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INSTALL report for GLAD on tokay2

This page was generated on 2018-10-17 08:32:15 -0400 (Wed, 17 Oct 2018).

Package 619/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GLAD 2.44.0
Philippe Hupe
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/GLAD
Branch: RELEASE_3_7
Last Commit: 029c2dc
Last Changed Date: 2018-04-30 10:35:00 -0400 (Mon, 30 Apr 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: GLAD
Version: 2.44.0
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/GLAD_2.44.0.tar.gz && rm -rf GLAD.buildbin-libdir && mkdir GLAD.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GLAD.buildbin-libdir GLAD_2.44.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL GLAD_2.44.0.zip && rm GLAD_2.44.0.tar.gz GLAD_2.44.0.zip
StartedAt: 2018-10-16 18:31:33 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 18:32:56 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 83.5 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/GLAD_2.44.0.tar.gz && rm -rf GLAD.buildbin-libdir && mkdir GLAD.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GLAD.buildbin-libdir GLAD_2.44.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL GLAD_2.44.0.zip && rm GLAD_2.44.0.tar.gz GLAD_2.44.0.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  385k  100  385k    0     0  6717k      0 --:--:-- --:--:-- --:--:-- 7703k

install for i386

* installing *source* package 'GLAD' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c BkpInfo.cpp -o BkpInfo.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c HaarSeg.cpp -o HaarSeg.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c MoveBkp.cpp -o MoveBkp.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c OutliersGNL.cpp -o OutliersGNL.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c chrBreakpoints.cpp -o chrBreakpoints.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c cutree.cpp -o cutree.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c daglad.cpp -o daglad.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c distance.cpp -o distance.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c filterBkp.cpp -o filterBkp.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c findCluster.cpp -o findCluster.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c glad-utils.cpp -o glad-utils.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c hclust.cpp -o hclust.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c laws.c -o laws.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c loopRemove.cpp -o loopRemove.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o GLAD.dll tmp.def BkpInfo.o HaarSeg.o MoveBkp.o OutliersGNL.o chrBreakpoints.o cutree.o daglad.o distance.o filterBkp.o findCluster.o glad-utils.o hclust.o laws.o loopRemove.o -L/i386/lib -lgsl -lgslcblas -lm -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/GLAD.buildbin-libdir/GLAD/libs/i386
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'GLAD'
    finding HTML links ... done
    ChrNumeric                              html  
    ColorBar                                html  
    GLAD-internal                           html  
    arrayCGH                                html  
    arrayPersp                              html  
    arrayPlot                               html  
    as.data.frame.profileCGH                html  
    as.profileCGH                           html  
    bladder                                 html  
    cytoband                                html  
    daglad                                  html  
    glad                                    html  
    hclust                                  html  
    kernel                                  html  
    myPalette                               html  
    plotProfile                             html  
    profileCGH                              html  
    snijders                                html  
    tkdaglad                                html  
    veltman                                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'GLAD' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c BkpInfo.cpp -o BkpInfo.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c HaarSeg.cpp -o HaarSeg.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c MoveBkp.cpp -o MoveBkp.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c OutliersGNL.cpp -o OutliersGNL.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c chrBreakpoints.cpp -o chrBreakpoints.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c cutree.cpp -o cutree.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c daglad.cpp -o daglad.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c distance.cpp -o distance.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c filterBkp.cpp -o filterBkp.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c findCluster.cpp -o findCluster.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c glad-utils.cpp -o glad-utils.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c hclust.cpp -o hclust.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c laws.c -o laws.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c loopRemove.cpp -o loopRemove.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o GLAD.dll tmp.def BkpInfo.o HaarSeg.o MoveBkp.o OutliersGNL.o chrBreakpoints.o cutree.o daglad.o distance.o filterBkp.o findCluster.o glad-utils.o hclust.o laws.o loopRemove.o -L/x64/lib -lgsl -lgslcblas -lm -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/GLAD.buildbin-libdir/GLAD/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GLAD' as GLAD_2.44.0.zip
* DONE (GLAD)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'GLAD' successfully unpacked and MD5 sums checked
In R CMD INSTALL