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BioC 3.2: BUILD BIN report for gdsfmt on perceval

This page was generated on 2015-10-27 17:36:58 -0400 (Tue, 27 Oct 2015).

Package 392/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gdsfmt 1.6.1
Xiuwen Zheng
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/gdsfmt
Last Changed Rev: 109914 / Revision: 109947
Last Changed Date: 2015-10-25 19:23:23 -0400 (Sun, 25 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK YES, new version is higher than in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK YES, new version is higher than in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK [ OK ]YES, new version is higher than in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK YES, new version is higher than in internal repository

Summary

Package: gdsfmt
Version: 1.6.1
Command: rm -rf gdsfmt.buildbin-libdir && mkdir gdsfmt.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh gdsfmt_1.6.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R gdsfmt.buildbin-libdir
StartedAt: 2015-10-27 11:32:44 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 11:34:30 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 105.8 seconds
RetCode: 0
Status:  OK 
PackageFile: gdsfmt_1.6.1.tgz
PackageFileSize: 1.2 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf gdsfmt.buildbin-libdir && mkdir gdsfmt.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh gdsfmt_1.6.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R gdsfmt.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=gdsfmt.buildbin-libdir gdsfmt_1.6.1.tar.gz'
>>>>>>> 

* installing *source* package ‘gdsfmt’ ...
** libs
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c R_CoreArray.cpp -o R_CoreArray.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c gdsfmt.cpp -o gdsfmt.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c CoreArray/CoreArray.cpp -o CoreArray/CoreArray.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c CoreArray/dAllocator.cpp -o CoreArray/dAllocator.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c CoreArray/dAny.cpp -o CoreArray/dAny.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c CoreArray/dBase.cpp -o CoreArray/dBase.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c CoreArray/dBitGDS.cpp -o CoreArray/dBitGDS.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c CoreArray/dEndian.cpp -o CoreArray/dEndian.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c CoreArray/dFile.cpp -o CoreArray/dFile.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c CoreArray/dParallel.cpp -o CoreArray/dParallel.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c CoreArray/dParallel_Ext.c -o CoreArray/dParallel_Ext.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c CoreArray/dPlatform.cpp -o CoreArray/dPlatform.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c CoreArray/dSerial.cpp -o CoreArray/dSerial.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c CoreArray/dStream.cpp -o CoreArray/dStream.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c CoreArray/dStruct.cpp -o CoreArray/dStruct.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c ZLIB/adler32.c -o ZLIB/adler32.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c ZLIB/compress.c -o ZLIB/compress.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c ZLIB/crc32.c -o ZLIB/crc32.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c ZLIB/deflate.c -o ZLIB/deflate.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c ZLIB/infback.c -o ZLIB/infback.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c ZLIB/inffast.c -o ZLIB/inffast.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c ZLIB/inflate.c -o ZLIB/inflate.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c ZLIB/inftrees.c -o ZLIB/inftrees.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c ZLIB/trees.c -o ZLIB/trees.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c ZLIB/uncompr.c -o ZLIB/uncompr.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c ZLIB/zutil.c -o ZLIB/zutil.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c LZ4/lz4.c -o LZ4/lz4.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c LZ4/lz4hc.c -o LZ4/lz4hc.o
LZ4/lz4.c:153: warning: ‘LZ4_readLE16’ defined but not used
LZ4/lz4.c:202: warning: ‘LZ4_copy4’ defined but not used
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c LZ4/lz4frame.c -o LZ4/lz4frame.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DUSING_R -I../inst/include -ICoreArray -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c LZ4/xxhash.c -o LZ4/xxhash.o
llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -L/usr/local/lib -o gdsfmt.so R_CoreArray.o gdsfmt.o CoreArray/CoreArray.o CoreArray/dAllocator.o CoreArray/dAny.o CoreArray/dBase.o CoreArray/dBitGDS.o CoreArray/dEndian.o CoreArray/dFile.o CoreArray/dParallel.o CoreArray/dParallel_Ext.o CoreArray/dPlatform.o CoreArray/dSerial.o CoreArray/dStream.o CoreArray/dStruct.o ZLIB/adler32.o ZLIB/compress.o ZLIB/crc32.o ZLIB/deflate.o ZLIB/infback.o ZLIB/inffast.o ZLIB/inflate.o ZLIB/inftrees.o ZLIB/trees.o ZLIB/uncompr.o ZLIB/zutil.o LZ4/lz4.o LZ4/lz4hc.o LZ4/lz4frame.o LZ4/xxhash.o -lpthread -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.2-bioc/meat/gdsfmt.buildbin-libdir/gdsfmt/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (gdsfmt)


>>>>>>> 
>>>>>>> FIXING LINKS FOR gdsfmt.buildbin-libdir/gdsfmt/libs//gdsfmt.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libgcc_s.1.dylib" "gdsfmt.buildbin-libdir/gdsfmt/libs//gdsfmt.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libgfortran.2.dylib" "gdsfmt.buildbin-libdir/gdsfmt/libs//gdsfmt.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libreadline.5.2.dylib" "gdsfmt.buildbin-libdir/gdsfmt/libs//gdsfmt.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.2/Resources/lib/libreadline.dylib" "gdsfmt.buildbin-libdir/gdsfmt/libs//gdsfmt.so"