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BioC 3.0: BUILD BIN report for DECIPHER on perceval

This page was generated on 2015-04-10 09:56:20 -0700 (Fri, 10 Apr 2015).

Package 226/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DECIPHER 1.12.0
Erik Wright
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/DECIPHER
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK [ OK ]
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: DECIPHER
Version: 1.12.0
Command: rm -rf DECIPHER.buildbin-libdir && mkdir DECIPHER.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh DECIPHER_1.12.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R DECIPHER.buildbin-libdir
StartedAt: 2015-04-10 08:06:32 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 08:06:59 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 27.0 seconds
RetCode: 0
Status:  OK 
PackageFile: DECIPHER_1.12.0.tgz
PackageFileSize: 3.04 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf DECIPHER.buildbin-libdir && mkdir DECIPHER.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh DECIPHER_1.12.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R DECIPHER.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=DECIPHER.buildbin-libdir DECIPHER_1.12.0.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/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c AlignProfiles.c -o AlignProfiles.o
AlignProfiles.c: In function ‘alignProfiles’:
AlignProfiles.c:189: warning: ignoring #pragma omp parallel
AlignProfiles.c: In function ‘alignProfilesAA’:
AlignProfiles.c:525: warning: ignoring #pragma omp parallel
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/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -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/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -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/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c CalculateFISH.c -o CalculateFISH.o
CalculateFISH.c: In function ‘calculateFISH’:
CalculateFISH.c:26: warning: missing braces around initializer
CalculateFISH.c:26: warning: (near initialization for ‘dH_DR[0]’)
CalculateFISH.c:32: warning: missing braces around initializer
CalculateFISH.c:32: warning: (near initialization for ‘dS_DR[0]’)
CalculateFISH.c:38: warning: missing braces around initializer
CalculateFISH.c:38: warning: (near initialization for ‘dH_DD[0]’)
CalculateFISH.c:44: warning: missing braces around initializer
CalculateFISH.c:44: warning: (near initialization for ‘dS_DD[0]’)
CalculateFISH.c:50: warning: missing braces around initializer
CalculateFISH.c:50: warning: (near initialization for ‘dH_RR[0]’)
CalculateFISH.c:56: warning: missing braces around initializer
CalculateFISH.c:56: warning: (near initialization for ‘dS_RR[0]’)
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/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c ClusterML.c -o ClusterML.o
ClusterML.c: In function ‘clusterML’:
ClusterML.c:422: warning: ignoring #pragma omp parallel
ClusterML.c:427: warning: ignoring #pragma omp parallel
ClusterML.c:432: warning: ignoring #pragma omp parallel
ClusterML.c:400: warning: unused variable ‘nthreads’
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/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c ClusterNJ.c -o ClusterNJ.o
ClusterNJ.c: In function ‘clusterNJ’:
ClusterNJ.c:267: warning: ignoring #pragma omp parallel
ClusterNJ.c:277: warning: ignoring #pragma omp critical
ClusterNJ.c:437: warning: ignoring #pragma omp parallel
ClusterNJ.c:449: warning: ignoring #pragma omp parallel
ClusterNJ.c:214: warning: unused variable ‘nthreads’
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/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c ClusterUPGMA.c -o ClusterUPGMA.o
ClusterUPGMA.c: In function ‘clusterUPGMA’:
ClusterUPGMA.c:185: warning: ignoring #pragma omp parallel
ClusterUPGMA.c:195: warning: ignoring #pragma omp critical
ClusterUPGMA.c:375: warning: ignoring #pragma omp parallel
ClusterUPGMA.c:387: warning: ignoring #pragma omp parallel
ClusterUPGMA.c:128: warning: unused variable ‘nthreads’
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/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -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/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -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/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c DesignProbes.c -o DesignProbes.o
DesignProbes.c: In function ‘designProbes’:
DesignProbes.c:71: warning: missing braces around initializer
DesignProbes.c:71: warning: (near initialization for ‘NN[0]’)
DesignProbes.c:78: warning: missing braces around initializer
DesignProbes.c:78: warning: (near initialization for ‘PM[0]’)
