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Package 443/658HostnameOS / ArchBUILDCHECKBUILD BIN
oligo 1.23.1
Benilton Carvalho
Snapshot Date: 2013-03-24 17:01:43 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/oligo
Last Changed Rev: 72253 / Revision: 74774
Last Changed Date: 2013-01-02 19:41:54 -0800 (Wed, 02 Jan 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 Leopard (10.5.8) / i386  OK  OK [ OK ]

Summary

Package: oligo
Version: 1.23.1
Command: rm -rf oligo.buildbin-libdir && mkdir oligo.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh oligo_1.23.1.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R oligo.buildbin-libdir
StartedAt: 2013-03-25 05:35:28 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 05:35:57 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 29.6 seconds
RetCode: 0
Status:  OK 
PackageFile: oligo_1.23.1.tgz
PackageFileSize: 5.455 MiB

Command output

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=oligo.buildbin-libdir oligo_1.23.1.tar.gz'
>>>>>>> 

* installing *source* package 'oligo' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -Wall -pedantic  -c DABG.c -o DABG.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -Wall -pedantic  -c ParserGzXYS.c -o ParserGzXYS.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -Wall -pedantic  -c ParserXYS.c -o ParserXYS.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -Wall -pedantic  -c baseProfile.c -o baseProfile.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -Wall -pedantic  -c basecontent.c -o basecontent.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -Wall -pedantic  -c chipbackground.c -o chipbackground.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -Wall -pedantic  -c mas5calls.c -o mas5calls.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -Wall -pedantic  -c rma2.c -o rma2.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -Wall -pedantic  -c rma_common.c -o rma_common.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -Wall -pedantic  -c trimmed.c -o trimmed.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 oligo.so DABG.o ParserGzXYS.o ParserXYS.o baseProfile.o basecontent.o chipbackground.o mas5calls.o rma2.o rma_common.o trimmed.o -lz -lgfortran -L/Library/Frameworks/R.framework/Resources/lib/i386 -lRlapack -L/Library/Frameworks/R.framework/Resources/lib/i386 -lRblas -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/oligo.buildbin-libdir/oligo/libs/i386
** R
** inst
** preparing package for lazy loading
Note: in method for 'pm<-' with signature
'object="TilingFeatureSet",subset="ANY",target="ANY",value="array"':
expanding the signature to include omitted arguments in definition: =
"missing"
Note: in method for 'mm<-' with signature
'object="TilingFeatureSet",subset="ANY",target="ANY",value="array"':
expanding the signature to include omitted arguments in definition: =
"missing"
** help
*** installing help indices
** building package indices
** installing vignettes
   'primer.Rnw' 
** testing if installed package can be loaded
* DONE (oligo)


>>>>>>> 
>>>>>>> FIXING LINKS FOR oligo.buildbin-libdir/oligo/libs/i386/oligo.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" "oligo.buildbin-libdir/oligo/libs/i386/oligo.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgfortran.2.dylib" "oligo.buildbin-libdir/oligo/libs/i386/oligo.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" "oligo.buildbin-libdir/oligo/libs/i386/oligo.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.dylib" "oligo.buildbin-libdir/oligo/libs/i386/oligo.so"


>>>>>>> 
>>>>>>> INSTALLATION OF x86_64 LIBS WITH 'R_ARCH=/x86_64 R CMD INSTALL --preclean --no-multiarch --no-test-load --library=oligo.buildbin-libdir --libs-only oligo_1.23.1.tar.gz'
>>>>>>> 

* installing *source* package 'oligo' ...
** 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 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -Wall -pedantic  -c DABG.c -o DABG.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -Wall -pedantic  -c ParserGzXYS.c -o ParserGzXYS.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -Wall -pedantic  -c ParserXYS.c -o ParserXYS.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -Wall -pedantic  -c baseProfile.c -o baseProfile.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -Wall -pedantic  -c basecontent.c -o basecontent.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -Wall -pedantic  -c chipbackground.c -o chipbackground.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -Wall -pedantic  -c mas5calls.c -o mas5calls.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -Wall -pedantic  -c rma2.c -o rma2.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -Wall -pedantic  -c rma_common.c -o rma_common.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -Wall -pedantic  -c trimmed.c -o trimmed.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 oligo.so DABG.o ParserGzXYS.o ParserXYS.o baseProfile.o basecontent.o chipbackground.o mas5calls.o rma2.o rma_common.o trimmed.o -lz -lgfortran -L/Library/Frameworks/R.framework/Resources/lib/x86_64 -lRlapack -L/Library/Frameworks/R.framework/Resources/lib/x86_64 -lRblas -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/oligo.buildbin-libdir/oligo/libs/x86_64
* DONE (oligo)


>>>>>>> 
>>>>>>> FIXING LINKS FOR oligo.buildbin-libdir/oligo/libs/x86_64/oligo.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" "oligo.buildbin-libdir/oligo/libs/x86_64/oligo.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libgfortran.2.dylib" "oligo.buildbin-libdir/oligo/libs/x86_64/oligo.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" "oligo.buildbin-libdir/oligo/libs/x86_64/oligo.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.0/Resources/lib/libreadline.dylib" "oligo.buildbin-libdir/oligo/libs/x86_64/oligo.so"