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Created January 15, 2013 01:53
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beagle failed to build on 10.8.2
################### verbose output #################################
brew install --HEAD beagle --with-cuda -v
==> Checking out http://beagle-lib.googlecode.com/svn/trunk/
svn up --force /Library/Caches/Homebrew/beagle--svn-HEAD
At revision 1092.
svn export --force /Library/Caches/Homebrew/beagle--svn-HEAD /private/tmp/beagle-UFvZ
Export complete.
==> Patching
/usr/bin/patch -f -p1 -i 000-homebrew.diff
patching file configure.ac
==> ./autogen.sh
./autogen.sh
glibtoolize: putting auxiliary files in AC_CONFIG_AUX_DIR, `.config'.
glibtoolize: copying file `.config/ltmain.sh'
glibtoolize: putting macros in AC_CONFIG_MACRO_DIR, `m4'.
glibtoolize: copying file `m4/libtool.m4'
glibtoolize: copying file `m4/ltoptions.m4'
glibtoolize: copying file `m4/ltsugar.m4'
glibtoolize: copying file `m4/ltversion.m4'
glibtoolize: copying file `m4/lt~obsolete.m4'
configure.ac:56: warning: AM_INIT_AUTOMAKE: two- and three-arguments forms are deprecated. For more info, see:
configure.ac:56: http://www.gnu.org/software/automake/manual/automake.html#Modernize-AM_INIT_AUTOMAKE-invocation
configure.ac:64: installing '.config/config.guess'
configure.ac:64: installing '.config/config.sub'
configure.ac:56: installing '.config/install-sh'
configure.ac:56: installing '.config/missing'
Makefile.am: installing './INSTALL'
examples/complextest/Makefile.am: installing '.config/depcomp'
parallel-tests: installing '.config/test-driver'
libhmsbeagle/GPU/kernels/Makefile.am:1: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
==> ./configure --prefix=/usr/local/Cellar/beagle/HEAD--with-cuda=/Developer/NVIDIA/CUDA-5.0/bin
./configure --prefix=/usr/local/Cellar/beagle/HEAD--with-cuda=/Developer/NVIDIA/CUDA-5.0/bin
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... .config/install-sh -c -d
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for gcc... cc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether cc accepts -g... yes
checking for cc option to accept ISO C89... none needed
checking for style of include used by make... GNU
checking dependency style of cc... gcc3
checking whether we are using the GNU C++ compiler... yes
checking whether c++ accepts -g... yes
checking dependency style of c++... gcc3
checking whether ln -s works... yes
checking build system type... x86_64-apple-darwin12.2.0
checking host system type... x86_64-apple-darwin12.2.0
checking how to print strings... printf
checking for a sed that does not truncate output... /usr/local/Library/ENV/4.3/sed
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for fgrep... /usr/bin/grep -F
checking for ld used by cc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... no
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm
checking the name lister (/usr/bin/nm) interface... BSD nm
checking the maximum length of command line arguments... 196608
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking how to convert x86_64-apple-darwin12.2.0 file names to x86_64-apple-darwin12.2.0 format... func_convert_file_noop
checking how to convert x86_64-apple-darwin12.2.0 file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... no
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... no
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm output from cc object... ok
checking for sysroot... no
checking for mt... no
checking if : is a manifest tool... no
checking for dsymutil... dsymutil
checking for nmedit... nmedit
checking for lipo... lipo
checking for otool... otool
checking for otool64... no
checking for -single_module linker flag... yes
checking for -exported_symbols_list linker flag... yes
checking for -force_load linker flag... yes
checking how to run the C preprocessor... cc -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if cc supports -fno-rtti -fno-exceptions... yes
checking for cc option to produce PIC... -fno-common -DPIC
checking if cc PIC flag -fno-common -DPIC works... yes
checking if cc static flag -static works... no
checking if cc supports -c -o file.o... yes
checking if cc supports -c -o file.o... (cached) yes
checking whether the cc linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin12.2.0 dyld
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking how to run the C++ preprocessor... c++ -E
checking for ld used by c++... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... no
checking whether the c++ linker (/usr/bin/ld) supports shared libraries... yes
checking for c++ option to produce PIC... -fno-common -DPIC
checking if c++ PIC flag -fno-common -DPIC works... yes
checking if c++ static flag -static works... no
checking if c++ supports -c -o file.o... yes
checking if c++ supports -c -o file.o... (cached) yes
checking whether the c++ linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... darwin12.2.0 dyld
checking how to hardcode library paths into programs... immediate
checking for library containing lt_dlinit... -lltdl
checking if gcc accepts -dumpversion option... yes
checking gcc version... 4.2.1
checking for /usr/local/cuda/... yes
checking for /usr/local/cuda/include... yes
checking for /usr/local/cuda/lib... yes
checking for nvcc... /Developer/NVIDIA/CUDA-5.0/bin/nvcc
checking for x86 cpuid output... unknown
checking for x86 cpuid 0x00000001 output... 20655:100800:29ae3ff:bfebfbff
checking whether mmx is supported... yes
checking whether sse is supported... yes
checking whether sse2 is supported... yes
checking whether sse3 is supported... yes
checking whether ssse3 is supported... yes
checking whether sse4.1 is supported... yes
