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BioC 2.12: BUILD BIN report for DECIPHER on petty

This page was generated on 2013-10-09 09:40:04 -0700 (Wed, 09 Oct 2013).

Package 169/671HostnameOS / ArchBUILDCHECKBUILD BIN
DECIPHER 1.6.0
Erik Wright
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/DECIPHER
Last Changed Rev: 75263 / Revision: 81334
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ OK ]

Summary

Package: DECIPHER
Version: 1.6.0
Command: rm -rf DECIPHER.buildbin-libdir && mkdir DECIPHER.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh DECIPHER_1.6.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R DECIPHER.buildbin-libdir
StartedAt: 2013-10-09 00:51:34 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 00:52:04 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 29.8 seconds
RetCode: 0
Status:  OK 
PackageFile: DECIPHER_1.6.0.tgz
PackageFileSize: 1.125 MiB

Command output

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=DECIPHER.buildbin-libdir DECIPHER_1.6.0.tar.gz'
>>>>>>> 

* installing *source* package 'DECIPHER' ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/stats/include"   -fPIC  -mtune=core2 -g -O2  -c Biostrings_stubs.c -o Biostrings_stubs.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/stats/include"   -fPIC  -mtune=core2 -g -O2  -c CalculateDeltaG.c -o CalculateDeltaG.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/stats/include"   -fPIC  -mtune=core2 -g -O2  -c ClusterML.c -o ClusterML.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/stats/include"   -fPIC  -mtune=core2 -g -O2  -c ClusterNJ.c -o ClusterNJ.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/stats/include"   -fPIC  -mtune=core2 -g -O2  -c ClusterUPGMA.c -o ClusterUPGMA.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/stats/include"   -fPIC  -mtune=core2 -g -O2  -c CommonGaps.c -o CommonGaps.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/stats/include"   -fPIC  -mtune=core2 -g -O2  -c ConsensusSequence.c -o ConsensusSequence.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/stats/include"   -fPIC  -mtune=core2 -g -O2  -c DistanceMatrix.c -o DistanceMatrix.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/stats/include"   -fPIC  -mtune=core2 -g -O2  -c MultiMatch.c -o MultiMatch.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/stats/include"   -fPIC  -mtune=core2 -g -O2  -c R_init_decipher.c -o R_init_decipher.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/stats/include"   -fPIC  -mtune=core2 -g -O2  -c ReplaceChars.c -o ReplaceChars.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/stats/include"   -fPIC  -mtune=core2 -g -O2  -c TerminalMismatch.c -o TerminalMismatch.o
llvm-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 -L/usr/local/lib -o DECIPHER.so Biostrings_stubs.o CalculateDeltaG.o ClusterML.o ClusterNJ.o ClusterUPGMA.o CommonGaps.o ConsensusSequence.o DistanceMatrix.o MultiMatch.o R_init_decipher.o ReplaceChars.o TerminalMismatch.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/DECIPHER.buildbin-libdir/DECIPHER/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DECIPHER)


>>>>>>> 
>>>>>>> FIXING LINKS FOR DECIPHER.buildbin-libdir/DECIPHER/libs//DECIPHER.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgcc_s.1.dylib" "DECIPHER.buildbin-libdir/DECIPHER/libs//DECIPHER.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgfortran.2.dylib" "DECIPHER.buildbin-libdir/DECIPHER/libs//DECIPHER.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.5.2.dylib" "DECIPHER.buildbin-libdir/DECIPHER/libs//DECIPHER.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.dylib" "DECIPHER.buildbin-libdir/DECIPHER/libs//DECIPHER.so"