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Package 55/467HostnameOS / ArchBUILDCHECKBUILD BIN
bgx 1.16.0
Ernest Turro
Snapshot Date: 2011-10-20 07:20:33 -0700 (Thu, 20 Oct 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_8/madman/Rpacks/bgx
Last Changed Rev: 54800 / Revision: 59457
Last Changed Date: 2011-04-13 15:27:35 -0700 (Wed, 13 Apr 2011)
lamb1 Linux (openSUSE 11.3) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK [ OK ]

Summary

Package: bgx
Version: 1.16.0
Command: rm -rf bgx.buildbin-libdir && mkdir bgx.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh bgx_1.16.0.tar.gz /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R bgx.buildbin-libdir
StartedAt: 2011-10-20 18:04:20 -0700 (Thu, 20 Oct 2011)
EndedAt: 2011-10-20 18:06:02 -0700 (Thu, 20 Oct 2011)
EllapsedTime: 102.0 seconds
RetCode: 0
Status:  OK 
PackageFile: bgx_1.16.0.tgz
PackageFileSize: 358.1 KiB

Command output

>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --library=bgx.buildbin-libdir bgx_1.16.0.tar.gz'
>>>>>>> 

* installing *source* package 'bgx' ...
checking for gcc... gcc-4.2 -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-4.2 -arch i386 -std=gnu99 accepts -g... yes
checking for gcc-4.2 -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-4.2 -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++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -I ../boostIncl -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -ffast-math -O3 -DUSING_R -c bgx.cc -o bgx.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -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-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -I ../boostIncl -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -g -O2  -ffast-math -O3 -c qnorm.c -o qnorm.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -I ../boostIncl -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -ffast-math -O3 -DUSING_R -c rundir.cc -o rundir.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -I ../boostIncl -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -ffast-math -O3 -DUSING_R -c sokal.cc -o sokal.o
g++-4.2 -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-2.8-bioc/meat/bgx.buildbin-libdir/bgx/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* 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/2.13/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/2.13/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/2.13/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/2.13/Resources/lib/libreadline.dylib" "bgx.buildbin-libdir/bgx/libs/i386/bgx.so"


>>>>>>> 
>>>>>>> INSTALLATION OF ppc LIBS WITH 'R_ARCH=/ppc R CMD INSTALL --preclean --library=bgx.buildbin-libdir --libs-only bgx_1.16.0.tar.gz'
>>>>>>> 

* installing *source* package 'bgx' ...
checking for gcc... gcc-4.2 -arch ppc -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-4.2 -arch ppc -std=gnu99 accepts -g... yes
checking for gcc-4.2 -arch ppc -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-4.2 -arch ppc -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 - ppc
g++-4.2 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -I ../boostIncl -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -ffast-math -O3 -DUSING_R -c bgx.cc -o bgx.o
g++-4.2 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -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-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -I ../boostIncl -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -g -O2  -ffast-math -O3 -c qnorm.c -o qnorm.o
g++-4.2 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -I ../boostIncl -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -ffast-math -O3 -DUSING_R -c rundir.cc -o rundir.o
g++-4.2 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/ppc -I ../boostIncl -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -ffast-math -O3 -DUSING_R -c sokal.cc -o sokal.o
g++-4.2 -arch ppc -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-2.8-bioc/meat/bgx.buildbin-libdir/bgx/libs/ppc

* DONE (bgx)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libgcc_s.1.dylib" "bgx.buildbin-libdir/bgx/libs/ppc/bgx.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libgfortran.2.dylib" "bgx.buildbin-libdir/bgx/libs/ppc/bgx.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libreadline.5.2.dylib" "bgx.buildbin-libdir/bgx/libs/ppc/bgx.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libreadline.dylib" "bgx.buildbin-libdir/bgx/libs/ppc/bgx.so"


>>>>>>> 
>>>>>>> INSTALLATION OF x86_64 LIBS WITH 'R_ARCH=/x86_64 R CMD INSTALL --preclean --library=bgx.buildbin-libdir --libs-only bgx_1.16.0.tar.gz'
>>>>>>> 

* installing *source* package 'bgx' ...
checking for gcc... gcc-4.2 -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-4.2 -arch x86_64 -std=gnu99 accepts -g... yes
checking for gcc-4.2 -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... a:756e6547:6c65746e:49656e69
checking for x86 cpuid 1 output... 6fb:20800:4e33d:bfebfbff
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-4.2 -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++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -I ../boostIncl -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -ffast-math -O3 -DUSING_R -c bgx.cc -o bgx.o
g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -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-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -I ../boostIncl -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -g -O2 -mpentiumpro  -ffast-math -O3 -c qnorm.c -o qnorm.o
g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -I ../boostIncl -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -ffast-math -O3 -DUSING_R -c rundir.cc -o rundir.o
g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/x86_64 -I ../boostIncl -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -ffast-math -O3 -DUSING_R -c sokal.cc -o sokal.o
g++-4.2 -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-2.8-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/2.13/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/2.13/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/2.13/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/2.13/Resources/lib/libreadline.dylib" "bgx.buildbin-libdir/bgx/libs/x86_64/bgx.so"