checking whether sse4.2 is supported... yes
checking whether avx is supported... no
checking whether C compiler accepts -mmmx... yes
checking whether C compiler accepts -msse... yes
checking whether C compiler accepts -msse2... yes
checking whether C compiler accepts -msse3... yes
checking whether C compiler accepts -mssse3... yes
checking whether C compiler accepts -msse4.1... yes
checking whether C compiler accepts -msse4.2... yes
checking cpuid.h usability... yes
checking cpuid.h presence... yes
checking for cpuid.h... yes
./configure: line 16568: enable-osx-leopard=yes: command not found
checking for javac... javac
checking for javac... /usr/bin/javac
checking symlink for /usr/bin/javac... /System/Library/Frameworks/JavaVM.framework/Versions/Current/Commands/javac
checking for doxygen... no
configure: WARNING: doxygen not found - will not generate any doxygen documentation
checking for perl... /usr/bin/perl
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating hmsbeagle-1.pc
config.status: creating libhmsbeagle/Makefile
config.status: creating libhmsbeagle/GPU/Makefile
config.status: creating libhmsbeagle/GPU/kernels/Makefile
config.status: creating libhmsbeagle/CPU/Makefile
config.status: creating libhmsbeagle/plugin/Makefile
config.status: creating examples/Makefile
config.status: creating examples/tinytest/Makefile
config.status: creating examples/complextest/Makefile
config.status: creating examples/oddstatetest/Makefile
config.status: creating examples/fourtaxon/Makefile
config.status: creating examples/genomictest/Makefile
config.status: creating examples/matrixtest/Makefile
config.status: creating libhmsbeagle/config.h
config.status: executing depfiles commands
config.status: executing libtool commands
==> make
make
Making all in libhmsbeagle
/usr/bin/make all-recursive
Making all in GPU
Making all in kernels
echo "// auto-generated header file with CUDA kernels PTX code" > BeagleCUDA_kernels.h
/Developer/NVIDIA/CUDA-5.0/bin/nvcc -o BeagleCUDA_kernels.ptx -ptx -DSTATE_COUNT=4 \
./kernels4.cu -O3 -m64 -D_POSIX_C_SOURCE -DHAVE_CONFIG_H -I/private/tmp/beagle-UFvZ -I/private/tmp/beagle-UFvZ
brew: superenv removed: -O3 -m64
brew: superenv removed: -O3 -m64
brew: superenv removed: -O3 -m64
echo "#define KERNELS_STRING_SP_4 \"\\" >> BeagleCUDA_kernels.h
cat BeagleCUDA_kernels.ptx | sed 's/\"/\\"/g' | sed 's/$/\\n\\/' >> BeagleCUDA_kernels.h
echo "\"" >> BeagleCUDA_kernels.h
for s in 16 32 48 64 80 128 192; do \
echo "Making state count = $s \n" ; \
(/Developer/NVIDIA/CUDA-5.0/bin/nvcc -o BeagleCUDA_kernels.ptx -ptx -DSTATE_COUNT=$s \
./kernelsX.cu -O3 -m64 -D_POSIX_C_SOURCE -DHAVE_CONFIG_H -I/private/tmp/beagle-UFvZ -I/private/tmp/beagle-UFvZ) || exit; \
echo "#define KERNELS_STRING_SP_$s \"\\" >> BeagleCUDA_kernels.h; \
cat BeagleCUDA_kernels.ptx | sed 's/\"/\\"/g' | sed 's/$/\\n\\/' >> BeagleCUDA_kernels.h; \
echo "\"" >> BeagleCUDA_kernels.h; \
done
Making state count = 16
brew: superenv removed: -O3 -m64
brew: superenv removed: -O3 -m64
brew: superenv removed: -O3 -m64
Making state count = 32
brew: superenv removed: -O3 -m64
brew: superenv removed: -O3 -m64
brew: superenv removed: -O3 -m64
Making state count = 48
brew: superenv removed: -O3 -m64
brew: superenv removed: -O3 -m64
brew: superenv removed: -O3 -m64
Making state count = 64
brew: superenv removed: -O3 -m64
brew: superenv removed: -O3 -m64
brew: superenv removed: -O3 -m64
Making state count = 80
brew: superenv removed: -O3 -m64
brew: superenv removed: -O3 -m64
brew: superenv removed: -O3 -m64
Making state count = 128
brew: superenv removed: -O3 -m64
brew: superenv removed: -O3 -m64
brew: superenv removed: -O3 -m64
Making state count = 192
brew: superenv removed: -O3 -m64
brew: superenv removed: -O3 -m64
brew: superenv removed: -O3 -m64
/Developer/NVIDIA/CUDA-5.0/bin/nvcc -o BeagleCUDA_kernels.ptx -ptx -arch compute_13 -DSTATE_COUNT=4 -DDOUBLE_PRECISION \
./kernels4.cu -O3 -m64 -D_POSIX_C_SOURCE -DHAVE_CONFIG_H -I/private/tmp/beagle-UFvZ -I/private/tmp/beagle-UFvZ
brew: superenv removed: -O3 -m64
brew: superenv removed: -O3 -m64
brew: superenv removed: -O3 -m64
echo "#define KERNELS_STRING_DP_4 \"\\" >> BeagleCUDA_kernels.h
cat BeagleCUDA_kernels.ptx | sed 's/\"/\\"/g' | sed 's/$/\\n\\/' >> BeagleCUDA_kernels.h
echo "\"" >> BeagleCUDA_kernels.h
for s in 16 32 48 64 80 128 192; do \
echo "Making state count = $s \n" ; \
(/Developer/NVIDIA/CUDA-5.0/bin/nvcc -o BeagleCUDA_kernels.ptx -ptx -arch compute_13 -DSTATE_COUNT=$s -DDOUBLE_PRECISION \
./kernelsX.cu -O3 -m64 -D_POSIX_C_SOURCE -DHAVE_CONFIG_H -I/private/tmp/beagle-UFvZ -I/private/tmp/beagle-UFvZ) || exit; \
echo "#define KERNELS_STRING_DP_$s \"\\" >> BeagleCUDA_kernels.h; \
cat BeagleCUDA_kernels.ptx | sed 's/\"/\\"/g' | sed 's/$/\\n\\/' >> BeagleCUDA_kernels.h; \
echo "\"" >> BeagleCUDA_kernels.h; \
done
Making state count = 16
brew: superenv removed: -O3 -m64
brew: superenv removed: -O3 -m64
brew: superenv removed: -O3 -m64
Making state count = 32
brew: superenv removed: -O3 -m64
brew: superenv removed: -O3 -m64
brew: superenv removed: -O3 -m64
Making state count = 48
brew: superenv removed: -O3 -m64
brew: superenv removed: -O3 -m64
brew: superenv removed: -O3 -m64
Making state count = 64
brew: superenv removed: -O3 -m64
brew: superenv removed: -O3 -m64
brew: superenv removed: -O3 -m64
Making state count = 80
brew: superenv removed: -O3 -m64
brew: superenv removed: -O3 -m64
brew: superenv removed: -O3 -m64
Making state count = 128
brew: superenv removed: -O3 -m64
brew: superenv removed: -O3 -m64
brew: superenv removed: -O3 -m64
Making state count = 192
brew: superenv removed: -O3 -m64
brew: superenv removed: -O3 -m64
brew: superenv removed: -O3 -m64
