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BioC 3.0: BUILD BIN report for bgx on perceval

This page was generated on 2015-04-10 09:53:29 -0700 (Fri, 10 Apr 2015).

Package 80/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bgx 1.32.0
Ernest Turro
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/bgx
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK [ OK ]
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: bgx
Version: 1.32.0
Command: rm -rf bgx.buildbin-libdir && mkdir bgx.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh bgx_1.32.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R bgx.buildbin-libdir
StartedAt: 2015-04-10 07:57:06 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 07:57:59 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 52.8 seconds
RetCode: 0
Status:  OK 
PackageFile: bgx_1.32.0.tgz
PackageFileSize: 237.2 KiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf bgx.buildbin-libdir && mkdir bgx.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh bgx_1.32.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R bgx.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=bgx.buildbin-libdir bgx_1.32.0.tar.gz'
>>>>>>> 

* installing *source* package ‘bgx’ ...
checking for gcc... llvm-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 llvm-gcc-4.2 -arch x86_64 -std=gnu99 accepts -g... yes
checking for llvm-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-darwin10.8.0
checking host system type... i386-apple-darwin10.8.0
checking for gcc architecture flag... 
checking for x86 cpuid 0 output... a:756e6547:6c65746e:49656e69
checking for x86 cpuid 1 output... 10676:3040800:ce3bd:bfebfbff
checking whether C compiler accepts -march=pentium3... no
checking whether C compiler accepts -mcpu=pentium3... no
checking whether C compiler accepts -mpentium3... 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 llvm-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
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I ../boostIncl -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -ffast-math -O3 -DUSING_R -c bgx.cc -o bgx.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I ../boostIncl -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -ffast-math -O3 -DUSING_R -c bgx_frontend.cc -o bgx_frontend.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I ../boostIncl -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -g -O2 -mpentiumpro  -ffast-math -O3 -c qnorm.c -o qnorm.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I ../boostIncl -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -ffast-math -O3 -DUSING_R -c rundir.cc -o rundir.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I ../boostIncl -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -ffast-math -O3 -DUSING_R -c sokal.cc -o sokal.o
llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -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-3.0-bioc/meat/bgx.buildbin-libdir/bgx/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (bgx)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libgcc_s.1.dylib" "bgx.buildbin-libdir/bgx/libs//bgx.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libgfortran.2.dylib" "bgx.buildbin-libdir/bgx/libs//bgx.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libreadline.5.2.dylib" "bgx.buildbin-libdir/bgx/libs//bgx.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libreadline.dylib" "bgx.buildbin-libdir/bgx/libs//bgx.so"