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Package 53/565HostnameOS / ArchBUILDCHECKBUILD BIN
beadarray 2.7.1
Mark Dunning
Snapshot Date: 2012-06-20 15:22:40 -0700 (Wed, 20 Jun 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/beadarray
Last Changed Rev: 65684 / Revision: 66885
Last Changed Date: 2012-05-03 10:13:32 -0700 (Thu, 03 May 2012)
lamb1 Linux (openSUSE 12.1) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK  OK [ OK ]
perceval Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: beadarray
Version: 2.7.1
Command: rm -rf beadarray.buildbin-libdir && mkdir beadarray.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh beadarray_2.7.1.tar.gz /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R beadarray.buildbin-libdir
StartedAt: 2012-06-21 04:34:39 -0700 (Thu, 21 Jun 2012)
EndedAt: 2012-06-21 04:35:17 -0700 (Thu, 21 Jun 2012)
EllapsedTime: 38.2 seconds
RetCode: 0
Status:  OK 
PackageFile: beadarray_2.7.1.tgz
PackageFileSize: 5.267 MiB

Command output

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=beadarray.buildbin-libdir beadarray_2.7.1.tar.gz'
>>>>>>> 

* installing *source* package 'beadarray' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c BASH.c -o BASH.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c HULK.c -o HULK.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c determiningGridPositions.c -o determiningGridPositions.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c findAllOutliers.c -o findAllOutliers.o
findAllOutliers.c: In function 'findBeadStatus':
findAllOutliers.c:155: warning: 'ma' may be used uninitialized in this function
findAllOutliers.c:155: warning: 'm' may be used uninitialized in this function
findAllOutliers.c: In function 'findAllOutliers':
findAllOutliers.c:226: warning: 'status' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c imageProcessing.c -o imageProcessing.o
imageProcessing.c: In function 'illuminaBackground':
imageProcessing.c:88: warning: ignoring #pragma omp parallel
imageProcessing.c: In function 'medianBackground':
imageProcessing.c:135: warning: ignoring #pragma omp parallel
imageProcessing.c: In function 'illuminaSharpen':
imageProcessing.c:244: warning: ignoring #pragma omp parallel
imageProcessing.c:251: warning: ignoring #pragma omp parallel
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o beadarray.so BASH.o HULK.o determiningGridPositions.o findAllOutliers.o imageProcessing.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.11-bioc/meat/beadarray.buildbin-libdir/beadarray/libs/i386
** R
** data
**  moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'ImageProcessing.rnw' 
   'beadarray.rnw' 
   'beadlevel.rnw' 
   'beadsummary.rnw' 
** testing if installed package can be loaded

* DONE (beadarray)


>>>>>>> 
>>>>>>> FIXING LINKS FOR beadarray.buildbin-libdir/beadarray/libs/i386/beadarray.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libgcc_s.1.dylib" "beadarray.buildbin-libdir/beadarray/libs/i386/beadarray.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libgfortran.2.dylib" "beadarray.buildbin-libdir/beadarray/libs/i386/beadarray.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libreadline.5.2.dylib" "beadarray.buildbin-libdir/beadarray/libs/i386/beadarray.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libreadline.dylib" "beadarray.buildbin-libdir/beadarray/libs/i386/beadarray.so"


>>>>>>> 
>>>>>>> INSTALLATION OF ppc LIBS WITH 'R_ARCH=/ppc R CMD INSTALL --preclean --no-multiarch --no-test-load --library=beadarray.buildbin-libdir --libs-only beadarray_2.7.1.tar.gz'
>>>>>>> 

* installing *source* package 'beadarray' ...
** libs
*** arch - ppc
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/ppc -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2  -c BASH.c -o BASH.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/ppc -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2  -c HULK.c -o HULK.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/ppc -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2  -c determiningGridPositions.c -o determiningGridPositions.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/ppc -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2  -c findAllOutliers.c -o findAllOutliers.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/ppc -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2  -c imageProcessing.c -o imageProcessing.o
gcc -arch ppc -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o beadarray.so BASH.o HULK.o determiningGridPositions.o findAllOutliers.o imageProcessing.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.11-bioc/meat/beadarray.buildbin-libdir/beadarray/libs/ppc

* DONE (beadarray)


>>>>>>> 
>>>>>>> FIXING LINKS FOR beadarray.buildbin-libdir/beadarray/libs/ppc/beadarray.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libgcc_s.1.dylib" "beadarray.buildbin-libdir/beadarray/libs/ppc/beadarray.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libgfortran.2.dylib" "beadarray.buildbin-libdir/beadarray/libs/ppc/beadarray.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libreadline.5.2.dylib" "beadarray.buildbin-libdir/beadarray/libs/ppc/beadarray.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libreadline.dylib" "beadarray.buildbin-libdir/beadarray/libs/ppc/beadarray.so"


>>>>>>> 
>>>>>>> INSTALLATION OF x86_64 LIBS WITH 'R_ARCH=/x86_64 R CMD INSTALL --preclean --no-multiarch --no-test-load --library=beadarray.buildbin-libdir --libs-only beadarray_2.7.1.tar.gz'
>>>>>>> 

* installing *source* package 'beadarray' ...
** libs
*** arch - x86_64
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2  -c BASH.c -o BASH.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2  -c HULK.c -o HULK.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2  -c determiningGridPositions.c -o determiningGridPositions.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2  -c findAllOutliers.c -o findAllOutliers.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/x86_64 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2  -c imageProcessing.c -o imageProcessing.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 beadarray.so BASH.o HULK.o determiningGridPositions.o findAllOutliers.o imageProcessing.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.11-bioc/meat/beadarray.buildbin-libdir/beadarray/libs/x86_64

* DONE (beadarray)


>>>>>>> 
>>>>>>> FIXING LINKS FOR beadarray.buildbin-libdir/beadarray/libs/x86_64/beadarray.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libgcc_s.1.dylib" "beadarray.buildbin-libdir/beadarray/libs/x86_64/beadarray.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libgfortran.2.dylib" "beadarray.buildbin-libdir/beadarray/libs/x86_64/beadarray.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libreadline.5.2.dylib" "beadarray.buildbin-libdir/beadarray/libs/x86_64/beadarray.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libreadline.dylib" "beadarray.buildbin-libdir/beadarray/libs/x86_64/beadarray.so"