/usr/bin/make all-am
make[5]: Nothing to be done for `all-am'.
/bin/sh ../../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I../../libhmsbeagle -I/private/tmp/beagle-UFvZ -I/private/tmp/beagle-UFvZ -I/System/Library/Frameworks/JavaVM.framework/Versions/Current/Headers -DDLS_MACOS -m64 -DCUDA -I/usr/local/cuda/include -O3 -MT libhmsbeagle_cuda_la-GPUImplHelper.lo -MD -MP -MF .deps/libhmsbeagle_cuda_la-GPUImplHelper.Tpo -c -o libhmsbeagle_cuda_la-GPUImplHelper.lo `test -f 'GPUImplHelper.cpp' || echo './'`GPUImplHelper.cpp
/bin/sh ../../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I../../libhmsbeagle -I/private/tmp/beagle-UFvZ -I/private/tmp/beagle-UFvZ -I/System/Library/Frameworks/JavaVM.framework/Versions/Current/Headers -DDLS_MACOS -m64 -DCUDA -I/usr/local/cuda/include -O3 -MT libhmsbeagle_cuda_la-GPUInterfaceCUDA.lo -MD -MP -MF .deps/libhmsbeagle_cuda_la-GPUInterfaceCUDA.Tpo -c -o libhmsbeagle_cuda_la-GPUInterfaceCUDA.lo `test -f 'GPUInterfaceCUDA.cpp' || echo './'`GPUInterfaceCUDA.cpp
/bin/sh ../../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I../../libhmsbeagle -I/private/tmp/beagle-UFvZ -I/private/tmp/beagle-UFvZ -I/System/Library/Frameworks/JavaVM.framework/Versions/Current/Headers -DDLS_MACOS -m64 -DCUDA -I/usr/local/cuda/include -O3 -MT libhmsbeagle_cuda_la-KernelLauncher.lo -MD -MP -MF .deps/libhmsbeagle_cuda_la-KernelLauncher.Tpo -c -o libhmsbeagle_cuda_la-KernelLauncher.lo `test -f 'KernelLauncher.cpp' || echo './'`KernelLauncher.cpp
/bin/sh ../../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I../../libhmsbeagle -I/private/tmp/beagle-UFvZ -I/private/tmp/beagle-UFvZ -I/System/Library/Frameworks/JavaVM.framework/Versions/Current/Headers -DDLS_MACOS -m64 -DCUDA -I/usr/local/cuda/include -O3 -MT libhmsbeagle_cuda_la-KernelResource.lo -MD -MP -MF .deps/libhmsbeagle_cuda_la-KernelResource.Tpo -c -o libhmsbeagle_cuda_la-KernelResource.lo `test -f 'KernelResource.cpp' || echo './'`KernelResource.cpp
libtool: compile: c++ -DHAVE_CONFIG_H -I. -I../../libhmsbeagle -I/private/tmp/beagle-UFvZ -I/private/tmp/beagle-UFvZ -I/System/Library/Frameworks/JavaVM.framework/Versions/Current/Headers -DDLS_MACOS -m64 -DCUDA -I/usr/local/cuda/include -O3 -MT libhmsbeagle_cuda_la-GPUImplHelper.lo -MD -MP -MF .deps/libhmsbeagle_cuda_la-GPUImplHelper.Tpo -c GPUImplHelper.cpp -fno-common -DPIC -o .libs/libhmsbeagle_cuda_la-GPUImplHelper.o
libtool: compile: c++ -DHAVE_CONFIG_H -I. -I../../libhmsbeagle -I/private/tmp/beagle-UFvZ -I/private/tmp/beagle-UFvZ -I/System/Library/Frameworks/JavaVM.framework/Versions/Current/Headers -DDLS_MACOS -m64 -DCUDA -I/usr/local/cuda/include -O3 -MT libhmsbeagle_cuda_la-KernelLauncher.lo -MD -MP -MF .deps/libhmsbeagle_cuda_la-KernelLauncher.Tpo -c KernelLauncher.cpp -fno-common -DPIC -o .libs/libhmsbeagle_cuda_la-KernelLauncher.o
libtool: compile: c++ -DHAVE_CONFIG_H -I. -I../../libhmsbeagle -I/private/tmp/beagle-UFvZ -I/private/tmp/beagle-UFvZ -I/System/Library/Frameworks/JavaVM.framework/Versions/Current/Headers -DDLS_MACOS -m64 -DCUDA -I/usr/local/cuda/include -O3 -MT libhmsbeagle_cuda_la-GPUInterfaceCUDA.lo -MD -MP -MF .deps/libhmsbeagle_cuda_la-GPUInterfaceCUDA.Tpo -c GPUInterfaceCUDA.cpp -fno-common -DPIC -o .libs/libhmsbeagle_cuda_la-GPUInterfaceCUDA.o
libtool: compile: c++ -DHAVE_CONFIG_H -I. -I../../libhmsbeagle -I/private/tmp/beagle-UFvZ -I/private/tmp/beagle-UFvZ -I/System/Library/Frameworks/JavaVM.framework/Versions/Current/Headers -DDLS_MACOS -m64 -DCUDA -I/usr/local/cuda/include -O3 -MT libhmsbeagle_cuda_la-KernelResource.lo -MD -MP -MF .deps/libhmsbeagle_cuda_la-KernelResource.Tpo -c KernelResource.cpp -fno-common -DPIC -o .libs/libhmsbeagle_cuda_la-KernelResource.o
brew: superenv removed: -m64 -O3
brew: superenv removed: -m64 -O3
brew: superenv removed: -m64 -O3
brew: superenv removed: -m64 -O3
mv -f .deps/libhmsbeagle_cuda_la-KernelResource.Tpo .deps/libhmsbeagle_cuda_la-KernelResource.Plo
/bin/sh ../../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I../../libhmsbeagle -I/private/tmp/beagle-UFvZ -I/private/tmp/beagle-UFvZ -I/System/Library/Frameworks/JavaVM.framework/Versions/Current/Headers -DDLS_MACOS -m64 -DCUDA -I/usr/local/cuda/include -O3 -MT libhmsbeagle_cuda_la-CUDAPlugin.lo -MD -MP -MF .deps/libhmsbeagle_cuda_la-CUDAPlugin.Tpo -c -o libhmsbeagle_cuda_la-CUDAPlugin.lo `test -f 'CUDAPlugin.cpp' || echo './'`CUDAPlugin.cpp
libtool: compile: c++ -DHAVE_CONFIG_H -I. -I../../libhmsbeagle -I/private/tmp/beagle-UFvZ -I/private/tmp/beagle-UFvZ -I/System/Library/Frameworks/JavaVM.framework/Versions/Current/Headers -DDLS_MACOS -m64 -DCUDA -I/usr/local/cuda/include -O3 -MT libhmsbeagle_cuda_la-CUDAPlugin.lo -MD -MP -MF .deps/libhmsbeagle_cuda_la-CUDAPlugin.Tpo -c CUDAPlugin.cpp -fno-common -DPIC -o .libs/libhmsbeagle_cuda_la-CUDAPlugin.o
brew: superenv removed: -m64 -O3
mv -f .deps/libhmsbeagle_cuda_la-KernelLauncher.Tpo .deps/libhmsbeagle_cuda_la-KernelLauncher.Plo
mv -f .deps/libhmsbeagle_cuda_la-GPUImplHelper.Tpo .deps/libhmsbeagle_cuda_la-GPUImplHelper.Plo
mv -f .deps/libhmsbeagle_cuda_la-GPUInterfaceCUDA.Tpo .deps/libhmsbeagle_cuda_la-GPUInterfaceCUDA.Plo
mv -f .deps/libhmsbeagle_cuda_la-CUDAPlugin.Tpo .deps/libhmsbeagle_cuda_la-CUDAPlugin.Plo
/bin/sh ../../libtool --tag=CXX --mode=link c++ -DDLS_MACOS -m64 -DCUDA -I/usr/local/cuda/include -O3 -version-info 1:1:0 -o libhmsbeagle-cuda.la -rpath /usr/local/Cellar/beagle/HEAD--with-cuda=/Developer/NVIDIA/CUDA-5.0/bin/lib libhmsbeagle_cuda_la-GPUImplHelper.lo libhmsbeagle_cuda_la-GPUInterfaceCUDA.lo libhmsbeagle_cuda_la-KernelLauncher.lo libhmsbeagle_cuda_la-KernelResource.lo libhmsbeagle_cuda_la-CUDAPlugin.lo -lcuda -L/usr/local/cuda/lib -lltdl
