bgx 1.20.0
Ernest Turro
| Snapshot Date: 2012-09-23 17:01:39 -0700 (Sun, 23 Sep 2012) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_10/madman/Rpacks/bgx | | Last Changed Rev: 64678 / Revision: 69725 | | Last Changed Date: 2012-03-30 15:05:02 -0700 (Fri, 30 Mar 2012) |
| lamb2 | Linux (openSUSE 11.4) / 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 ] |
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=bgx.buildbin-libdir bgx_1.20.0.tar.gz'
>>>>>>>
* installing *source* package 'bgx' ...
checking for gcc... gcc -arch i386 -std=gnu99
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -arch i386 -std=gnu99 accepts -g... yes
checking for gcc -arch i386 -std=gnu99 option to accept ISO C89... none needed
checking for C compiler vendor... gnu
checking whether C compiler accepts -ffast-math... yes
checking whether C compiler accepts -O3... yes
checking build system type... i386-apple-darwin9.8.0
checking host system type... i386-apple-darwin9.8.0
checking for gcc architecture flag...
checking for x86 cpuid 0 output... unknown
checking for x86 cpuid 1 output... unknown
checking for gcc architecture flag... unknown
checking for gcc -arch i386 -std=gnu99 option to accept ISO C99... none needed
checking for main in -lm... yes
Untarring Boost header files...
checking for an ANSI C-conforming const... yes
checking for inline... inline
configure: creating ./config.status
config.status: creating src/Makevars
** libs
*** arch - i386
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -I ../boostIncl -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -ffast-math -O3 -DUSING_R -c bgx.cc -o bgx.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -I ../boostIncl -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -ffast-math -O3 -DUSING_R -c bgx_frontend.cc -o bgx_frontend.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 ../boostIncl -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -g -O2 -ffast-math -O3 -c qnorm.c -o qnorm.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -I ../boostIncl -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -ffast-math -O3 -DUSING_R -c rundir.cc -o rundir.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG -I ../boostIncl -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -ffast-math -O3 -DUSING_R -c sokal.cc -o sokal.o
g++ -arch i386 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o bgx.so bgx.o bgx_frontend.o qnorm.o rundir.o sokal.o -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
rm -r ../boostIncl
installing to /Users/biocbuild/bbs-2.10-bioc/meat/bgx.buildbin-libdir/bgx/libs/i386
** R
** inst
** preparing package for lazy loading
BiocInstaller version 1.4.7, ?biocLite for help
** help
*** installing help indices
** building package indices
** installing vignettes
'bgx.Rnw'
** testing if installed package can be loaded
BiocInstaller version 1.4.7, ?biocLite for help
* DONE (bgx)
>>>>>>>
>>>>>>> FIXING LINKS FOR bgx.buildbin-libdir/bgx/libs/i386/bgx.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" "bgx.buildbin-libdir/bgx/libs/i386/bgx.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libgfortran.2.dylib" "bgx.buildbin-libdir/bgx/libs/i386/bgx.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" "bgx.buildbin-libdir/bgx/libs/i386/bgx.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libreadline.dylib" "bgx.buildbin-libdir/bgx/libs/i386/bgx.so"
>>>>>>>
>>>>>>> INSTALLATION OF x86_64 LIBS WITH 'R_ARCH=/x86_64 R CMD INSTALL --preclean --no-multiarch --no-test-load --library=bgx.buildbin-libdir --libs-only bgx_1.20.0.tar.gz'
>>>>>>>
* installing *source* package 'bgx' ...
checking for gcc... gcc -arch x86_64 -std=gnu99
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -arch x86_64 -std=gnu99 accepts -g... yes
checking for gcc -arch x86_64 -std=gnu99 option to accept ISO C89... none needed
checking for C compiler vendor... gnu
checking whether C compiler accepts -ffast-math... yes
checking whether C compiler accepts -O3... yes
checking build system type... i386-apple-darwin9.8.0
checking host system type... i386-apple-darwin9.8.0
checking for gcc architecture flag...
checking for x86 cpuid 0 output... b:756e6547:6c65746e:49656e69
checking for x86 cpuid 1 output... 106a5:13100800:9ce3bd:bfebfbff
checking whether C compiler accepts -march=pentium2... no
checking whether C compiler accepts -mcpu=pentium2... no
checking whether C compiler accepts -mpentium2... no
checking whether C compiler accepts -march=pentiumpro... no
checking whether C compiler accepts -mcpu=pentiumpro... no
checking whether C compiler accepts -mpentiumpro... yes
checking for gcc architecture flag... -mpentiumpro
checking for gcc -arch x86_64 -std=gnu99 option to accept ISO C99... none needed
checking for main in -lm... yes
Untarring Boost header files...
checking for an ANSI C-conforming const... yes
checking for inline... inline
configure: creating ./config.status
config.status: creating src/Makevars
** libs
*** arch - x86_64
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/x86_64 -DNDEBUG -I ../boostIncl -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -ffast-math -O3 -DUSING_R -c bgx.cc -o bgx.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/x86_64 -DNDEBUG -I ../boostIncl -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -ffast-math -O3 -DUSING_R -c bgx_frontend.cc -o bgx_frontend.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 ../boostIncl -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -g -O2 -mpentiumpro -ffast-math -O3 -c qnorm.c -o qnorm.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/x86_64 -DNDEBUG -I ../boostIncl -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -ffast-math -O3 -DUSING_R -c rundir.cc -o rundir.o
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/x86_64 -DNDEBUG -I ../boostIncl -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -ffast-math -O3 -DUSING_R -c sokal.cc -o sokal.o
g++ -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o bgx.so bgx.o bgx_frontend.o qnorm.o rundir.o sokal.o -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
rm -r ../boostIncl
installing to /Users/biocbuild/bbs-2.10-bioc/meat/bgx.buildbin-libdir/bgx/libs/x86_64
* DONE (bgx)
>>>>>>>
>>>>>>> FIXING LINKS FOR bgx.buildbin-libdir/bgx/libs/x86_64/bgx.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" "bgx.buildbin-libdir/bgx/libs/x86_64/bgx.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libgfortran.2.dylib" "bgx.buildbin-libdir/bgx/libs/x86_64/bgx.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" "bgx.buildbin-libdir/bgx/libs/x86_64/bgx.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/libreadline.dylib" "bgx.buildbin-libdir/bgx/libs/x86_64/bgx.so"