DesignProbes.c:85: warning: missing braces around initializer
DesignProbes.c:85: warning: (near initialization for ‘sMM[0]’)
DesignProbes.c:256: warning: ignoring #pragma omp parallel
DesignProbes.c:707: warning: ignoring #pragma omp critical
DesignProbes.c:58: warning: unused variable ‘nthreads’
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/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c DistanceMatrix.c -o DistanceMatrix.o
DistanceMatrix.c: In function ‘distMatrix’:
DistanceMatrix.c:293: warning: ignoring #pragma omp parallel
DistanceMatrix.c:239: warning: unused variable ‘nthreads’
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/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c EnumerateSequence.c -o EnumerateSequence.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/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c GC_Content.c -o GC_Content.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/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c InsertGaps.c -o InsertGaps.o
InsertGaps.c: In function ‘insertGaps’:
InsertGaps.c:83: warning: ignoring #pragma omp parallel
InsertGaps.c:47: warning: unused variable ‘nthreads’
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/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c IntDist.c -o IntDist.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/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c MeltPolymer.c -o MeltPolymer.o
MeltPolymer.c: In function ‘meltPolymer’:
MeltPolymer.c:80: warning: missing braces around initializer
MeltPolymer.c:80: warning: (near initialization for ‘dH[0]’)
MeltPolymer.c:89: warning: missing braces around initializer
MeltPolymer.c:89: warning: (near initialization for ‘dS[0]’)
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/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c MultiMatch.c -o MultiMatch.o
MultiMatch.c: In function ‘intMatch’:
MultiMatch.c:190: warning: ignoring #pragma omp parallel
MultiMatch.c:184: warning: unused variable ‘nthreads’
MultiMatch.c: In function ‘firstMatchUpper’:
MultiMatch.c:217: warning: ignoring #pragma omp parallel
MultiMatch.c:215: warning: unused variable ‘nthreads’
MultiMatch.c: In function ‘matchLists’:
MultiMatch.c:258: warning: ignoring #pragma omp parallel
MultiMatch.c:244: warning: unused variable ‘nthreads’
MultiMatch.c: In function ‘matchOrder’:
MultiMatch.c:363: warning: ignoring #pragma omp parallel
MultiMatch.c:349: warning: unused variable ‘nthreads’
MultiMatch.c: In function ‘matchOrderDual’:
MultiMatch.c:566: warning: ignoring #pragma omp parallel
MultiMatch.c:563: warning: unused variable ‘nthreads’
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/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c NNLS.c -o NNLS.o
NNLS.c: In function ‘NNLS’:
NNLS.c:89: warning: ignoring #pragma omp parallel
NNLS.c:49: warning: unused variable ‘nthreads’
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/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -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/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -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/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c TerminalMismatch.c -o TerminalMismatch.o
TerminalMismatch.c: In function ‘terminalMismatch’:
TerminalMismatch.c:47: warning: ignoring #pragma omp parallel
TerminalMismatch.c:40: warning: unused variable ‘nthreads’
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/3.1/Resources/library/Biostrings/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/RSQLite/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRanges/include" -I"/Library/Frameworks/R.framework/Versions/3.1/Resources/library/XVector/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -c XVector_stubs.c -o XVector_stubs.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/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -L/usr/local/lib -o DECIPHER.so AlignProfiles.o Biostrings_stubs.o CalculateDeltaG.o CalculateFISH.o ClusterML.o ClusterNJ.o ClusterUPGMA.o CommonGaps.o ConsensusSequence.o DesignProbes.o DistanceMatrix.o EnumerateSequence.o GC_Content.o InsertGaps.o IntDist.o MeltPolymer.o MultiMatch.o NNLS.o R_init_decipher.o ReplaceChars.o TerminalMismatch.o XVector_stubs.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.0-bioc/meat/DECIPHER.buildbin-libdir/DECIPHER/libs
** R
** data
** 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/3.1/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/3.1/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/3.1/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/3.1/Resources/lib/libreadline.dylib" "DECIPHER.buildbin-libdir/DECIPHER/libs//DECIPHER.so"