libtool: link: c++ -dynamiclib -Wl,-undefined -Wl,dynamic_lookup -o .libs/libhmsbeagle-cuda.1.dylib .libs/libhmsbeagle_cuda_la-GPUImplHelper.o .libs/libhmsbeagle_cuda_la-GPUInterfaceCUDA.o .libs/libhmsbeagle_cuda_la-KernelLauncher.o .libs/libhmsbeagle_cuda_la-KernelResource.o .libs/libhmsbeagle_cuda_la-CUDAPlugin.o -lcuda -L/usr/local/cuda/lib -lltdl -m64 -O3 -install_name /usr/local/Cellar/beagle/HEAD--with-cuda=/Developer/NVIDIA/CUDA-5.0/bin/lib/libhmsbeagle-cuda.1.dylib -compatibility_version 2 -current_version 2.1 -Wl,-single_module
brew: superenv removed: -m64 -O3
libtool: link: (cd ".libs" && rm -f "libhmsbeagle-cuda.dylib" && ln -s "libhmsbeagle-cuda.1.dylib" "libhmsbeagle-cuda.dylib")
libtool: link: ( cd ".libs" && rm -f "libhmsbeagle-cuda.la" && ln -s "../libhmsbeagle-cuda.la" "libhmsbeagle-cuda.la" )
Making all in CPU
/bin/sh ../../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I../../libhmsbeagle -I/private/tmp/beagle-UFvZ -I/private/tmp/beagle-UFvZ -I/System/Library/Frameworks/JavaVM.framework/Versions/Current/Headers -DDLS_MACOS -m64 -O3 -MT libhmsbeagle_cpu_la-BeagleCPUPlugin.lo -MD -MP -MF .deps/libhmsbeagle_cpu_la-BeagleCPUPlugin.Tpo -c -o libhmsbeagle_cpu_la-BeagleCPUPlugin.lo `test -f 'BeagleCPUPlugin.cpp' || echo './'`BeagleCPUPlugin.cpp
/bin/sh ../../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I../../libhmsbeagle -I/private/tmp/beagle-UFvZ -I/private/tmp/beagle-UFvZ -I/System/Library/Frameworks/JavaVM.framework/Versions/Current/Headers -DDLS_MACOS -m64 -msse2 -O3 -MT libhmsbeagle_cpu_sse_la-BeagleCPUSSEPlugin.lo -MD -MP -MF .deps/libhmsbeagle_cpu_sse_la-BeagleCPUSSEPlugin.Tpo -c -o libhmsbeagle_cpu_sse_la-BeagleCPUSSEPlugin.lo `test -f 'BeagleCPUSSEPlugin.cpp' || echo './'`BeagleCPUSSEPlugin.cpp
libtool: compile: c++ -DHAVE_CONFIG_H -I. -I../../libhmsbeagle -I/private/tmp/beagle-UFvZ -I/private/tmp/beagle-UFvZ -I/System/Library/Frameworks/JavaVM.framework/Versions/Current/Headers -DDLS_MACOS -m64 -msse2 -O3 -MT libhmsbeagle_cpu_sse_la-BeagleCPUSSEPlugin.lo -MD -MP -MF .deps/libhmsbeagle_cpu_sse_la-BeagleCPUSSEPlugin.Tpo -c BeagleCPUSSEPlugin.cpp -fno-common -DPIC -o .libs/libhmsbeagle_cpu_sse_la-BeagleCPUSSEPlugin.o
libtool: compile: c++ -DHAVE_CONFIG_H -I. -I../../libhmsbeagle -I/private/tmp/beagle-UFvZ -I/private/tmp/beagle-UFvZ -I/System/Library/Frameworks/JavaVM.framework/Versions/Current/Headers -DDLS_MACOS -m64 -O3 -MT libhmsbeagle_cpu_la-BeagleCPUPlugin.lo -MD -MP -MF .deps/libhmsbeagle_cpu_la-BeagleCPUPlugin.Tpo -c BeagleCPUPlugin.cpp -fno-common -DPIC -o .libs/libhmsbeagle_cpu_la-BeagleCPUPlugin.o
brew: superenv removed: -m64 -O3
brew: superenv removed: -m64 -O3
mv -f .deps/libhmsbeagle_cpu_sse_la-BeagleCPUSSEPlugin.Tpo .deps/libhmsbeagle_cpu_sse_la-BeagleCPUSSEPlugin.Plo
/bin/sh ../../libtool --tag=CXX --mode=link c++ -DDLS_MACOS -m64 -msse2 -O3 -version-info 1:1:0 -o libhmsbeagle-cpu-sse.la -rpath /usr/local/Cellar/beagle/HEAD--with-cuda=/Developer/NVIDIA/CUDA-5.0/bin/lib libhmsbeagle_cpu_sse_la-BeagleCPUSSEPlugin.lo -lltdl
mv -f .deps/libhmsbeagle_cpu_la-BeagleCPUPlugin.Tpo .deps/libhmsbeagle_cpu_la-BeagleCPUPlugin.Plo
/bin/sh ../../libtool --tag=CXX --mode=link c++ -DDLS_MACOS -m64 -O3 -version-info 1:1:0 -o libhmsbeagle-cpu.la -rpath /usr/local/Cellar/beagle/HEAD--with-cuda=/Developer/NVIDIA/CUDA-5.0/bin/lib libhmsbeagle_cpu_la-BeagleCPUPlugin.lo -lltdl
libtool: link: c++ -dynamiclib -Wl,-undefined -Wl,dynamic_lookup -o .libs/libhmsbeagle-cpu-sse.1.dylib .libs/libhmsbeagle_cpu_sse_la-BeagleCPUSSEPlugin.o -lltdl -m64 -msse2 -O3 -install_name /usr/local/Cellar/beagle/HEAD--with-cuda=/Developer/NVIDIA/CUDA-5.0/bin/lib/libhmsbeagle-cpu-sse.1.dylib -compatibility_version 2 -current_version 2.1 -Wl,-single_module
brew: superenv removed: -m64 -O3
libtool: link: c++ -dynamiclib -Wl,-undefined -Wl,dynamic_lookup -o .libs/libhmsbeagle-cpu.1.dylib .libs/libhmsbeagle_cpu_la-BeagleCPUPlugin.o -lltdl -m64 -O3 -install_name /usr/local/Cellar/beagle/HEAD--with-cuda=/Developer/NVIDIA/CUDA-5.0/bin/lib/libhmsbeagle-cpu.1.dylib -compatibility_version 2 -current_version 2.1 -Wl,-single_module
brew: superenv removed: -m64 -O3
libtool: link: (cd ".libs" && rm -f "libhmsbeagle-cpu-sse.dylib" && ln -s "libhmsbeagle-cpu-sse.1.dylib" "libhmsbeagle-cpu-sse.dylib")
libtool: link: ( cd ".libs" && rm -f "libhmsbeagle-cpu-sse.la" && ln -s "../libhmsbeagle-cpu-sse.la" "libhmsbeagle-cpu-sse.la" )
libtool: link: (cd ".libs" && rm -f "libhmsbeagle-cpu.dylib" && ln -s "libhmsbeagle-cpu.1.dylib" "libhmsbeagle-cpu.dylib")
libtool: link: ( cd ".libs" && rm -f "libhmsbeagle-cpu.la" && ln -s "../libhmsbeagle-cpu.la" "libhmsbeagle-cpu.la" )
Making all in plugin
/bin/sh ../../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I../../libhmsbeagle -I../.. -I../.. -I/System/Library/Frameworks/JavaVM.framework/Versions/Current/Headers -DDLS_MACOS -m64 -O3 -MT libplugin_la-Plugin.lo -MD -MP -MF .deps/libplugin_la-Plugin.Tpo -c -o libplugin_la-Plugin.lo `test -f 'Plugin.cpp' || echo './'`Plugin.cpp
/bin/sh ../../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I../../libhmsbeagle -I../.. -I../.. -I/System/Library/Frameworks/JavaVM.framework/Versions/Current/Headers -DDLS_MACOS -m64 -O3 -MT libplugin_la-UnixSharedLibrary.lo -MD -MP -MF .deps/libplugin_la-UnixSharedLibrary.Tpo -c -o libplugin_la-UnixSharedLibrary.lo `test -f 'UnixSharedLibrary.cpp' || echo './'`UnixSharedLibrary.cpp
libtool: compile: c++ -DHAVE_CONFIG_H -I. -I../../libhmsbeagle -I../.. -I../.. -I/System/Library/Frameworks/JavaVM.framework/Versions/Current/Headers -DDLS_MACOS -m64 -O3 -MT libplugin_la-UnixSharedLibrary.lo -MD -MP -MF .deps/libplugin_la-UnixSharedLibrary.Tpo -c UnixSharedLibrary.cpp -fno-common -DPIC -o .libs/libplugin_la-UnixSharedLibrary.o
