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Package 196/479HostnameOS / ArchBUILDCHECKBUILD BIN
GenomicRanges 1.5.16
Biocore Team c/o BioC user list
Snapshot Date: 2011-07-06 19:21:50 -0700 (Wed, 06 Jul 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GenomicRanges
Last Changed Rev: 56570 / Revision: 56603
Last Changed Date: 2011-07-05 14:16:40 -0700 (Tue, 05 Jul 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK  OK [ OK ]

Summary

Package: GenomicRanges
Version: 1.5.16
Command: mkdir GenomicRanges.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh GenomicRanges_1.5.16.tar.gz /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R GenomicRanges.buildbin-libdir
StartedAt: 2011-07-07 06:40:04 -0700 (Thu, 07 Jul 2011)
EndedAt: 2011-07-07 06:40:26 -0700 (Thu, 07 Jul 2011)
EllapsedTime: 22.4 seconds
RetCode: 0
Status:  OK 
PackageFile: GenomicRanges_1.5.16.tgz
PackageFileSize: 1.392 MiB

Command output

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --library=GenomicRanges.buildbin-libdir GenomicRanges_1.5.16.tar.gz'
>>>>>>> 

* installing *source* package 'GenomicRanges' ...
** libs
*** arch - i386
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c IRanges_stubs.c -o IRanges_stubs.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c R_init_GenomicRanges.c -o R_init_GenomicRanges.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/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:1168: warning: 'n' may be used uninitialized in this function
cigar_utils.c: In function 'cigar_to_width':
cigar_utils.c:841: warning: 'width' may be used uninitialized in this function
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/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:207: warning: 'nlocs' may be used uninitialized in this function
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
gcc-4.2 -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-2.9-bioc/meat/GenomicRanges.buildbin-libdir/GenomicRanges/libs/i386
*** arch - ppc
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c IRanges_stubs.c -o IRanges_stubs.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c R_init_GenomicRanges.c -o R_init_GenomicRanges.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/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:1168: warning: 'n' may be used uninitialized in this function
cigar_utils.c: In function 'cigar_to_width':
cigar_utils.c:841: warning: 'width' may be used uninitialized in this function
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/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:207: warning: 'nlocs' may be used uninitialized in this function
gcc-4.2 -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-2.9-bioc/meat/GenomicRanges.buildbin-libdir/GenomicRanges/libs/ppc
*** arch - x86_64
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c IRanges_stubs.c -o IRanges_stubs.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include"   -fPIC  -g -O2 -Wall -pedantic -c R_init_GenomicRanges.c -o R_init_GenomicRanges.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/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:1168: warning: 'n' may be used uninitialized in this function
cigar_utils.c: In function 'cigar_to_width':
cigar_utils.c:841: warning: 'width' may be used uninitialized in this function
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/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:207: warning: 'nlocs' may be used uninitialized in this function
gcc-4.2 -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-2.9-bioc/meat/GenomicRanges.buildbin-libdir/GenomicRanges/libs/x86_64
** R
** inst
** preparing package for lazy loading

Attaching package: 'IRanges'

The following object(s) are masked from 'package:base':

    Map, cbind, eval, intersect, mapply, order, paste, pmax, pmax.int,
    pmin, pmin.int, rbind, rep.int, setdiff, table, union

** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'GenomicRangesIntroduction.Rnw' 
   'GenomicRangesUseCases.Rnw' 
   'countGenomicOverlaps.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/2.14/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/2.14/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/2.14/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/2.14/Resources/lib/libreadline.dylib" "GenomicRanges.buildbin-libdir/GenomicRanges/libs/i386/GenomicRanges.so"


>>>>>>> 
>>>>>>> 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/2.14/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/2.14/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/2.14/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/2.14/Resources/lib/libreadline.dylib" "GenomicRanges.buildbin-libdir/GenomicRanges/libs/ppc/GenomicRanges.so"


>>>>>>> 
>>>>>>> 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/2.14/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/2.14/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/2.14/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/2.14/Resources/lib/libreadline.dylib" "GenomicRanges.buildbin-libdir/GenomicRanges/libs/x86_64/GenomicRanges.so"