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INSTALL report for rhdf5 on tokay2

This page was generated on 2019-10-16 12:26:04 -0400 (Wed, 16 Oct 2019).

Package 1371/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rhdf5 2.28.1
Mike Smith
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/rhdf5
Branch: RELEASE_3_9
Last Commit: e230fa3
Last Changed Date: 2019-10-10 09:09:17 -0400 (Thu, 10 Oct 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: rhdf5
Version: 2.28.1
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/rhdf5_2.28.1.tar.gz && rm -rf rhdf5.buildbin-libdir && mkdir rhdf5.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=rhdf5.buildbin-libdir rhdf5_2.28.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL rhdf5_2.28.1.zip && rm rhdf5_2.28.1.tar.gz rhdf5_2.28.1.zip
StartedAt: 2019-10-15 18:43:30 -0400 (Tue, 15 Oct 2019)
EndedAt: 2019-10-15 18:44:57 -0400 (Tue, 15 Oct 2019)
EllapsedTime: 87.3 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/rhdf5_2.28.1.tar.gz && rm -rf rhdf5.buildbin-libdir && mkdir rhdf5.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=rhdf5.buildbin-libdir rhdf5_2.28.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL rhdf5_2.28.1.zip && rm rhdf5_2.28.1.tar.gz rhdf5_2.28.1.zip
###
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install for i386