libtool: compile: c++ -DHAVE_CONFIG_H -I. -I../../libhmsbeagle -I../.. -I../.. -I/System/Library/Frameworks/JavaVM.framework/Versions/Current/Headers -DDLS_MACOS -m64 -O3 -MT libplugin_la-Plugin.lo -MD -MP -MF .deps/libplugin_la-Plugin.Tpo -c Plugin.cpp -fno-common -DPIC -o .libs/libplugin_la-Plugin.o
brew: superenv removed: -m64 -O3
brew: superenv removed: -m64 -O3
mv -f .deps/libplugin_la-Plugin.Tpo .deps/libplugin_la-Plugin.Plo
mv -f .deps/libplugin_la-UnixSharedLibrary.Tpo .deps/libplugin_la-UnixSharedLibrary.Plo
/bin/sh ../../libtool --tag=CXX --mode=link c++ -DDLS_MACOS -m64 -O3 -o libplugin.la libplugin_la-Plugin.lo libplugin_la-UnixSharedLibrary.lo -lltdl
libtool: link: ar cru .libs/libplugin.a .libs/libplugin_la-Plugin.o .libs/libplugin_la-UnixSharedLibrary.o
libtool: link: ranlib .libs/libplugin.a
libtool: link: ( cd ".libs" && rm -f "libplugin.la" && ln -s "../libplugin.la" "libplugin.la" )
/bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/System/Library/Frameworks/JavaVM.framework/Versions/Current/Headers -DDLS_MACOS -m64 -O3 -MT libhmsbeagle_la-beagle.lo -MD -MP -MF .deps/libhmsbeagle_la-beagle.Tpo -c -o libhmsbeagle_la-beagle.lo `test -f 'beagle.cpp' || echo './'`beagle.cpp
/bin/sh ../libtool --tag=CXX --mode=compile c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/System/Library/Frameworks/JavaVM.framework/Versions/Current/Headers -DDLS_MACOS -m64 -O3 -MT libhmsbeagle_jni_la-beagle_BeagleJNIWrapper.lo -MD -MP -MF .deps/libhmsbeagle_jni_la-beagle_BeagleJNIWrapper.Tpo -c -o libhmsbeagle_jni_la-beagle_BeagleJNIWrapper.lo `test -f 'JNI/beagle_BeagleJNIWrapper.cpp' || echo './'`JNI/beagle_BeagleJNIWrapper.cpp
libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/System/Library/Frameworks/JavaVM.framework/Versions/Current/Headers -DDLS_MACOS -m64 -O3 -MT libhmsbeagle_la-beagle.lo -MD -MP -MF .deps/libhmsbeagle_la-beagle.Tpo -c beagle.cpp -fno-common -DPIC -o .libs/libhmsbeagle_la-beagle.o
libtool: compile: c++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/System/Library/Frameworks/JavaVM.framework/Versions/Current/Headers -DDLS_MACOS -m64 -O3 -MT libhmsbeagle_jni_la-beagle_BeagleJNIWrapper.lo -MD -MP -MF .deps/libhmsbeagle_jni_la-beagle_BeagleJNIWrapper.Tpo -c JNI/beagle_BeagleJNIWrapper.cpp -fno-common -DPIC -o .libs/libhmsbeagle_jni_la-beagle_BeagleJNIWrapper.o
brew: superenv removed: -m64 -O3
brew: superenv removed: -m64 -O3
mv -f .deps/libhmsbeagle_jni_la-beagle_BeagleJNIWrapper.Tpo .deps/libhmsbeagle_jni_la-beagle_BeagleJNIWrapper.Plo
/bin/sh ../libtool --tag=CXX --mode=link c++ -DDLS_MACOS -m64 -O3 -module -avoid-version -shrext .jnilib -o libhmsbeagle-jni.la -rpath /usr/local/Cellar/beagle/HEAD--with-cuda=/Developer/NVIDIA/CUDA-5.0/bin/lib libhmsbeagle_jni_la-beagle_BeagleJNIWrapper.lo -lhmsbeagle -lltdl
libtool: link: c++ -Wl,-undefined -Wl,dynamic_lookup -o .libs/libhmsbeagle-jni.jnilib -bundle .libs/libhmsbeagle_jni_la-beagle_BeagleJNIWrapper.o -lhmsbeagle -lltdl -m64 -O3
brew: superenv removed: -m64 -O3
ld: library not found for -lhmsbeagle
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[3]: *** [libhmsbeagle-jni.la] Error 1
make[3]: *** Waiting for unfinished jobs....
mv -f .deps/libhmsbeagle_la-beagle.Tpo .deps/libhmsbeagle_la-beagle.Plo
make[2]: *** [all-recursive] Error 1
make[1]: *** [all] Error 2
make: *** [all-recursive] Error 1
==> Configuration
HOMEBREW_VERSION: 0.9.3
HEAD: 9bf47d705a41777275910a5948077073be9dad4d
CPU: quad-core 64-bit arrandale
OS X: 10.8.2-x86_64
Xcode: 4.5.2
CLT: 4.5.0.0.1.1249367152
X11: 2.7.4 => /opt/X11
==> ENV
CC: cc
CXX: c++
MAKEFLAGS: -j4
CMAKE_PREFIX_PATH: /usr/local
CMAKE_INCLUDE_PATH: /usr/include/libxml2:/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers/
CMAKE_LIBRARY_PATH: /System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries
PKG_CONFIG_PATH: /usr/local/lib/pkgconfig:/usr/local/Library/ENV/pkgconfig/mountain_lion
ACLOCAL_PATH: /usr/local/share/aclocal
OBJC: cc
PATH: /usr/local/Library/ENV/4.3:/usr/local/opt/autoconf/bin:/usr/local/opt/automake/bin:/usr/local/opt/libtool/bin:/usr/local/opt/python/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/Cellar/python/2.7.3/bin:/usr/local/bin:/usr/local/sbin:/Users/crd1859/bin:/Users/crd1859/.rvm/gems/ruby-1.9.3-p194/bin:/Users/crd1859/.rvm/gems/ruby-1.9.3-p194@global/bin:/Users/crd1859/.rvm/rubies/ruby-1.9.3-p194/bin:/Users/crd1859/.rvm/bin:/Developer/NVIDIA/CUDA-5.0/bin:/Users/crd1859/.pythonbrew/bin:/Users/crd1859/.pythonbrew/pythons/Python-2.7.2/bin:/Users/crd1859/perl5/perlbrew/bin:/Users/crd1859/perl5/perlbrew/perls/perl-5.16.0/bin
Error: beagle did not build
Logs: /Users/crd1859/Library/Logs/Homebrew/beagle/config.log
##################################################################
######### config.log ##############
This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.
It was created by libhmsbeagle configure 1.0.0, which was
generated by GNU Autoconf 2.69. Invocation command line was
$ ./configure --prefix=/usr/local/Cellar/beagle/HEAD--with-cuda=/Developer/NVIDIA/CUDA-5.0/bin
## --------- ##
## Platform. ##
## --------- ##
hostname = Peter-Fieldss-MacBook-Pro.local
uname -m = x86_64
uname -r = 12.2.0
uname -s = Darwin
uname -v = Darwin Kernel Version 12.2.0: Sat Aug 25 00:48:52 PDT 2012; root:xnu-2050.18.24~1/RELEASE_X86_64
/usr/bin/uname -p = i386
/bin/uname -X = unknown
/bin/arch = unknown
/usr/bin/arch -k = unknown
/usr/convex/getsysinfo = unknown
/usr/bin/hostinfo = Mach kernel version:
Darwin Kernel Version 12.2.0: Sat Aug 25 00:48:52 PDT 2012; root:xnu-2050.18.24~1/RELEASE_X86_64
Kernel configured for up to 4 processors.
2 processors are physically available.
4 processors are logically available.
