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Package 582/609HostnameOS / ArchBUILDCHECKBUILD BIN
TransView 1.0.7
Julius Muller
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/TransView
Last Changed Rev: 73106 / Revision: 74773
Last Changed Date: 2013-02-03 07:25:33 -0800 (Sun, 03 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: TransView
Version: 1.0.7
Command: rm -rf TransView.buildbin-libdir && mkdir TransView.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh TransView_1.0.7.tar.gz /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R TransView.buildbin-libdir
StartedAt: 2013-03-25 02:10:39 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 02:11:07 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 28.5 seconds
RetCode: 0
Status:  OK 
PackageFile: TransView_1.0.7.tgz
PackageFileSize: 1.667 MiB

Command output

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=TransView.buildbin-libdir TransView_1.0.7.tar.gz'
>>>>>>> 

* installing *source* package 'TransView' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include"   -fPIC  -g -O2 -Wall -pedantic  -c R_init_TransView.c -o R_init_TransView.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include"   -fPIC  -g -O2 -Wall -pedantic  -c construct_dc.c -o construct_dc.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include"   -fPIC  -g -O2 -Wall -pedantic  -c parse_sam.c -o parse_sam.o
parse_sam.c: In function 'seq_density':
parse_sam.c:282: warning: comparison is always false due to limited range of data type
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include"   -fPIC  -g -O2 -Wall -pedantic  -c slice_dc.c -o slice_dc.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include"   -fPIC  -g -O2 -Wall -pedantic  -c visuals.c -o visuals.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 TransView.so R_init_TransView.o construct_dc.o parse_sam.o slice_dc.o visuals.o /Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/usrlib/i386/libbam.a -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.11-bioc/meat/TransView.buildbin-libdir/TransView/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'TransView.Rnw' 
** testing if installed package can be loaded

* DONE (TransView)


>>>>>>> 
>>>>>>> FIXING LINKS FOR TransView.buildbin-libdir/TransView/libs/i386/TransView.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" "TransView.buildbin-libdir/TransView/libs/i386/TransView.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libgfortran.2.dylib" "TransView.buildbin-libdir/TransView/libs/i386/TransView.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" "TransView.buildbin-libdir/TransView/libs/i386/TransView.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libreadline.dylib" "TransView.buildbin-libdir/TransView/libs/i386/TransView.so"


>>>>>>> 
>>>>>>> INSTALLATION OF x86_64 LIBS WITH 'R_ARCH=/x86_64 R CMD INSTALL --preclean --no-multiarch --no-test-load --library=TransView.buildbin-libdir --libs-only TransView_1.0.7.tar.gz'
>>>>>>> 

* installing *source* package 'TransView' ...
** 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 -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include"   -fPIC  -g -O2 -Wall -pedantic  -c R_init_TransView.c -o R_init_TransView.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include"   -fPIC  -g -O2 -Wall -pedantic  -c construct_dc.c -o construct_dc.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include"   -fPIC  -g -O2 -Wall -pedantic  -c parse_sam.c -o parse_sam.o
parse_sam.c: In function 'seq_density':
parse_sam.c:282: warning: comparison is always false due to limited range of data type
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include"   -fPIC  -g -O2 -Wall -pedantic  -c slice_dc.c -o slice_dc.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/include"   -fPIC  -g -O2 -Wall -pedantic  -c visuals.c -o visuals.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 TransView.so R_init_TransView.o construct_dc.o parse_sam.o slice_dc.o visuals.o /Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rsamtools/usrlib/x86_64/libbam.a -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.11-bioc/meat/TransView.buildbin-libdir/TransView/libs/x86_64

* DONE (TransView)


>>>>>>> 
>>>>>>> FIXING LINKS FOR TransView.buildbin-libdir/TransView/libs/x86_64/TransView.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" "TransView.buildbin-libdir/TransView/libs/x86_64/TransView.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libgfortran.2.dylib" "TransView.buildbin-libdir/TransView/libs/x86_64/TransView.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" "TransView.buildbin-libdir/TransView/libs/x86_64/TransView.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libreadline.dylib" "TransView.buildbin-libdir/TransView/libs/x86_64/TransView.so"