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Package 129/514HostnameOS / ArchBUILDCHECKBUILD BIN
DECIPHER 1.0.0
Erik Wright
Snapshot Date: 2012-03-23 18:21:46 -0700 (Fri, 23 Mar 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/DECIPHER
Last Changed Rev: 59920 / Revision: 64395
Last Changed Date: 2011-10-31 15:59:03 -0700 (Mon, 31 Oct 2011)
wilson2 Linux (openSUSE 11.4) / 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 ]

Summary

Package: DECIPHER
Version: 1.0.0
Command: rm -rf DECIPHER.buildbin-libdir && mkdir DECIPHER.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh DECIPHER_1.0.0.tar.gz /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R DECIPHER.buildbin-libdir
StartedAt: 2012-03-24 05:12:30 -0700 (Sat, 24 Mar 2012)
EndedAt: 2012-03-24 05:12:58 -0700 (Sat, 24 Mar 2012)
EllapsedTime: 28.1 seconds
RetCode: 0
Status:  OK 
PackageFile: DECIPHER_1.0.0.tgz
PackageFileSize: 745.1 KiB

Command output

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=DECIPHER.buildbin-libdir DECIPHER_1.0.0.tar.gz'
>>>>>>> 

* installing *source* package 'DECIPHER' ...
** libs
*** arch - i386
gcc -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/stats/include"   -fPIC  -g -O2 -Wall -pedantic -c ClusterNJ.c -o ClusterNJ.o
ClusterNJ.c: In function 'clusterNJ':
ClusterNJ.c:263: warning: ignoring #pragma omp parallel
ClusterNJ.c:273: warning: ignoring #pragma omp critical
ClusterNJ.c:433: warning: ignoring #pragma omp parallel
ClusterNJ.c:445: warning: ignoring #pragma omp parallel
ClusterNJ.c: In function 'reclusterNJ':
ClusterNJ.c:590: warning: 'longestLeaf' may be used uninitialized in this function
ClusterNJ.c: In function 'clusterNJ':
ClusterNJ.c:195: warning: 'utilsPackage' may be used uninitialized in this function
ClusterNJ.c:195: warning: 'percentComplete' may be used uninitialized in this function
ClusterNJ.c:194: warning: 'total' may be used uninitialized in this function
ClusterNJ.c:193: warning: 'rPercentComplete' may be used uninitialized in this function
ClusterNJ.c:192: warning: 'minC' may be used uninitialized in this function
ClusterNJ.c:192: warning: 'minR' may be used uninitialized in this function
ClusterNJ.c:506: warning: 'longestLeaf' may be used uninitialized in this function
gcc -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/stats/include"   -fPIC  -g -O2 -Wall -pedantic -c ClusterUPGMA.c -o ClusterUPGMA.o
ClusterUPGMA.c: In function 'clusterUPGMA':
ClusterUPGMA.c:180: warning: ignoring #pragma omp parallel
ClusterUPGMA.c:190: warning: ignoring #pragma omp critical
ClusterUPGMA.c:340: warning: ignoring #pragma omp parallel
ClusterUPGMA.c:352: warning: ignoring #pragma omp parallel
ClusterUPGMA.c:124: warning: 'utilsPackage' may be used uninitialized in this function
ClusterUPGMA.c:124: warning: 'percentComplete' may be used uninitialized in this function
ClusterUPGMA.c:123: warning: 'total' may be used uninitialized in this function
ClusterUPGMA.c:122: warning: 'rPercentComplete' may be used uninitialized in this function
ClusterUPGMA.c:121: warning: 'minC' may be used uninitialized in this function
ClusterUPGMA.c:121: warning: 'minR' may be used uninitialized in this function
gcc -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/stats/include"   -fPIC  -g -O2 -Wall -pedantic -c DistanceMatrix.c -o DistanceMatrix.o
DistanceMatrix.c: In function 'distMatrix':
DistanceMatrix.c:171: warning: ignoring #pragma omp parallel
DistanceMatrix.c:133: warning: 'utilsPackage' may be used uninitialized in this function
DistanceMatrix.c:133: warning: 'percentComplete' may be used uninitialized in this function
DistanceMatrix.c:131: warning: 'rPercentComplete' may be used uninitialized in this function
gcc -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.14/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 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-2.9-bioc/meat/DECIPHER.buildbin-libdir/DECIPHER/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   '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/2.14/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/2.14/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/2.14/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/2.14/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_1.0.0.tar.gz'
>>>>>>> 