Processor type: i486 (Intel 80486)
Processors active: 0 1 2 3
Primary memory available: 8.00 gigabytes
Default processor set: 142 tasks, 847 threads, 4 processors
Load average: 2.64, Mach factor: 1.64
/bin/machine = unknown
/usr/bin/oslevel = unknown
/bin/universe = unknown
PATH: /usr/local/Library/ENV/4.3
PATH: /usr/local/opt/autoconf/bin
PATH: /usr/local/opt/automake/bin
PATH: /usr/local/opt/libtool/bin
PATH: /usr/local/opt/python/bin
PATH: /usr/bin
PATH: /bin
PATH: /usr/sbin
PATH: /sbin
PATH: /usr/local/Cellar/python/2.7.3/bin
PATH: /usr/local/bin
PATH: /usr/local/sbin
PATH: /Users/crd1859/bin
PATH: /Users/crd1859/.rvm/gems/ruby-1.9.3-p194/bin
PATH: /Users/crd1859/.rvm/gems/ruby-1.9.3-p194@global/bin
PATH: /Users/crd1859/.rvm/rubies/ruby-1.9.3-p194/bin
PATH: /Users/crd1859/.rvm/bin
PATH: /Developer/NVIDIA/CUDA-5.0/bin
PATH: /Users/crd1859/.pythonbrew/bin
PATH: /Users/crd1859/.pythonbrew/pythons/Python-2.7.2/bin
PATH: /Users/crd1859/perl5/perlbrew/bin
PATH: /Users/crd1859/perl5/perlbrew/perls/perl-5.16.0/bin
## ----------- ##
## Core tests. ##
## ----------- ##
configure:2550: checking for a BSD-compatible install
configure:2618: result: /usr/bin/install -c
configure:2629: checking whether build environment is sane
configure:2684: result: yes
configure:2835: checking for a thread-safe mkdir -p
configure:2874: result: .config/install-sh -c -d
configure:2881: checking for gawk
configure:2911: result: no
configure:2881: checking for mawk
configure:2911: result: no
configure:2881: checking for nawk
configure:2911: result: no
configure:2881: checking for awk
configure:2897: found /usr/bin/awk
configure:2908: result: awk
configure:2919: checking whether make sets $(MAKE)
configure:2941: result: yes
configure:2970: checking whether make supports nested variables
configure:2987: result: yes
configure:3107: checking for gcc
configure:3134: result: cc
configure:3363: checking for C compiler version
configure:3372: cc --version >&5
Apple clang version 4.1 (tags/Apple/clang-421.11.66) (based on LLVM 3.1svn)
Target: x86_64-apple-darwin12.2.0
Thread model: posix
configure:3383: $? = 0
configure:3372: cc -v >&5
Apple clang version 4.1 (tags/Apple/clang-421.11.66) (based on LLVM 3.1svn)
Target: x86_64-apple-darwin12.2.0
Thread model: posix
clang: warning: argument unused during compilation: '-isystem /usr/local/include'
clang: warning: argument unused during compilation: '-isystem /usr/include/libxml2'
clang: warning: argument unused during compilation: '-isystem /System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers/'
clang: warning: argument unused during compilation: '-L/usr/local/lib'
clang: warning: argument unused during compilation: '-L/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries'
configure:3383: $? = 0
configure:3372: cc -V >&5
clang: error: unsupported option '-V -isystem/usr/local/include'
clang: error: no input files
configure:3383: $? = 1
configure:3372: cc -qversion >&5
clang: error: no input files
configure:3383: $? = 1
configure:3403: checking whether the C compiler works
configure:3425: cc conftest.c >&5
configure:3429: $? = 0
configure:3477: result: yes
configure:3480: checking for C compiler default output file name
configure:3482: result: a.out
configure:3488: checking for suffix of executables
configure:3495: cc -o conftest conftest.c >&5
configure:3499: $? = 0
configure:3521: result:
configure:3543: checking whether we are cross compiling
configure:3551: cc -o conftest conftest.c >&5
configure:3555: $? = 0
configure:3562: ./conftest
configure:3566: $? = 0
configure:3581: result: no
configure:3586: checking for suffix of object files
configure:3608: cc -c conftest.c >&5
configure:3612: $? = 0
configure:3633: result: o
configure:3637: checking whether we are using the GNU C compiler
configure:3656: cc -c conftest.c >&5
configure:3656: $? = 0
configure:3665: result: yes
configure:3674: checking whether cc accepts -g
configure:3694: cc -c -g conftest.c >&5
configure:3694: $? = 0
configure:3735: result: yes
configure:3752: checking for cc option to accept ISO C89
configure:3815: cc -c -g -O2 conftest.c >&5
configure:3815: $? = 0
configure:3828: result: none needed
configure:3859: checking for style of include used by make
configure:3887: result: GNU
configure:3913: checking dependency style of cc
configure:4024: result: gcc3
configure:4151: checking for C++ compiler version
configure:4160: c++ --version >&5
Apple clang version 4.1 (tags/Apple/clang-421.11.66) (based on LLVM 3.1svn)
Target: x86_64-apple-darwin12.2.0
Thread model: posix
configure:4171: $? = 0
configure:4160: c++ -v >&5
Apple clang version 4.1 (tags/Apple/clang-421.11.66) (based on LLVM 3.1svn)
Target: x86_64-apple-darwin12.2.0
Thread model: posix
clang: warning: argument unused during compilation: '-isystem /usr/local/include'
clang: warning: argument unused during compilation: '-isystem /usr/include/libxml2'
clang: warning: argument unused during compilation: '-isystem /System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers/'
clang: warning: argument unused during compilation: '-L/usr/local/lib'
clang: warning: argument unused during compilation: '-L/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries'
configure:4171: $? = 0
configure:4160: c++ -V >&5
clang: error: unsupported option '-V -isystem/usr/local/include'
clang: error: no input files
configure:4171: $? = 1
configure:4160: c++ -qversion >&5
clang: error: no input files
configure:4171: $? = 1
configure:4175: checking whether we are using the GNU C++ compiler
configure:4194: c++ -c -O3 conftest.cpp >&5
configure:4194: $? = 0
configure:4203: result: yes
configure:4212: checking whether c++ accepts -g
configure:4232: c++ -c -g conftest.cpp >&5
configure:4232: $? = 0
configure:4273: result: yes
configure:4298: checking dependency style of c++
configure:4409: result: gcc3
configure:4425: checking whether ln -s works
configure:4429: result: yes
configure:4524: checking build system type
configure:4538: result: x86_64-apple-darwin12.2.0
configure:4558: checking host system type
configure:4571: result: x86_64-apple-darwin12.2.0
configure:4612: checking how to print strings
configure:4639: result: printf
configure:4660: checking for a sed that does not truncate output
configure:4724: result: /usr/local/Library/ENV/4.3/sed
configure:4742: checking for grep that handles long lines and -e
configure:4800: result: /usr/bin/grep
configure:4805: checking for egrep
configure:4867: result: /usr/bin/grep -E
configure:4872: checking for fgrep
configure:4934: result: /usr/bin/grep -F
configure:4969: checking for ld used by cc
configure:5036: result: /usr/bin/ld
configure:5043: checking if the linker (/usr/bin/ld) is GNU ld
configure:5058: result: no
configure:5070: checking for BSD- or MS-compatible name lister (nm)
configure:5119: result: /usr/bin/nm
configure:5249: checking the name lister (/usr/bin/nm) interface
configure:5256: cc -c -g -O2 conftest.c >&5
configure:5259: /usr/bin/nm "conftest.o"
configure:5262: output
000000000000020c S _some_variable
configure:5269: result: BSD nm
configure:5273: checking the maximum length of command line arguments
configure:5403: result: 196608
configure:5420: checking whether the shell understands some XSI constructs
configure:5430: result: yes
configure:5434: checking whether the shell understands "+="
configure:5440: result: yes
configure:5475: checking how to convert x86_64-apple-darwin12.2.0 file names to x86_64-apple-darwin12.2.0 format
configure:5515: result: func_convert_file_noop
configure:5522: checking how to convert x86_64-apple-darwin12.2.0 file names to toolchain format
configure:5542: result: func_convert_file_noop
