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Package 145/609HostnameOS / ArchBUILDCHECKBUILD BIN
crlmm 1.16.9
Benilton S Carvalho , Robert Scharpf , Matt Ritchie
Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/crlmm
Last Changed Rev: 71383 / Revision: 74773
Last Changed Date: 2012-11-21 06:32:51 -0800 (Wed, 21 Nov 2012)
lamb1 Linux (openSUSE 12.1) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Leopard (10.5.8) / i386  OK  OK [ OK ]

Summary

Package: crlmm
Version: 1.16.9
Command: rm -rf crlmm.buildbin-libdir && mkdir crlmm.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh crlmm_1.16.9.tar.gz /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R crlmm.buildbin-libdir
StartedAt: 2013-03-25 01:50:22 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 01:50:55 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 32.5 seconds
RetCode: 0
Status:  OK 
PackageFile: crlmm_1.16.9.tgz
PackageFileSize: 4.371 MiB

Command output

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=crlmm.buildbin-libdir crlmm_1.16.9.tar.gz'
>>>>>>> 

* installing *source* package 'crlmm' ...
** 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    -fPIC  -g -O2 -Wall -pedantic  -c gtypeCaller.c -o gtypeCaller.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    -fPIC  -g -O2 -Wall -pedantic  -c init.c -o init.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    -fPIC  -g -O2 -Wall -pedantic  -c trimmed.c -o trimmed.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    -fPIC  -g -O2 -Wall -pedantic  -c utils.c -o utils.o
utils.c: In function 'mad_median':
utils.c:124: warning: unused variable 'n_ignore'
utils.c: In function 'normalizeBAF':
utils.c:178: warning: suggest parentheses around comparison in operand of &
utils.c:180: warning: suggest parentheses around comparison in operand of &
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o crlmm.so gtypeCaller.o init.o trimmed.o utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.11-bioc/meat/crlmm.buildbin-libdir/crlmm/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'AffyGW.Rnw' 
   'CopyNumberOverview.Rnw' 
   'IlluminaPreprocessCN.Rnw' 
   'Infrastructure.Rnw' 
   'genotyping.Rnw' 
   'gtypeDownstream.Rnw' 
** testing if installed package can be loaded

* DONE (crlmm)


>>>>>>> 
>>>>>>> FIXING LINKS FOR crlmm.buildbin-libdir/crlmm/libs/i386/crlmm.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" "crlmm.buildbin-libdir/crlmm/libs/i386/crlmm.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libgfortran.2.dylib" "crlmm.buildbin-libdir/crlmm/libs/i386/crlmm.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" "crlmm.buildbin-libdir/crlmm/libs/i386/crlmm.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libreadline.dylib" "crlmm.buildbin-libdir/crlmm/libs/i386/crlmm.so"


>>>>>>> 
>>>>>>> INSTALLATION OF x86_64 LIBS WITH 'R_ARCH=/x86_64 R CMD INSTALL --preclean --no-multiarch --no-test-load --library=crlmm.buildbin-libdir --libs-only crlmm_1.16.9.tar.gz'
>>>>>>> 

* installing *source* package 'crlmm' ...
** 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    -fPIC  -g -O2 -Wall -pedantic  -c gtypeCaller.c -o gtypeCaller.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    -fPIC  -g -O2 -Wall -pedantic  -c init.c -o init.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    -fPIC  -g -O2 -Wall -pedantic  -c trimmed.c -o trimmed.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    -fPIC  -g -O2 -Wall -pedantic  -c utils.c -o utils.o
utils.c: In function 'mad_median':
utils.c:124: warning: unused variable 'n_ignore'
utils.c: In function 'normalizeBAF':
utils.c:178: warning: suggest parentheses around comparison in operand of &
utils.c:180: warning: suggest parentheses around comparison in operand of &
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 crlmm.so gtypeCaller.o init.o trimmed.o utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.11-bioc/meat/crlmm.buildbin-libdir/crlmm/libs/x86_64

* DONE (crlmm)


>>>>>>> 
>>>>>>> FIXING LINKS FOR crlmm.buildbin-libdir/crlmm/libs/x86_64/crlmm.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" "crlmm.buildbin-libdir/crlmm/libs/x86_64/crlmm.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libgfortran.2.dylib" "crlmm.buildbin-libdir/crlmm/libs/x86_64/crlmm.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" "crlmm.buildbin-libdir/crlmm/libs/x86_64/crlmm.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libreadline.dylib" "crlmm.buildbin-libdir/crlmm/libs/x86_64/crlmm.so"