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Package 13/658HostnameOS / ArchBUILDCHECKBUILD BIN
affy 1.37.4
Rafael A. Irizarry
Snapshot Date: 2013-03-24 17:01:43 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/affy
Last Changed Rev: 73893 / Revision: 74774
Last Changed Date: 2013-03-04 09:49:21 -0800 (Mon, 04 Mar 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: affy
Version: 1.37.4
Command: rm -rf affy.buildbin-libdir && mkdir affy.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh affy_1.37.4.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R affy.buildbin-libdir
StartedAt: 2013-03-25 05:15:57 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 05:16:12 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 15.1 seconds
RetCode: 0
Status:  OK 
PackageFile: affy_1.37.4.tgz
PackageFileSize: 1.402 MiB

Command output

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=affy.buildbin-libdir affy_1.37.4.tar.gz'
>>>>>>> 

* installing *source* package 'affy' ...
creating cache ./config.cache
checking how to run the C preprocessor... cc -E
checking for main in -lz... yes
checking for zlib.h... yes
checking if zlib version >= 1.1.3... yes
updating cache ./config.cache
creating ./config.status
creating src/Makevars
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -DHAVE_ZLIB=1  -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 -DHAVE_ZLIB=1  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -Wall -pedantic  -c getall_locations.c -o getall_locations.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -DHAVE_ZLIB=1  -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 -DHAVE_ZLIB=1  -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 -DHAVE_ZLIB=1  -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 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o affy.so chipbackground.o getall_locations.o mas5calls.o rma2.o rma_common.o -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/affy.buildbin-libdir/affy/libs/i386
** R
** data
** demo
** inst
** preparing package for lazy loading
Creating a generic function for 'open' from package 'base' in package 'affy'
Creating a generic function for 'close' from package 'base' in package 'affy'
Creating a generic function for 'barplot' from package 'graphics' in package 'affy'
** help
*** installing help indices
** building package indices
** installing vignettes
   'affy.Rnw' 
   'builtinMethods.Rnw' 
   'customMethods.Rnw' 
   'vim.Rnw' 
** testing if installed package can be loaded
* DONE (affy)


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


>>>>>>> 
>>>>>>> INSTALLATION OF x86_64 LIBS WITH 'R_ARCH=/x86_64 R CMD INSTALL --preclean --no-multiarch --no-test-load --library=affy.buildbin-libdir --libs-only affy_1.37.4.tar.gz'
>>>>>>> 

* installing *source* package 'affy' ...
creating cache ./config.cache
checking how to run the C preprocessor... cc -E
checking for main in -lz... yes
checking for zlib.h... yes
checking if zlib version >= 1.1.3... yes
updating cache ./config.cache
creating ./config.status
creating src/Makevars
** 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 -DHAVE_ZLIB=1  -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 -DHAVE_ZLIB=1  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/preprocessCore/include"   -fPIC  -g -O2 -Wall -pedantic  -c getall_locations.c -o getall_locations.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -DNDEBUG -DHAVE_ZLIB=1  -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 -DHAVE_ZLIB=1  -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 -DHAVE_ZLIB=1  -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 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o affy.so chipbackground.o getall_locations.o mas5calls.o rma2.o rma_common.o -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/affy.buildbin-libdir/affy/libs/x86_64
* DONE (affy)


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