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Package 283/609HostnameOS / ArchBUILDCHECKBUILD BIN
hapFabia 1.0.6
Sepp Hochreiter
Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/hapFabia
Last Changed Rev: 73724 / Revision: 74773
Last Changed Date: 2013-02-25 03:12:31 -0800 (Mon, 25 Feb 2013)
lamb1 Linux (openSUSE 12.1) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Leopard (10.5.8) / i386  OK  OK [ OK ]

Summary

Package: hapFabia
Version: 1.0.6
Command: rm -rf hapFabia.buildbin-libdir && mkdir hapFabia.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh hapFabia_1.0.6.tar.gz /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R hapFabia.buildbin-libdir
StartedAt: 2013-03-25 01:55:11 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 01:55:23 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 12.1 seconds
RetCode: 0
Status:  OK 
PackageFile: hapFabia_1.0.6.tgz
PackageFileSize: 1.629 MiB

Command output

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=hapFabia.buildbin-libdir hapFabia_1.0.6.tar.gz'
>>>>>>> 

* installing *source* package 'hapFabia' ...
rmdir: inst/commandLine/i386: No such file or directory
rmdir: inst/commandLine/x86_64: No such file or directory
rmdir: inst/commandLine/ppc: No such file or directory
rmdir: inst/commandLine/ppc64: No such file or directory
rmdir: inst/commandLine: No such file or directory
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c interfaceR.c -o interfaceR.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c split_sparse_matrixB.c -o split_sparse_matrixB.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c vcftoFABIAB.c -o vcftoFABIAB.o
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o hapFabia.so interfaceR.o split_sparse_matrixB.o vcftoFABIAB.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
gcc -arch i386 -std=gnu99 -c ./commandLine/split_sparse_matrix.c -o ./commandLine/split_sparse_matrix.o -g -O2 -Wall -pedantic 
gcc -arch i386 -std=gnu99 -c split_sparse_matrixB.c -o ./commandLine/split_sparse_matrixB.o -g -O2 -Wall -pedantic 
gcc -arch i386 -std=gnu99 ./commandLine/split_sparse_matrix.o ./commandLine/split_sparse_matrixB.o -o ./commandLine/split_sparse_matrix
mv ./commandLine/split_sparse_matrix ../inst/commandLine//i386
gcc -arch i386 -std=gnu99 -c ./commandLine/vcftoFABIA.c -o ./commandLine/vcftoFABIA.o -g -O2 -Wall -pedantic 
gcc -arch i386 -std=gnu99 -c vcftoFABIAB.c -o ./commandLine/vcftoFABIAB.o -g -O2 -Wall -pedantic 
gcc -arch i386 -std=gnu99 ./commandLine/vcftoFABIA.o ./commandLine/vcftoFABIAB.o -o ./commandLine/vcftoFABIA
mv ./commandLine/vcftoFABIA ../inst/commandLine//i386
installing to /Users/biocbuild/bbs-2.11-bioc/meat/hapFabia.buildbin-libdir/hapFabia/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'hapfabia.Rnw' 
** testing if installed package can be loaded

* DONE (hapFabia)


>>>>>>> 
>>>>>>> FIXING LINKS FOR hapFabia.buildbin-libdir/hapFabia/libs/i386/hapFabia.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libgcc_s.1.dylib" "hapFabia.buildbin-libdir/hapFabia/libs/i386/hapFabia.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libgfortran.2.dylib" "hapFabia.buildbin-libdir/hapFabia/libs/i386/hapFabia.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libreadline.5.2.dylib" "hapFabia.buildbin-libdir/hapFabia/libs/i386/hapFabia.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libreadline.dylib" "hapFabia.buildbin-libdir/hapFabia/libs/i386/hapFabia.so"


>>>>>>> 
>>>>>>> INSTALLATION OF x86_64 LIBS WITH 'R_ARCH=/x86_64 R CMD INSTALL --preclean --no-multiarch --no-test-load --library=hapFabia.buildbin-libdir --libs-only hapFabia_1.0.6.tar.gz'
>>>>>>> 

* installing *source* package 'hapFabia' ...
rmdir: inst/commandLine/i386: No such file or directory
rmdir: inst/commandLine/x86_64: No such file or directory
rmdir: inst/commandLine/ppc: No such file or directory
rmdir: inst/commandLine/ppc64: No such file or directory
rmdir: inst/commandLine: No such file or directory
** libs
*** arch - x86_64
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c interfaceR.c -o interfaceR.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c split_sparse_matrixB.c -o split_sparse_matrixB.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c vcftoFABIAB.c -o vcftoFABIAB.o
gcc -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o hapFabia.so interfaceR.o split_sparse_matrixB.o vcftoFABIAB.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
gcc -arch x86_64 -std=gnu99 -c ./commandLine/split_sparse_matrix.c -o ./commandLine/split_sparse_matrix.o -g -O2 -Wall -pedantic 
gcc -arch x86_64 -std=gnu99 -c split_sparse_matrixB.c -o ./commandLine/split_sparse_matrixB.o -g -O2 -Wall -pedantic 
gcc -arch x86_64 -std=gnu99 ./commandLine/split_sparse_matrix.o ./commandLine/split_sparse_matrixB.o -o ./commandLine/split_sparse_matrix
mv ./commandLine/split_sparse_matrix ../inst/commandLine//x86_64
gcc -arch x86_64 -std=gnu99 -c ./commandLine/vcftoFABIA.c -o ./commandLine/vcftoFABIA.o -g -O2 -Wall -pedantic 
gcc -arch x86_64 -std=gnu99 -c vcftoFABIAB.c -o ./commandLine/vcftoFABIAB.o -g -O2 -Wall -pedantic 
gcc -arch x86_64 -std=gnu99 ./commandLine/vcftoFABIA.o ./commandLine/vcftoFABIAB.o -o ./commandLine/vcftoFABIA
mv ./commandLine/vcftoFABIA ../inst/commandLine//x86_64
installing to /Users/biocbuild/bbs-2.11-bioc/meat/hapFabia.buildbin-libdir/hapFabia/libs/x86_64

* DONE (hapFabia)


>>>>>>> 
>>>>>>> FIXING LINKS FOR hapFabia.buildbin-libdir/hapFabia/libs/x86_64/hapFabia.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libgcc_s.1.dylib" "hapFabia.buildbin-libdir/hapFabia/libs/x86_64/hapFabia.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libgfortran.2.dylib" "hapFabia.buildbin-libdir/hapFabia/libs/x86_64/hapFabia.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libreadline.5.2.dylib" "hapFabia.buildbin-libdir/hapFabia/libs/x86_64/hapFabia.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libreadline.dylib" "hapFabia.buildbin-libdir/hapFabia/libs/x86_64/hapFabia.so"