OK ] OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: GenoGAM
Version: 2.4.0
Command: C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/GenoGAM_2.4.0.tar.gz && rm -rf GenoGAM.buildbin-libdir && mkdir GenoGAM.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GenoGAM.buildbin-libdir GenoGAM_2.4.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL GenoGAM_2.4.0.zip && rm GenoGAM_2.4.0.tar.gz GenoGAM_2.4.0.zip
StartedAt: 2020-04-14 19:40:29 -0400 (Tue, 14 Apr 2020)
EndedAt: 2020-04-14 19:42:22 -0400 (Tue, 14 Apr 2020)
EllapsedTime: 113.1 seconds
RetCode: 0
Status:  OK  

Command output

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### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/GenoGAM_2.4.0.tar.gz && rm -rf GenoGAM.buildbin-libdir && mkdir GenoGAM.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GenoGAM.buildbin-libdir GenoGAM_2.4.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL GenoGAM_2.4.0.zip && rm GenoGAM_2.4.0.tar.gz GenoGAM_2.4.0.zip
###
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100 3286k  100 3286k    0     0  50.0M      0 --:--:-- --:--:-- --:--:-- 53.4M

install for i386

* installing *source* package 'GenoGAM' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I../inst/include -DARMA_64BIT_WORD=1 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"  -fopenmp    -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I../inst/include -DARMA_64BIT_WORD=1 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"  -fopenmp    -O2 -Wall  -mtune=core2 -c matrixMult.cpp -o matrixMult.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o GenoGAM.dll tmp.def RcppExports.o matrixMult.o -fopenmp -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/GenoGAM.buildbin-libdir/00LOCK-GenoGAM/00new/GenoGAM/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'S4Vectors::na.omit' by 'stats::na.omit' when loading 'GenoGAM'
** help
*** installing help indices
  converting help for package 'GenoGAM'
    finding HTML links ... done
    Coordinates-class                       html  
    GenoGAM-class                           html  
    GenoGAM                                 html  
    GenoGAMDataSet-class                    html  
Rd warning: C:/Users/biocbuild/bbs-3.10-bioc/tmpdir/RtmpYfVVmO/R.INSTALL20ec78525f48/GenoGAM/man/GenoGAMDataSet-class.Rd:139: file link 'GenoGAMSettings' in package 'GenoGAM' does not exist and so has been treated as a topic
    GenoGAMDataSet-metrics                  html  
    GenoGAMDataSet-subsetting               html  
    GenoGAMDataSetList-class                html  
    GenoGAMDataSetList-metrics              html  
    GenoGAMDataSetList-subsetting           html  
    GenoGAMFamily-class                     html  
    GenoGAMList-class                       html  
    GenoGAMList-subsetting                  html  
    GenoGAMSettings-class                   html  
    asCoordinates                           html  
    callPeaks                               html  
    computeRegionSignificance               html  
    computeSignificance                     html  
    computeSizeFactors                      html  
    fitGenoGAM                              html  
    makeTestGenoGAM                         html  
    makeTestGenoGAMDataSet                  html  
    makeTestGenoGAMDataSetList              html  
    makeTestGenoGAMList                     html  
    plotGenoGAM                             html  
    readData                                html  
    writeToBEDFile                          html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'S4Vectors::na.omit' by 'stats::na.omit' when loading 'GenoGAM'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'S4Vectors::na.omit' by 'stats::na.omit' when loading 'GenoGAM'
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'GenoGAM' ...
** libs
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I../inst/include -DARMA_64BIT_WORD=1 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"  -fopenmp    -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I../inst/include -DARMA_64BIT_WORD=1 -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"  -fopenmp    -O2 -Wall  -mtune=core2 -c matrixMult.cpp -o matrixMult.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o GenoGAM.dll tmp.def RcppExports.o matrixMult.o -fopenmp -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/GenoGAM.buildbin-libdir/GenoGAM/libs/x64
** testing if installed package can be loaded
Warning: replacing previous import 'S4Vectors::na.omit' by 'stats::na.omit' when loading 'GenoGAM'
* MD5 sums
packaged installation of 'GenoGAM' as GenoGAM_2.4.0.zip
* DONE (GenoGAM)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'GenoGAM' successfully unpacked and MD5 sums checked