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Package 121/609HostnameOS / ArchBUILDCHECKBUILD BIN
cn.farms 1.6.0
Andreas Mitterecker
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/cn.farms
Last Changed Rev: 70050 / Revision: 74773
Last Changed Date: 2012-10-01 15:16:24 -0700 (Mon, 01 Oct 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: cn.farms
Version: 1.6.0
Command: rm -rf cn.farms.buildbin-libdir && mkdir cn.farms.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh cn.farms_1.6.0.tar.gz /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R cn.farms.buildbin-libdir
StartedAt: 2013-03-25 01:49:44 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 01:50:13 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 28.5 seconds
RetCode: 0
Status:  OK 
PackageFile: cn.farms_1.6.0.tgz
PackageFileSize: 2.289 MiB

Command output

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=cn.farms.buildbin-libdir cn.farms_1.6.0.tar.gz'
>>>>>>> 

* installing *source* package 'cn.farms' ...
** 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 R_init_cnfarms.c -o R_init_cnfarms.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c laplace.cpp -o laplace.o
laplace.cpp: In function 'SEXPREC* momentsGauss(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
laplace.cpp:442: warning: unused variable 'method'
laplace.cpp: In function 'void computeParameters(double, double, double, double, double, double, int&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&)':
laplace.cpp:199: warning: 'I1right' may be used uninitialized in this function
laplace.cpp:198: warning: 'I1left' may be used uninitialized in this function
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 sparse_farms.c -o sparse_farms.o
g++ -arch i386 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o cn.farms.so R_init_cnfarms.o laplace.o sparse_farms.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.11-bioc/meat/cn.farms.buildbin-libdir/cn.farms/libs/i386
** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'cn.farms.Rnw' 
** testing if installed package can be loaded

* DONE (cn.farms)


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


>>>>>>> 
>>>>>>> INSTALLATION OF x86_64 LIBS WITH 'R_ARCH=/x86_64 R CMD INSTALL --preclean --no-multiarch --no-test-load --library=cn.farms.buildbin-libdir --libs-only cn.farms_1.6.0.tar.gz'
>>>>>>> 

* installing *source* package 'cn.farms' ...
** 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 R_init_cnfarms.c -o R_init_cnfarms.o
g++ -arch x86_64 -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 -fasm-blocks  -c laplace.cpp -o laplace.o
laplace.cpp: In function 'SEXPREC* momentsGauss(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
laplace.cpp:442: warning: unused variable 'method'
laplace.cpp: In function 'void computeParameters(double, double, double, double, double, double, int&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&)':
laplace.cpp:199: warning: 'I1right' may be used uninitialized in this function
laplace.cpp:198: warning: 'I1left' may be used uninitialized in this function
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 sparse_farms.c -o sparse_farms.o
g++ -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o cn.farms.so R_init_cnfarms.o laplace.o sparse_farms.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.11-bioc/meat/cn.farms.buildbin-libdir/cn.farms/libs/x86_64

* DONE (cn.farms)


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