* installing *source* package 'DECIPHER' ...
** libs
*** arch - ppc
gcc -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/stats/include"   -fPIC  -g -O2 -Wall -pedantic -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/stats/include"   -fPIC  -g -O2 -Wall -pedantic -c ClusterML.c -o ClusterML.o
gcc -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/stats/include"   -fPIC  -g -O2 -Wall -pedantic -c ClusterNJ.c -o ClusterNJ.o
ClusterNJ.c: In function 'clusterNJ':
ClusterNJ.c:263: warning: ignoring #pragma omp parallel
ClusterNJ.c:273: warning: ignoring #pragma omp critical
ClusterNJ.c:433: warning: ignoring #pragma omp parallel
ClusterNJ.c:445: warning: ignoring #pragma omp parallel
ClusterNJ.c: In function 'reclusterNJ':
ClusterNJ.c:590: warning: 'longestLeaf' may be used uninitialized in this function
ClusterNJ.c: In function 'clusterNJ':
ClusterNJ.c:195: warning: 'utilsPackage' may be used uninitialized in this function
ClusterNJ.c:195: warning: 'percentComplete' may be used uninitialized in this function
ClusterNJ.c:194: warning: 'total' may be used uninitialized in this function
ClusterNJ.c:193: warning: 'rPercentComplete' may be used uninitialized in this function
ClusterNJ.c:192: warning: 'minC' may be used uninitialized in this function
ClusterNJ.c:192: warning: 'minR' may be used uninitialized in this function
ClusterNJ.c:506: warning: 'longestLeaf' may be used uninitialized in this function
gcc -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/stats/include"   -fPIC  -g -O2 -Wall -pedantic -c ClusterUPGMA.c -o ClusterUPGMA.o
ClusterUPGMA.c: In function 'clusterUPGMA':
ClusterUPGMA.c:180: warning: ignoring #pragma omp parallel
ClusterUPGMA.c:190: warning: ignoring #pragma omp critical
ClusterUPGMA.c:340: warning: ignoring #pragma omp parallel
ClusterUPGMA.c:352: warning: ignoring #pragma omp parallel
ClusterUPGMA.c:124: warning: 'utilsPackage' may be used uninitialized in this function
ClusterUPGMA.c:124: warning: 'percentComplete' may be used uninitialized in this function
ClusterUPGMA.c:123: warning: 'total' may be used uninitialized in this function
ClusterUPGMA.c:122: warning: 'rPercentComplete' may be used uninitialized in this function
ClusterUPGMA.c:121: warning: 'minC' may be used uninitialized in this function
ClusterUPGMA.c:121: warning: 'minR' may be used uninitialized in this function
gcc -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/stats/include"   -fPIC  -g -O2 -Wall -pedantic -c CommonGaps.c -o CommonGaps.o
gcc -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/stats/include"   -fPIC  -g -O2 -Wall -pedantic -c ConsensusSequence.c -o ConsensusSequence.o
gcc -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/stats/include"   -fPIC  -g -O2 -Wall -pedantic -c DistanceMatrix.c -o DistanceMatrix.o
DistanceMatrix.c: In function 'distMatrix':
DistanceMatrix.c:171: warning: ignoring #pragma omp parallel
DistanceMatrix.c:133: warning: 'utilsPackage' may be used uninitialized in this function
DistanceMatrix.c:133: warning: 'percentComplete' may be used uninitialized in this function
DistanceMatrix.c:131: warning: 'rPercentComplete' may be used uninitialized in this function
gcc -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/stats/include"   -fPIC  -g -O2 -Wall -pedantic -c R_init_decipher.c -o R_init_decipher.o
gcc -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/stats/include"   -fPIC  -g -O2 -Wall -pedantic -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 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-2.9-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/2.14/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/2.14/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/2.14/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/2.14/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_1.0.0.tar.gz'
>>>>>>> 

