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BioC 2.12: BUILD BIN report for Rsubread on petty

This page was generated on 2013-10-09 09:39:58 -0700 (Wed, 09 Oct 2013).

Package 571/671HostnameOS / ArchBUILDCHECKBUILD BIN
Rsubread 1.10.5
Wei Shi
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/Rsubread
Last Changed Rev: 77915 / Revision: 81334
Last Changed Date: 2013-06-25 16:58:04 -0700 (Tue, 25 Jun 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 N O T   S U P P O R T E D
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK [ OK ]

Summary

Package: Rsubread
Version: 1.10.5
Command: rm -rf Rsubread.buildbin-libdir && mkdir Rsubread.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Rsubread_1.10.5.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R Rsubread.buildbin-libdir
StartedAt: 2013-10-09 01:04:24 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 01:04:47 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 22.4 seconds
RetCode: 0
Status:  OK 
PackageFile: Rsubread_1.10.5.tgz
PackageFileSize: 6.461 MiB

Command output

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=Rsubread.buildbin-libdir Rsubread_1.10.5.tar.gz'
>>>>>>> 

* installing *source* package 'Rsubread' ...
@@@@@ The operating system is Darwin.
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D MACOS  -fPIC  -mtune=core2 -g -O2  -c HelperFunctions.c -o HelperFunctions.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D MACOS  -fPIC  -mtune=core2 -g -O2  -c R_wrapper.c -o R_wrapper.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D MACOS  -fPIC  -mtune=core2 -g -O2  -c SNPCalling.c -o SNPCalling.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D MACOS  -fPIC  -mtune=core2 -g -O2  -c aligner.c -o aligner.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D MACOS  -fPIC  -mtune=core2 -g -O2  -c atgcContent.c -o atgcContent.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D MACOS  -fPIC  -mtune=core2 -g -O2  -c detectionCall.c -o detectionCall.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D MACOS  -fPIC  -mtune=core2 -g -O2  -c detectionCallAnnotation.c -o detectionCallAnnotation.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D MACOS  -fPIC  -mtune=core2 -g -O2  -c exon-algorithms.c -o exon-algorithms.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D MACOS  -fPIC  -mtune=core2 -g -O2  -c exon-align.c -o exon-align.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D MACOS  -fPIC  -mtune=core2 -g -O2  -c fullscan.c -o fullscan.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D MACOS  -fPIC  -mtune=core2 -g -O2  -c gene-algorithms.c -o gene-algorithms.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D MACOS  -fPIC  -mtune=core2 -g -O2  -c gene-value-index.c -o gene-value-index.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D MACOS  -fPIC  -mtune=core2 -g -O2  -c hashtable.c -o hashtable.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D MACOS  -fPIC  -mtune=core2 -g -O2  -c index-builder.c -o index-builder.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D MACOS  -fPIC  -mtune=core2 -g -O2  -c input-files.c -o input-files.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D MACOS  -fPIC  -mtune=core2 -g -O2  -c processExons.c -o processExons.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D MACOS  -fPIC  -mtune=core2 -g -O2  -c propmapped.c -o propmapped.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D MACOS  -fPIC  -mtune=core2 -g -O2  -c qualityScores.c -o qualityScores.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D MACOS  -fPIC  -mtune=core2 -g -O2  -c readSummary.c -o readSummary.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D MACOS  -fPIC  -mtune=core2 -g -O2  -c removeDupReads.c -o removeDupReads.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D MACOS  -fPIC  -mtune=core2 -g -O2  -c sam2bed.c -o sam2bed.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D MACOS  -fPIC  -mtune=core2 -g -O2  -c sambam-file.c -o sambam-file.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include   -DMAKE_FOR_EXON -D MACOS  -fPIC  -mtune=core2 -g -O2  -c sorted-hashtable.c -o sorted-hashtable.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 Rsubread.so HelperFunctions.o R_wrapper.o SNPCalling.o aligner.o atgcContent.o detectionCall.o detectionCallAnnotation.o exon-algorithms.o exon-align.o fullscan.o gene-algorithms.o gene-value-index.o hashtable.o index-builder.o input-files.o processExons.o propmapped.o qualityScores.o readSummary.o removeDupReads.o sam2bed.o sambam-file.o sorted-hashtable.o -lpthread -DMAKE_FOR_EXON -D MACOS -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/Rsubread.buildbin-libdir/Rsubread/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Rsubread)


>>>>>>> 
>>>>>>> FIXING LINKS FOR Rsubread.buildbin-libdir/Rsubread/libs//Rsubread.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" "Rsubread.buildbin-libdir/Rsubread/libs//Rsubread.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgfortran.2.dylib" "Rsubread.buildbin-libdir/Rsubread/libs//Rsubread.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" "Rsubread.buildbin-libdir/Rsubread/libs//Rsubread.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.dylib" "Rsubread.buildbin-libdir/Rsubread/libs//Rsubread.so"