configure:5549: checking for /usr/bin/ld option to reload object files
configure:5556: result: -r
configure:5630: checking for objdump
configure:5660: result: no
configure:5689: checking how to recognize dependent libraries
configure:5891: result: pass_all
configure:5976: checking for dlltool
configure:6006: result: no
configure:6036: checking how to associate runtime and link libraries
configure:6063: result: printf %s\n
configure:6124: checking for ar
configure:6140: found /usr/bin/ar
configure:6151: result: ar
configure:6188: checking for archiver @FILE support
configure:6205: cc -c -g -O2 conftest.c >&5
configure:6205: $? = 0
configure:6208: ar cru libconftest.a @conftest.lst >&5
ar: @conftest.lst: No such file or directory
configure:6211: $? = 1
configure:6231: result: no
configure:6289: checking for strip
configure:6305: found /usr/bin/strip
configure:6316: result: strip
configure:6388: checking for ranlib
configure:6404: found /usr/bin/ranlib
configure:6415: result: ranlib
configure:6517: checking command to parse /usr/bin/nm output from cc object
configure:6637: cc -c -g -O2 conftest.c >&5
configure:6640: $? = 0
configure:6644: /usr/bin/nm conftest.o \| sed -n -e 's/^.*[ ]\([BCDEGRST][BCDEGRST]*\)[ ][ ]*\([_A-Za-z][_A-Za-z0-9]*\)$/\1 \2 \2/p' | sed '/ __gnu_lto/d' \> conftest.nm
configure:6647: $? = 0
cannot find nm_test_var in conftest.nm
configure:6637: cc -c -g -O2 conftest.c >&5
configure:6640: $? = 0
configure:6644: /usr/bin/nm conftest.o \| sed -n -e 's/^.*[ ]\([BCDEGRST][BCDEGRST]*\)[ ][ ]*_\([_A-Za-z][_A-Za-z0-9]*\)$/\1 _\2 \2/p' | sed '/ __gnu_lto/d' \> conftest.nm
configure:6647: $? = 0
configure:6713: cc -o conftest -g -O2 conftest.c conftstm.o >&5
configure:6716: $? = 0
configure:6754: result: ok
configure:6791: checking for sysroot
configure:6821: result: no
configure:7077: checking for mt
configure:7107: result: no
configure:7127: checking if : is a manifest tool
configure:7133: : '-?'
configure:7141: result: no
configure:7197: checking for dsymutil
configure:7213: found /usr/bin/dsymutil
configure:7224: result: dsymutil
configure:7289: checking for nmedit
configure:7305: found /usr/bin/nmedit
configure:7316: result: nmedit
configure:7381: checking for lipo
configure:7397: found /usr/bin/lipo
configure:7408: result: lipo
configure:7473: checking for otool
configure:7489: found /usr/bin/otool
configure:7500: result: otool
configure:7565: checking for otool64
configure:7595: result: no
configure:7640: checking for -single_module linker flag
cc -g -O2 -o libconftest.dylib -dynamiclib -Wl,-single_module conftest.c
configure:7673: result: yes
configure:7676: checking for -exported_symbols_list linker flag
configure:7696: cc -o conftest -g -O2 -Wl,-exported_symbols_list,conftest.sym conftest.c >&5
configure:7696: $? = 0
configure:7706: result: yes
configure:7709: checking for -force_load linker flag
cc -g -O2 -c -o conftest.o conftest.c
ar cru libconftest.a conftest.o
ranlib libconftest.a
cc -g -O2 -o conftest conftest.c -Wl,-force_load,./libconftest.a
configure:7741: result: yes
configure:7783: checking how to run the C preprocessor
configure:7814: cc -E conftest.c
configure:7814: $? = 0
configure:7828: cc -E conftest.c
conftest.c:9:10: fatal error: 'ac_nonexistent.h' file not found
#include <ac_nonexistent.h>
^
1 error generated.
configure:7828: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "libhmsbeagle"
| #define PACKAGE_TARNAME "libhmsbeagle"
| #define PACKAGE_VERSION "1.0.0"
| #define PACKAGE_STRING "libhmsbeagle 1.0.0"
| #define PACKAGE_BUGREPORT "beagle-dev@googlegroups.com"
| #define PACKAGE_URL ""
| /* end confdefs.h. */
| #include <ac_nonexistent.h>
configure:7853: result: cc -E
configure:7873: cc -E conftest.c
configure:7873: $? = 0
configure:7887: cc -E conftest.c
conftest.c:9:10: fatal error: 'ac_nonexistent.h' file not found
#include <ac_nonexistent.h>
^
1 error generated.
configure:7887: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "libhmsbeagle"
| #define PACKAGE_TARNAME "libhmsbeagle"
| #define PACKAGE_VERSION "1.0.0"
| #define PACKAGE_STRING "libhmsbeagle 1.0.0"
| #define PACKAGE_BUGREPORT "beagle-dev@googlegroups.com"
| #define PACKAGE_URL ""
| /* end confdefs.h. */
| #include <ac_nonexistent.h>
configure:7916: checking for ANSI C header files
configure:7936: cc -c -g -O2 conftest.c >&5
configure:7936: $? = 0
configure:8009: cc -o conftest -g -O2 conftest.c >&5
configure:8009: $? = 0
configure:8009: ./conftest
configure:8009: $? = 0
configure:8020: result: yes
configure:8033: checking for sys/types.h
configure:8033: cc -c -g -O2 conftest.c >&5
configure:8033: $? = 0
configure:8033: result: yes
configure:8033: checking for sys/stat.h
configure:8033: cc -c -g -O2 conftest.c >&5
configure:8033: $? = 0
configure:8033: result: yes
configure:8033: checking for stdlib.h
configure:8033: cc -c -g -O2 conftest.c >&5
configure:8033: $? = 0
configure:8033: result: yes
configure:8033: checking for string.h
configure:8033: cc -c -g -O2 conftest.c >&5
configure:8033: $? = 0
configure:8033: result: yes
configure:8033: checking for memory.h
configure:8033: cc -c -g -O2 conftest.c >&5
configure:8033: $? = 0
configure:8033: result: yes
configure:8033: checking for strings.h
configure:8033: cc -c -g -O2 conftest.c >&5
configure:8033: $? = 0
configure:8033: result: yes
configure:8033: checking for inttypes.h
configure:8033: cc -c -g -O2 conftest.c >&5
configure:8033: $? = 0
configure:8033: result: yes
configure:8033: checking for stdint.h
configure:8033: cc -c -g -O2 conftest.c >&5
configure:8033: $? = 0
configure:8033: result: yes
configure:8033: checking for unistd.h
configure:8033: cc -c -g -O2 conftest.c >&5
configure:8033: $? = 0
configure:8033: result: yes
configure:8047: checking for dlfcn.h
configure:8047: cc -c -g -O2 conftest.c >&5
configure:8047: $? = 0
configure:8047: result: yes
configure:8234: checking for objdir
configure:8249: result: .libs
configure:8520: checking if cc supports -fno-rtti -fno-exceptions
configure:8538: cc -c -g -O2 -fno-rtti -fno-exceptions conftest.c >&5
configure:8542: $? = 0
configure:8555: result: yes
configure:8882: checking for cc option to produce PIC
configure:8889: result: -fno-common -DPIC
configure:8897: checking if cc PIC flag -fno-common -DPIC works
configure:8915: cc -c -g -O2 -fno-common -DPIC -DPIC conftest.c >&5
configure:8919: $? = 0
configure:8932: result: yes
configure:8961: checking if cc static flag -static works
configure:8989: result: no
configure:9004: checking if cc supports -c -o file.o
configure:9025: cc -c -g -O2 -o out/conftest2.o conftest.c >&5
configure:9029: $? = 0
configure:9051: result: yes
configure:9059: checking if cc supports -c -o file.o
configure:9106: result: yes
configure:9139: checking whether the cc linker (/usr/bin/ld) supports shared libraries
configure:10292: result: yes
configure:10532: checking dynamic linker characteristics
configure:11265: result: darwin12.2.0 dyld
configure:11372: checking how to hardcode library paths into programs
configure:11397: result: immediate
configure:11937: checking whether stripping libraries is possible
configure:11951: result: yes
configure:11977: checking if libtool supports shared libraries
configure:11979: result: yes
configure:11982: checking whether to build shared libraries
configure:12003: result: yes
configure:12006: checking whether to build static libraries
configure:12010: result: no
configure:12033: checking how to run the C++ preprocessor
configure:12060: c++ -E conftest.cpp
configure:12060: $? = 0
configure:12074: c++ -E conftest.cpp
conftest.cpp:21:10: fatal error: 'ac_nonexistent.h' file not found
#include <ac_nonexistent.h>
^
1 error generated.