* installing *source* package 'rhdf5' ...
** using staged installation
** libs
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/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O3 -Wall  -std=gnu99 -mtune=generic -c H5.c -o H5.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/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O3 -Wall  -std=gnu99 -mtune=generic -c H5A.c -o H5A.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/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O3 -Wall  -std=gnu99 -mtune=generic -c H5D.c -o H5D.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/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O3 -Wall  -std=gnu99 -mtune=generic -c H5E.c -o H5E.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/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O3 -Wall  -std=gnu99 -mtune=generic -c H5F.c -o H5F.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/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O3 -Wall  -std=gnu99 -mtune=generic -c H5G.c -o H5G.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/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O3 -Wall  -std=gnu99 -mtune=generic -c H5I.c -o H5I.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/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O3 -Wall  -std=gnu99 -mtune=generic -c H5L.c -o H5L.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/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O3 -Wall  -std=gnu99 -mtune=generic -c H5O.c -o H5O.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/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O3 -Wall  -std=gnu99 -mtune=generic -c H5P.c -o H5P.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/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O3 -Wall  -std=gnu99 -mtune=generic -c H5S.c -o H5S.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/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O3 -Wall  -std=gnu99 -mtune=generic -c H5T.c -o H5T.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/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O3 -Wall  -std=gnu99 -mtune=generic -c H5Z.c -o H5Z.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/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O3 -Wall  -std=gnu99 -mtune=generic -c H5constants.c -o H5constants.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c HandleList.cpp -o HandleList.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/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O3 -Wall  -std=gnu99 -mtune=generic -c HandleListWrap.c -o HandleListWrap.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/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O3 -Wall  -std=gnu99 -mtune=generic -c h5dump.c -o h5dump.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/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O3 -Wall  -std=gnu99 -mtune=generic -c h5ls.c -o h5ls.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/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O3 -Wall  -std=gnu99 -mtune=generic -c h5testLock.c -o h5testLock.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/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O3 -Wall  -std=gnu99 -mtune=generic -c h5writeDataFrame.c -o h5writeDataFrame.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/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O3 -Wall  -std=gnu99 -mtune=generic -c printdatatype.c -o printdatatype.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/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O3 -Wall  -std=gnu99 -mtune=generic -c wrap.c -o wrap.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o rhdf5.dll tmp.def H5.o H5A.o H5D.o H5E.o H5F.o H5G.o H5I.o H5L.o H5O.o H5P.o H5S.o H5T.o H5Z.o H5constants.o HandleList.o HandleListWrap.o h5dump.o h5ls.o h5testLock.o h5writeDataFrame.o printdatatype.o wrap.o -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/library/Rhdf5lib/lib/i386 -lhdf5_cpp -lhdf5 -lszip -lz -lpsapi -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/rhdf5.buildbin-libdir/00LOCK-rhdf5/00new/rhdf5/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'rhdf5'
    finding HTML links ... done
    H5                                      html  
    H5A                                     html  
    H5D                                     html  
    H5F                                     html  
    H5G                                     html  
    H5I                                     html  
    H5IdComponent-class                     html  
    H5L                                     html  
    H5O                                     html  
    H5P                                     html  
    H5P_DATASET_ACCESS                      html  
    H5P_DATASET_CREATE                      html  
    H5P_LINK_CREATE                         html  
    H5S                                     html  
    H5T                                     html  
    h5closeAll                              html  
    h5const                                 html  
    h5createAttribute                       html  
    h5createDataset                         html  
    h5createFile                            html  
    h5createGroup                           html  
    h5delete                                html  
    h5errorHandling                         html  
    h5fileLocking                           html  
    h5listIdentifier                        html  
    h5ls                                    html  
    h5save                                  html  
    h5set_extent                            html  
    h5version                               html  
    h5write                                 html  
    methods-And                             html  
    methods-Dollar1                         html  
    methods-Dollar2                         html  
    methods-subset1                         html  
    methods-subset2                         html  
    rhdf5                                   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 'rhdf5' ...
** libs
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/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O2 -Wall  -std=gnu99 -mtune=generic -c H5.c -o H5.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/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O2 -Wall  -std=gnu99 -mtune=generic -c H5A.c -o H5A.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/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O2 -Wall  -std=gnu99 -mtune=generic -c H5D.c -o H5D.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/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O2 -Wall  -std=gnu99 -mtune=generic -c H5E.c -o H5E.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/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O2 -Wall  -std=gnu99 -mtune=generic -c H5F.c -o H5F.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/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O2 -Wall  -std=gnu99 -mtune=generic -c H5G.c -o H5G.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/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O2 -Wall  -std=gnu99 -mtune=generic -c H5I.c -o H5I.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/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O2 -Wall  -std=gnu99 -mtune=generic -c H5L.c -o H5L.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/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O2 -Wall  -std=gnu99 -mtune=generic -c H5O.c -o H5O.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/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O2 -Wall  -std=gnu99 -mtune=generic -c H5P.c -o H5P.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/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O2 -Wall  -std=gnu99 -mtune=generic -c H5S.c -o H5S.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/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O2 -Wall  -std=gnu99 -mtune=generic -c H5T.c -o H5T.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/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O2 -Wall  -std=gnu99 -mtune=generic -c H5Z.c -o H5Z.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/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O2 -Wall  -std=gnu99 -mtune=generic -c H5constants.c -o H5constants.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhdf5lib/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c HandleList.cpp -o HandleList.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/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O2 -Wall  -std=gnu99 -mtune=generic -c HandleListWrap.c -o HandleListWrap.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/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O2 -Wall  -std=gnu99 -mtune=generic -c h5dump.c -o h5dump.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/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O2 -Wall  -std=gnu99 -mtune=generic -c h5ls.c -o h5ls.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/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O2 -Wall  -std=gnu99 -mtune=generic -c h5testLock.c -o h5testLock.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/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O2 -Wall  -std=gnu99 -mtune=generic -c h5writeDataFrame.c -o h5writeDataFrame.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/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O2 -Wall  -std=gnu99 -mtune=generic -c printdatatype.c -o printdatatype.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/Rhdf5lib/include"   -I"C:/extsoft/include"  "-w"   -O2 -Wall  -std=gnu99 -mtune=generic -c wrap.c -o wrap.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o rhdf5.dll tmp.def H5.o H5A.o H5D.o H5E.o H5F.o H5G.o H5I.o H5L.o H5O.o H5P.o H5S.o H5T.o H5Z.o H5constants.o HandleList.o HandleListWrap.o h5dump.o h5ls.o h5testLock.o h5writeDataFrame.o printdatatype.o wrap.o -LC:/Users/BIOCBU~1/BBS-3~1.9-B/R/library/Rhdf5lib/lib/x64 -lhdf5_cpp -lhdf5 -lszip -lz -lpsapi -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/rhdf5.buildbin-libdir/rhdf5/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'rhdf5' as rhdf5_2.28.1.zip
* DONE (rhdf5)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'rhdf5' successfully unpacked and MD5 sums checked