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Package 232/565HostnameOS / ArchBUILDCHECKBUILD BIN
GenomicRanges 1.9.28
Bioconductor Package Maintainer
Snapshot Date: 2012-06-20 15:22:40 -0700 (Wed, 20 Jun 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges
Last Changed Rev: 66881 / Revision: 66885
Last Changed Date: 2012-06-20 13:17:38 -0700 (Wed, 20 Jun 2012)
lamb1 Linux (openSUSE 12.1) / x86_64  OK  WARNINGS 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS [ OK ]
perceval Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS  OK 

Summary

Package: GenomicRanges
Version: 1.9.28
Command: rm -rf GenomicRanges.buildbin-libdir && mkdir GenomicRanges.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh GenomicRanges_1.9.28.tar.gz /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R GenomicRanges.buildbin-libdir
StartedAt: 2012-06-21 04:51:59 -0700 (Thu, 21 Jun 2012)
EndedAt: 2012-06-21 04:52:32 -0700 (Thu, 21 Jun 2012)
EllapsedTime: 33.6 seconds
RetCode: 0
Status:  OK 
PackageFile: GenomicRanges_1.9.28.tgz
PackageFileSize: 3.051 MiB

Command output

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=GenomicRanges.buildbin-libdir GenomicRanges_1.9.28.tar.gz'
>>>>>>> 

* installing *source* package 'GenomicRanges' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c IRanges_stubs.c -o IRanges_stubs.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c R_init_GenomicRanges.c -o R_init_GenomicRanges.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c cigar_utils.c -o cigar_utils.o
cigar_utils.c: In function 'ref_locs_to_query_locs':
cigar_utils.c:1096: warning: 'n' may be used uninitialized in this function
cigar_utils.c: In function 'cigar_to_width':
cigar_utils.c:763: warning: 'width' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic  -c transcript_utils.c -o transcript_utils.o
transcript_utils.c: In function 'tlocs2rlocs':
transcript_utils.c:119: warning: 'end' may be used uninitialized in this function
transcript_utils.c:119: note: 'end' was declared here
transcript_utils.c:119: warning: 'start' may be used uninitialized in this function
transcript_utils.c:119: note: 'start' was declared here
transcript_utils.c:208: warning: 'nlocs' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o GenomicRanges.so IRanges_stubs.o R_init_GenomicRanges.o cigar_utils.o transcript_utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.11-bioc/meat/GenomicRanges.buildbin-libdir/GenomicRanges/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'GenomicRangesIntroduction.Rnw' 
   'GenomicRangesUseCases.Rnw' 
   'OverlapEncodings.Rnw' 
   'summarizeOverlaps.Rnw' 
** testing if installed package can be loaded

* DONE (GenomicRanges)


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


>>>>>>> 
>>>>>>> INSTALLATION OF ppc LIBS WITH 'R_ARCH=/ppc R CMD INSTALL --preclean --no-multiarch --no-test-load --library=GenomicRanges.buildbin-libdir --libs-only GenomicRanges_1.9.28.tar.gz'
>>>>>>> 

* installing *source* package 'GenomicRanges' ...
** libs
*** arch - ppc
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/ppc -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include"   -fPIC  -g -O2  -c IRanges_stubs.c -o IRanges_stubs.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/ppc -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include"   -fPIC  -g -O2  -c R_init_GenomicRanges.c -o R_init_GenomicRanges.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/ppc -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include"   -fPIC  -g -O2  -c cigar_utils.c -o cigar_utils.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/ppc -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include"   -fPIC  -g -O2  -c transcript_utils.c -o transcript_utils.o
gcc -arch ppc -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o GenomicRanges.so IRanges_stubs.o R_init_GenomicRanges.o cigar_utils.o transcript_utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.11-bioc/meat/GenomicRanges.buildbin-libdir/GenomicRanges/libs/ppc

* DONE (GenomicRanges)


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


>>>>>>> 
>>>>>>> INSTALLATION OF x86_64 LIBS WITH 'R_ARCH=/x86_64 R CMD INSTALL --preclean --no-multiarch --no-test-load --library=GenomicRanges.buildbin-libdir --libs-only GenomicRanges_1.9.28.tar.gz'
>>>>>>> 

* installing *source* package 'GenomicRanges' ...
** libs
*** arch - x86_64
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include"   -fPIC  -g -O2  -c IRanges_stubs.c -o IRanges_stubs.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include"   -fPIC  -g -O2  -c R_init_GenomicRanges.c -o R_init_GenomicRanges.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include"   -fPIC  -g -O2  -c cigar_utils.c -o cigar_utils.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include"   -fPIC  -g -O2  -c transcript_utils.c -o transcript_utils.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 GenomicRanges.so IRanges_stubs.o R_init_GenomicRanges.o cigar_utils.o transcript_utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.11-bioc/meat/GenomicRanges.buildbin-libdir/GenomicRanges/libs/x86_64

* DONE (GenomicRanges)


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