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This page was generated on 2021-09-13 15:06:27 -0400 (Mon, 13 Sep 2021).

INSTALL results for GenoGAM on tokay2

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- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GenoGAM.git to
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raw results

Package 734/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenoGAM 2.10.0  (landing page)
Georg Stricker
Snapshot Date: 2021-09-12 04:50:10 -0400 (Sun, 12 Sep 2021)
git_url: https://git.bioconductor.org/packages/GenoGAM
git_branch: RELEASE_3_13
git_last_commit: 3b86b0c
git_last_commit_date: 2021-05-19 12:19:19 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: GenoGAM
Version: 2.10.0
Command: C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/GenoGAM_2.10.0.tar.gz && rm -rf GenoGAM.buildbin-libdir && mkdir GenoGAM.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GenoGAM.buildbin-libdir GenoGAM_2.10.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL GenoGAM_2.10.0.zip && rm GenoGAM_2.10.0.tar.gz GenoGAM_2.10.0.zip
StartedAt: 2021-09-12 09:09:31 -0400 (Sun, 12 Sep 2021)
EndedAt: 2021-09-12 09:11:47 -0400 (Sun, 12 Sep 2021)
EllapsedTime: 135.8 seconds
RetCode: 0
Status:   OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/GenoGAM_2.10.0.tar.gz && rm -rf GenoGAM.buildbin-libdir && mkdir GenoGAM.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GenoGAM.buildbin-libdir GenoGAM_2.10.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL GenoGAM_2.10.0.zip && rm GenoGAM_2.10.0.tar.gz GenoGAM_2.10.0.zip
###
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##############################################################################


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install for i386

* installing *source* package 'GenoGAM' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I../inst/include -DARMA_64BIT_WORD=1 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include'   -I"c:/extsoft/include"  -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I../inst/include -DARMA_64BIT_WORD=1 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include'   -I"c:/extsoft/include"  -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c matrixMult.cpp -o matrixMult.o
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o GenoGAM.dll tmp.def RcppExports.o matrixMult.o -fopenmp -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.13-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 'HDF5Array::h5ls' by 'rhdf5::h5ls' when loading 'GenoGAM'
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  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/GenoGAM.buildbin-libdir/00LOCK-GenoGAM/00new/GenoGAM/help/GenoGAM.html
    GenoGAMDataSet-class                    html  
    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  
REDIRECT:topic	 Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.13-bioc/meat/GenoGAM.buildbin-libdir/00LOCK-GenoGAM/00new/GenoGAM/help/genogam.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 'HDF5Array::h5ls' by 'rhdf5::h5ls' when loading 'GenoGAM'
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 'HDF5Array::h5ls' by 'rhdf5::h5ls' when loading 'GenoGAM'
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:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I../inst/include -DARMA_64BIT_WORD=1 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"  -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG -I../inst/include -DARMA_64BIT_WORD=1 -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.13-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"  -fopenmp    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c matrixMult.cpp -o matrixMult.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o GenoGAM.dll tmp.def RcppExports.o matrixMult.o -fopenmp -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/GenoGAM.buildbin-libdir/GenoGAM/libs/x64
** testing if installed package can be loaded
Warning: replacing previous import 'HDF5Array::h5ls' by 'rhdf5::h5ls' when loading 'GenoGAM'
Warning: replacing previous import 'S4Vectors::na.omit' by 'stats::na.omit' when loading 'GenoGAM'
* MD5 sums
packaged installation of 'GenoGAM' as GenoGAM_2.10.0.zip
* DONE (GenoGAM)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'GenoGAM' successfully unpacked and MD5 sums checked