DECIPHER 1.3.1 Erik Wright
Snapshot Date: 2012-06-20 15:22:40 -0700 (Wed, 20 Jun 2012) | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/DECIPHER | Last Changed Rev: 66763 / Revision: 66885 | Last Changed Date: 2012-06-15 14:46:54 -0700 (Fri, 15 Jun 2012) |
| lamb1 | Linux (openSUSE 12.1) / x86_64 | OK | OK | |
moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
pitt | Mac OS X Leopard (10.5.8) / i386 | OK | OK | [ OK ] |
perceval | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=DECIPHER.buildbin-libdir DECIPHER_1.3.1.tar.gz'
>>>>>>>
* installing *source* package 'DECIPHER' ...
** 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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/stats/include" -fPIC -g -O2 -Wall -pedantic -c Biostrings_stubs.c -o Biostrings_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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/stats/include" -fPIC -g -O2 -Wall -pedantic -c CalculateDeltaG.c -o CalculateDeltaG.o
CalculateDeltaG.c: In function 'calculateDeltaG':
CalculateDeltaG.c:26: warning: 's2' may be used uninitialized in this function
CalculateDeltaG.c:26: warning: 's1' 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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/stats/include" -fPIC -g -O2 -Wall -pedantic -c ClusterML.c -o ClusterML.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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/stats/include" -fPIC -g -O2 -Wall -pedantic -c ClusterNJ.c -o ClusterNJ.o
ClusterNJ.c: In function 'clusterNJ':
ClusterNJ.c:266: warning: ignoring #pragma omp parallel
ClusterNJ.c:276: warning: ignoring #pragma omp critical
ClusterNJ.c:436: warning: ignoring #pragma omp parallel
ClusterNJ.c:448: warning: ignoring #pragma omp parallel
ClusterNJ.c: In function 'reclusterNJ':
ClusterNJ.c:593: warning: 'longestLeaf' may be used uninitialized in this function
ClusterNJ.c: In function 'clusterNJ':
ClusterNJ.c:198: warning: 'utilsPackage' may be used uninitialized in this function
ClusterNJ.c:198: warning: 'percentComplete' may be used uninitialized in this function
ClusterNJ.c:197: warning: 'total' may be used uninitialized in this function
ClusterNJ.c:196: warning: 'rPercentComplete' may be used uninitialized in this function
ClusterNJ.c:195: warning: 'minC' may be used uninitialized in this function
ClusterNJ.c:195: warning: 'minR' may be used uninitialized in this function
ClusterNJ.c:509: warning: 'longestLeaf' 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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/stats/include" -fPIC -g -O2 -Wall -pedantic -c ClusterUPGMA.c -o ClusterUPGMA.o
ClusterUPGMA.c: In function 'clusterUPGMA':
ClusterUPGMA.c:183: warning: ignoring #pragma omp parallel
ClusterUPGMA.c:193: warning: ignoring #pragma omp critical
ClusterUPGMA.c:343: warning: ignoring #pragma omp parallel
ClusterUPGMA.c:355: warning: ignoring #pragma omp parallel
ClusterUPGMA.c:127: warning: 'utilsPackage' may be used uninitialized in this function
ClusterUPGMA.c:127: warning: 'percentComplete' may be used uninitialized in this function
ClusterUPGMA.c:126: warning: 'total' may be used uninitialized in this function
ClusterUPGMA.c:125: warning: 'rPercentComplete' may be used uninitialized in this function
ClusterUPGMA.c:124: warning: 'minC' may be used uninitialized in this function
ClusterUPGMA.c:124: warning: 'minR' 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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/stats/include" -fPIC -g -O2 -Wall -pedantic -c CommonGaps.c -o CommonGaps.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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/stats/include" -fPIC -g -O2 -Wall -pedantic -c ConsensusSequence.c -o ConsensusSequence.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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/stats/include" -fPIC -g -O2 -Wall -pedantic -c DistanceMatrix.c -o DistanceMatrix.o
DistanceMatrix.c: In function 'distMatrix':
DistanceMatrix.c:174: warning: ignoring #pragma omp parallel
DistanceMatrix.c:136: warning: 'utilsPackage' may be used uninitialized in this function
DistanceMatrix.c:136: warning: 'percentComplete' may be used uninitialized in this function
DistanceMatrix.c:134: warning: 'rPercentComplete' 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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/stats/include" -fPIC -g -O2 -Wall -pedantic -c R_init_decipher.c -o R_init_decipher.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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/stats/include" -fPIC -g -O2 -Wall -pedantic -c ReplaceChars.c -o ReplaceChars.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 DECIPHER.so Biostrings_stubs.o CalculateDeltaG.o ClusterML.o ClusterNJ.o ClusterUPGMA.o CommonGaps.o ConsensusSequence.o DistanceMatrix.o R_init_decipher.o ReplaceChars.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.11-bioc/meat/DECIPHER.buildbin-libdir/DECIPHER/libs/i386
** R
** data
** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
'DECIPHERing.Rnw'
'FindChimeras.Rnw'
** testing if installed package can be loaded
* DONE (DECIPHER)
>>>>>>>
>>>>>>> FIXING LINKS FOR DECIPHER.buildbin-libdir/DECIPHER/libs/i386/DECIPHER.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" "DECIPHER.buildbin-libdir/DECIPHER/libs/i386/DECIPHER.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libgfortran.2.dylib" "DECIPHER.buildbin-libdir/DECIPHER/libs/i386/DECIPHER.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" "DECIPHER.buildbin-libdir/DECIPHER/libs/i386/DECIPHER.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libreadline.dylib" "DECIPHER.buildbin-libdir/DECIPHER/libs/i386/DECIPHER.so"
>>>>>>>
>>>>>>> INSTALLATION OF ppc LIBS WITH 'R_ARCH=/ppc R CMD INSTALL --preclean --no-multiarch --no-test-load --library=DECIPHER.buildbin-libdir --libs-only DECIPHER_1.3.1.tar.gz'
>>>>>>>
* installing *source* package 'DECIPHER' ...
