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Package 40/419HostnameOS / ArchBUILDCHECKBUILD BIN
beadarray 2.0.6
Mark Dunning
Snapshot Date: 2011-03-30 23:22:56 -0700 (Wed, 30 Mar 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_7/madman/Rpacks/beadarray
Last Changed Rev: 53565 / Revision: 54281
Last Changed Date: 2011-03-10 02:48:20 -0800 (Thu, 10 Mar 2011)
lamb2 Linux (openSUSE 11.2) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK [ OK ]

Summary

Package: beadarray
Version: 2.0.6
Command: /Users/biocbuild/BBS/utils/build-universal.sh beadarray_2.0.6.tar.gz /Library/Frameworks/R.framework/Versions/2.12/Resources/bin/R beadarray.buildbin-libdir
StartedAt: 2011-03-31 08:27:38 -0700 (Thu, 31 Mar 2011)
EndedAt: 2011-03-31 08:28:00 -0700 (Thu, 31 Mar 2011)
EllapsedTime: 21.6 seconds
RetCode: 0
Status:  OK 
PackageFile: beadarray_2.0.6.tgz
PackageFileSize: 11.35 MiB

Command output

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --library=beadarray.buildbin-libdir beadarray_2.0.6.tar.gz'
>>>>>>> 

* installing *source* package ‘beadarray’ ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386  -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/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386  -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/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c determiningGridPositions.c -o determiningGridPositions.o
determiningGridPositions.c: In function ‘roundLocsFileValues’:
determiningGridPositions.c:7: warning: unused variable ‘vecLength’
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c findAllOutliers.c -o findAllOutliers.o
findAllOutliers.c: In function ‘findBeadStatus’:
findAllOutliers.c:161: warning: ‘ma’ may be used uninitialized in this function
findAllOutliers.c:161: warning: ‘m’ may be used uninitialized in this function
findAllOutliers.c: In function ‘findAllOutliers’:
findAllOutliers.c:234: warning: ‘status’ may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c imageProcessing.c -o imageProcessing.o
imageProcessing.c: In function ‘illuminaBackground’:
imageProcessing.c:68: warning: statement with no effect
imageProcessing.c:70: warning: ignoring #pragma omp parallel
imageProcessing.c:51: warning: unused variable ‘tmp’
imageProcessing.c:49: warning: unused variable ‘k’
imageProcessing.c:49: warning: unused variable ‘j’
imageProcessing.c: In function ‘illuminaSharpen’:
imageProcessing.c:166: warning: ignoring #pragma omp parallel
imageProcessing.c:168: warning: ignoring #pragma omp for
imageProcessing.c:175: warning: ignoring #pragma omp for
imageProcessing.c:154: warning: unused variable ‘chunk’
imageProcessing.c:154: warning: unused variable ‘nthreads’
imageProcessing.c:154: warning: unused variable ‘tid’
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-2.7-bioc/meat/beadarray.buildbin-libdir/beadarray/libs/i386
*** arch - ppc
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c BASH.c -o BASH.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c HULK.c -o HULK.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c determiningGridPositions.c -o determiningGridPositions.o
determiningGridPositions.c: In function ‘roundLocsFileValues’:
determiningGridPositions.c:7: warning: unused variable ‘vecLength’
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c findAllOutliers.c -o findAllOutliers.o
findAllOutliers.c: In function ‘findBeadStatus’:
findAllOutliers.c:161: warning: ‘ma’ may be used uninitialized in this function
findAllOutliers.c:161: warning: ‘m’ may be used uninitialized in this function
findAllOutliers.c: In function ‘findAllOutliers’:
findAllOutliers.c:234: warning: ‘status’ may be used uninitialized in this function
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c imageProcessing.c -o imageProcessing.o
imageProcessing.c: In function ‘illuminaBackground’:
imageProcessing.c:68: warning: statement with no effect
imageProcessing.c:70: warning: ignoring #pragma omp parallel
imageProcessing.c:51: warning: unused variable ‘tmp’
imageProcessing.c:49: warning: unused variable ‘k’
imageProcessing.c:49: warning: unused variable ‘j’
imageProcessing.c: In function ‘illuminaSharpen’:
imageProcessing.c:166: warning: ignoring #pragma omp parallel
imageProcessing.c:168: warning: ignoring #pragma omp for
imageProcessing.c:175: warning: ignoring #pragma omp for
imageProcessing.c:154: warning: unused variable ‘chunk’
imageProcessing.c:154: warning: unused variable ‘nthreads’
imageProcessing.c:154: warning: unused variable ‘tid’
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-2.7-bioc/meat/beadarray.buildbin-libdir/beadarray/libs/ppc
*** arch - x86_64
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/x86_64  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c BASH.c -o BASH.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/x86_64  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c HULK.c -o HULK.o
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/x86_64  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c determiningGridPositions.c -o determiningGridPositions.o
determiningGridPositions.c: In function ‘roundLocsFileValues’:
determiningGridPositions.c:7: warning: unused variable ‘vecLength’
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/x86_64  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c findAllOutliers.c -o findAllOutliers.o
findAllOutliers.c: In function ‘findBeadStatus’:
findAllOutliers.c:161: warning: ‘ma’ may be used uninitialized in this function
findAllOutliers.c:161: warning: ‘m’ may be used uninitialized in this function
findAllOutliers.c: In function ‘findAllOutliers’:
findAllOutliers.c:234: warning: ‘status’ may be used uninitialized in this function
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/x86_64  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c imageProcessing.c -o imageProcessing.o
imageProcessing.c: In function ‘illuminaBackground’:
imageProcessing.c:68: warning: statement with no effect
imageProcessing.c:70: warning: ignoring #pragma omp parallel
imageProcessing.c:51: warning: unused variable ‘tmp’
imageProcessing.c:49: warning: unused variable ‘k’
imageProcessing.c:49: warning: unused variable ‘j’
imageProcessing.c: In function ‘illuminaSharpen’:
imageProcessing.c:166: warning: ignoring #pragma omp parallel
imageProcessing.c:168: warning: ignoring #pragma omp for
imageProcessing.c:175: warning: ignoring #pragma omp for
imageProcessing.c:154: warning: unused variable ‘chunk’
imageProcessing.c:154: warning: unused variable ‘nthreads’
imageProcessing.c:154: warning: unused variable ‘tid’
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-2.7-bioc/meat/beadarray.buildbin-libdir/beadarray/libs/x86_64
** R
** data
** inst
** preparing package for lazy loading

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Creating a new generic function for "boxplot" in "beadarray"
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
Welcome to beadarray version 2.0.6
There have been major changes to beadarray since Bioconductor 2.6 (April 2010). Please see package vignette for details

* 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/2.12/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/2.12/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/2.12/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/2.12/Resources/lib/libreadline.dylib" "beadarray.buildbin-libdir/beadarray/libs/i386/beadarray.so"


>>>>>>> 
>>>>>>> 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/2.12/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/2.12/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/2.12/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/2.12/Resources/lib/libreadline.dylib" "beadarray.buildbin-libdir/beadarray/libs/ppc/beadarray.so"


>>>>>>> 
>>>>>>> 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/2.12/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/2.12/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/2.12/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/2.12/Resources/lib/libreadline.dylib" "beadarray.buildbin-libdir/beadarray/libs/x86_64/beadarray.so"