* installing *source* package 'DECIPHER' ...
** 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  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/stats/include"   -fPIC  -g -O2 -Wall -pedantic -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/stats/include"   -fPIC  -g -O2 -Wall -pedantic -c ClusterML.c -o ClusterML.o
gcc -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/stats/include"   -fPIC  -g -O2 -Wall -pedantic -c ClusterNJ.c -o ClusterNJ.o
ClusterNJ.c: In function 'clusterNJ':
ClusterNJ.c:263: warning: ignoring #pragma omp parallel
ClusterNJ.c:273: warning: ignoring #pragma omp critical
ClusterNJ.c:433: warning: ignoring #pragma omp parallel
ClusterNJ.c:445: warning: ignoring #pragma omp parallel
ClusterNJ.c: In function 'reclusterNJ':
ClusterNJ.c:590: warning: 'longestLeaf' may be used uninitialized in this function
ClusterNJ.c: In function 'clusterNJ':
ClusterNJ.c:195: warning: 'utilsPackage' may be used uninitialized in this function
ClusterNJ.c:195: warning: 'percentComplete' may be used uninitialized in this function
ClusterNJ.c:194: warning: 'total' may be used uninitialized in this function
ClusterNJ.c:193: warning: 'rPercentComplete' may be used uninitialized in this function
ClusterNJ.c:192: warning: 'minC' may be used uninitialized in this function
ClusterNJ.c:192: warning: 'minR' may be used uninitialized in this function
ClusterNJ.c:506: warning: 'longestLeaf' may be used uninitialized in this function
gcc -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/stats/include"   -fPIC  -g -O2 -Wall -pedantic -c ClusterUPGMA.c -o ClusterUPGMA.o
ClusterUPGMA.c: In function 'clusterUPGMA':
ClusterUPGMA.c:180: warning: ignoring #pragma omp parallel
ClusterUPGMA.c:190: warning: ignoring #pragma omp critical
ClusterUPGMA.c:340: warning: ignoring #pragma omp parallel
ClusterUPGMA.c:352: warning: ignoring #pragma omp parallel
ClusterUPGMA.c:124: warning: 'utilsPackage' may be used uninitialized in this function
ClusterUPGMA.c:124: warning: 'percentComplete' may be used uninitialized in this function
ClusterUPGMA.c:123: warning: 'total' may be used uninitialized in this function
ClusterUPGMA.c:122: warning: 'rPercentComplete' may be used uninitialized in this function
ClusterUPGMA.c:121: warning: 'minC' may be used uninitialized in this function
ClusterUPGMA.c:121: warning: 'minR' may be used uninitialized in this function
gcc -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/stats/include"   -fPIC  -g -O2 -Wall -pedantic -c CommonGaps.c -o CommonGaps.o
gcc -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/stats/include"   -fPIC  -g -O2 -Wall -pedantic -c ConsensusSequence.c -o ConsensusSequence.o
gcc -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/stats/include"   -fPIC  -g -O2 -Wall -pedantic -c DistanceMatrix.c -o DistanceMatrix.o
DistanceMatrix.c: In function 'distMatrix':
DistanceMatrix.c:171: warning: ignoring #pragma omp parallel
DistanceMatrix.c:133: warning: 'utilsPackage' may be used uninitialized in this function
DistanceMatrix.c:133: warning: 'percentComplete' may be used uninitialized in this function
DistanceMatrix.c:131: warning: 'rPercentComplete' may be used uninitialized in this function
gcc -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/stats/include"   -fPIC  -g -O2 -Wall -pedantic -c R_init_decipher.c -o R_init_decipher.o
gcc -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/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/stats/include"   -fPIC  -g -O2 -Wall -pedantic -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 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-2.9-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/2.14/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/2.14/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/2.14/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/2.14/Resources/lib/libreadline.dylib" "DECIPHER.buildbin-libdir/DECIPHER/libs/x86_64/DECIPHER.so"