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INSTALL report for GLAD on tokay1

This page was generated on 2020-04-15 12:17:03 -0400 (Wed, 15 Apr 2020).

Package 708/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GLAD 2.50.0
Philippe Hupe
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/GLAD
Branch: RELEASE_3_10
Last Commit: 34b2862
Last Changed Date: 2019-10-29 13:07:30 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64 [ OK ] OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  ERROR  skipped  skipped 

Summary

Package: GLAD
Version: 2.50.0
Command: C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/GLAD_2.50.0.tar.gz && rm -rf GLAD.buildbin-libdir && mkdir GLAD.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GLAD.buildbin-libdir GLAD_2.50.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL GLAD_2.50.0.zip && rm GLAD_2.50.0.tar.gz GLAD_2.50.0.zip
StartedAt: 2020-04-14 18:41:22 -0400 (Tue, 14 Apr 2020)
EndedAt: 2020-04-14 18:42:23 -0400 (Tue, 14 Apr 2020)
EllapsedTime: 61.2 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/GLAD_2.50.0.tar.gz && rm -rf GLAD.buildbin-libdir && mkdir GLAD.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GLAD.buildbin-libdir GLAD_2.50.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL GLAD_2.50.0.zip && rm GLAD_2.50.0.tar.gz GLAD_2.50.0.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  382k  100  382k    0     0  13.9M      0 --:--:-- --:--:-- --:--:-- 16.2M

install for i386

* installing *source* package 'GLAD' ...
** using staged installation

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


** libs
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c BkpInfo.cpp -o BkpInfo.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c HaarSeg.cpp -o HaarSeg.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c MoveBkp.cpp -o MoveBkp.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c OutliersGNL.cpp -o OutliersGNL.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c chrBreakpoints.cpp -o chrBreakpoints.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c cutree.cpp -o cutree.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c daglad.cpp -o daglad.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c distance.cpp -o distance.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c filterBkp.cpp -o filterBkp.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c findCluster.cpp -o findCluster.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c glad-utils.cpp -o glad-utils.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c hclust.cpp -o hclust.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c laws.c -o laws.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I/src/include -I/i386/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c loopRemove.cpp -o loopRemove.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -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-3~1.10-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/GLAD.buildbin-libdir/00LOCK-GLAD/00new/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  
    veltman                                 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 'GLAD' ...

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


** libs
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c BkpInfo.cpp -o BkpInfo.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c HaarSeg.cpp -o HaarSeg.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c MoveBkp.cpp -o MoveBkp.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c OutliersGNL.cpp -o OutliersGNL.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c chrBreakpoints.cpp -o chrBreakpoints.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c cutree.cpp -o cutree.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c daglad.cpp -o daglad.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c distance.cpp -o distance.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c filterBkp.cpp -o filterBkp.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c findCluster.cpp -o findCluster.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c glad-utils.cpp -o glad-utils.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c hclust.cpp -o hclust.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c laws.c -o laws.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I/src/include -I/x64/include    -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c loopRemove.cpp -o loopRemove.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -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-3~1.10-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/GLAD.buildbin-libdir/GLAD/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GLAD' as GLAD_2.50.0.zip
* DONE (GLAD)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'GLAD' successfully unpacked and MD5 sums checked