** 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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/stats/include" -fPIC -g -O2 -c Biostrings_stubs.c -o Biostrings_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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/stats/include" -fPIC -g -O2 -c CalculateDeltaG.c -o CalculateDeltaG.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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/stats/include" -fPIC -g -O2 -c ClusterML.c -o ClusterML.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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/stats/include" -fPIC -g -O2 -c ClusterNJ.c -o ClusterNJ.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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/stats/include" -fPIC -g -O2 -c ClusterUPGMA.c -o ClusterUPGMA.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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/stats/include" -fPIC -g -O2 -c CommonGaps.c -o CommonGaps.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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/stats/include" -fPIC -g -O2 -c ConsensusSequence.c -o ConsensusSequence.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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/stats/include" -fPIC -g -O2 -c DistanceMatrix.c -o DistanceMatrix.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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/stats/include" -fPIC -g -O2 -c R_init_decipher.c -o R_init_decipher.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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/stats/include" -fPIC -g -O2 -c ReplaceChars.c -o ReplaceChars.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 DECIPHER.so Biostrings_stubs.o CalculateDeltaG.o ClusterML.o ClusterNJ.o ClusterUPGMA.o CommonGaps.o ConsensusSequence.o DistanceMatrix.o R_init_decipher.o ReplaceChars.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.11-bioc/meat/DECIPHER.buildbin-libdir/DECIPHER/libs/ppc
* DONE (DECIPHER)
>>>>>>>
>>>>>>> FIXING LINKS FOR DECIPHER.buildbin-libdir/DECIPHER/libs/ppc/DECIPHER.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" "DECIPHER.buildbin-libdir/DECIPHER/libs/ppc/DECIPHER.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libgfortran.2.dylib" "DECIPHER.buildbin-libdir/DECIPHER/libs/ppc/DECIPHER.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" "DECIPHER.buildbin-libdir/DECIPHER/libs/ppc/DECIPHER.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libreadline.dylib" "DECIPHER.buildbin-libdir/DECIPHER/libs/ppc/DECIPHER.so"
>>>>>>>
>>>>>>> INSTALLATION OF x86_64 LIBS WITH 'R_ARCH=/x86_64 R CMD INSTALL --preclean --no-multiarch --no-test-load --library=DECIPHER.buildbin-libdir --libs-only DECIPHER_1.3.1.tar.gz'
>>>>>>>
* installing *source* package 'DECIPHER' ...
** 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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/stats/include" -fPIC -g -O2 -c Biostrings_stubs.c -o Biostrings_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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/stats/include" -fPIC -g -O2 -c CalculateDeltaG.c -o CalculateDeltaG.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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/stats/include" -fPIC -g -O2 -c ClusterML.c -o ClusterML.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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/stats/include" -fPIC -g -O2 -c ClusterNJ.c -o ClusterNJ.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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/stats/include" -fPIC -g -O2 -c ClusterUPGMA.c -o ClusterUPGMA.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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/stats/include" -fPIC -g -O2 -c CommonGaps.c -o CommonGaps.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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/stats/include" -fPIC -g -O2 -c ConsensusSequence.c -o ConsensusSequence.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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/stats/include" -fPIC -g -O2 -c DistanceMatrix.c -o DistanceMatrix.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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/stats/include" -fPIC -g -O2 -c R_init_decipher.c -o R_init_decipher.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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/stats/include" -fPIC -g -O2 -c ReplaceChars.c -o ReplaceChars.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 DECIPHER.so Biostrings_stubs.o CalculateDeltaG.o ClusterML.o ClusterNJ.o ClusterUPGMA.o CommonGaps.o ConsensusSequence.o DistanceMatrix.o R_init_decipher.o ReplaceChars.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.11-bioc/meat/DECIPHER.buildbin-libdir/DECIPHER/libs/x86_64
* DONE (DECIPHER)
>>>>>>>
>>>>>>> FIXING LINKS FOR DECIPHER.buildbin-libdir/DECIPHER/libs/x86_64/DECIPHER.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" "DECIPHER.buildbin-libdir/DECIPHER/libs/x86_64/DECIPHER.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libgfortran.2.dylib" "DECIPHER.buildbin-libdir/DECIPHER/libs/x86_64/DECIPHER.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" "DECIPHER.buildbin-libdir/DECIPHER/libs/x86_64/DECIPHER.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libreadline.dylib" "DECIPHER.buildbin-libdir/DECIPHER/libs/x86_64/DECIPHER.so"