configure:12074: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "libhmsbeagle"
| #define PACKAGE_TARNAME "libhmsbeagle"
| #define PACKAGE_VERSION "1.0.0"
| #define PACKAGE_STRING "libhmsbeagle 1.0.0"
| #define PACKAGE_BUGREPORT "beagle-dev@googlegroups.com"
| #define PACKAGE_URL ""
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define LT_OBJDIR ".libs/"
| /* end confdefs.h. */
| #include <ac_nonexistent.h>
configure:12099: result: c++ -E
configure:12119: c++ -E conftest.cpp
configure:12119: $? = 0
configure:12133: c++ -E conftest.cpp
conftest.cpp:21:10: fatal error: 'ac_nonexistent.h' file not found
#include <ac_nonexistent.h>
^
1 error generated.
configure:12133: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "libhmsbeagle"
| #define PACKAGE_TARNAME "libhmsbeagle"
| #define PACKAGE_VERSION "1.0.0"
| #define PACKAGE_STRING "libhmsbeagle 1.0.0"
| #define PACKAGE_BUGREPORT "beagle-dev@googlegroups.com"
| #define PACKAGE_URL ""
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define LT_OBJDIR ".libs/"
| /* end confdefs.h. */
| #include <ac_nonexistent.h>
configure:12302: checking for ld used by c++
configure:12369: result: /usr/bin/ld
configure:12376: checking if the linker (/usr/bin/ld) is GNU ld
configure:12391: result: no
configure:12446: checking whether the c++ linker (/usr/bin/ld) supports shared libraries
configure:13451: result: yes
configure:13487: c++ -c -O3 conftest.cpp >&5
configure:13490: $? = 0
configure:14010: checking for c++ option to produce PIC
configure:14017: result: -fno-common -DPIC
configure:14025: checking if c++ PIC flag -fno-common -DPIC works
configure:14043: c++ -c -O3 -fno-common -DPIC -DPIC conftest.cpp >&5
configure:14047: $? = 0
configure:14060: result: yes
configure:14083: checking if c++ static flag -static works
configure:14111: result: no
configure:14123: checking if c++ supports -c -o file.o
configure:14144: c++ -c -O3 -o out/conftest2.o conftest.cpp >&5
configure:14148: $? = 0
configure:14170: result: yes
configure:14175: checking if c++ supports -c -o file.o
configure:14222: result: yes
configure:14252: checking whether the c++ linker (/usr/bin/ld) supports shared libraries
configure:14288: result: yes
configure:14429: checking dynamic linker characteristics
configure:15096: result: darwin12.2.0 dyld
configure:15149: checking how to hardcode library paths into programs
configure:15174: result: immediate
configure:15250: checking for library containing lt_dlinit
configure:15281: cc -o conftest -g -O2 conftest.c >&5
Undefined symbols for architecture x86_64:
"_lt_dlinit", referenced from:
_main in conftest-sF6vXV.o
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
configure:15281: $? = 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "libhmsbeagle"
| #define PACKAGE_TARNAME "libhmsbeagle"
| #define PACKAGE_VERSION "1.0.0"
| #define PACKAGE_STRING "libhmsbeagle 1.0.0"
| #define PACKAGE_BUGREPORT "beagle-dev@googlegroups.com"
| #define PACKAGE_URL ""
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define LT_OBJDIR ".libs/"
| /* end confdefs.h. */
|
| /* Override any GCC internal prototype to avoid an error.
| Use char because int might match the return type of a GCC
| builtin and then its argument prototype would still apply. */
| #ifdef __cplusplus
| extern "C"
| #endif
| char lt_dlinit ();
| int
| main ()
| {
| return lt_dlinit ();
| ;
| return 0;
| }
configure:15281: cc -o conftest -g -O2 conftest.c -lltdl >&5
configure:15281: $? = 0
configure:15298: result: -lltdl
configure:15378: checking if gcc accepts -dumpversion option
configure:15403: cat conftest.c 1>&5
int main()
{
return 0;
}
configure:15406: $? = 0
configure:15410: cc -dumpversion -c conftest.c 1>&5
4.2.1
configure:15413: $? = 0
configure:15416: result: yes
configure:15443: checking gcc version
configure:15457: result: 4.2.1
configure:15738: checking for /usr/local/cuda/
configure:15751: result: yes
configure:15757: checking for /usr/local/cuda/include
configure:15770: result: yes
configure:15776: checking for /usr/local/cuda/lib
configure:15789: result: yes
configure:15817: checking for nvcc
configure:15836: found /Developer/NVIDIA/CUDA-5.0/bin/nvcc
configure:15849: result: /Developer/NVIDIA/CUDA-5.0/bin/nvcc
configure:15904: checking for x86 cpuid output
configure:15933: cc -o conftest -g -O2 conftest.c -lltdl >&5
conftest.c:27:15: error: expected expression
int op = , eax, ebx, ecx, edx;
^
1 error generated.
configure:15933: $? = 1
configure: program exited with status 1
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "libhmsbeagle"
| #define PACKAGE_TARNAME "libhmsbeagle"
| #define PACKAGE_VERSION "1.0.0"
| #define PACKAGE_STRING "libhmsbeagle 1.0.0"
| #define PACKAGE_BUGREPORT "beagle-dev@googlegroups.com"
| #define PACKAGE_URL ""
| #define STDC_HEADERS 1
| #define HAVE_SYS_TYPES_H 1
| #define HAVE_SYS_STAT_H 1
| #define HAVE_STDLIB_H 1
| #define HAVE_STRING_H 1
| #define HAVE_MEMORY_H 1
| #define HAVE_STRINGS_H 1
| #define HAVE_INTTYPES_H 1
| #define HAVE_STDINT_H 1
| #define HAVE_UNISTD_H 1
| #define HAVE_DLFCN_H 1
| #define LT_OBJDIR ".libs/"
| #define HAVE_LIBLTDL "1"
| /* end confdefs.h. */
| #include <stdio.h>
| int
| main ()
| {
|
| int op = , eax, ebx, ecx, edx;
| FILE *f;
| __asm__("cpuid"
| : "=a" (eax), "=b" (ebx), "=c" (ecx), "=d" (edx)
| : "a" (op));
| f = fopen("conftest_cpuid", "w"); if (!f) return 1;
| fprintf(f, "%x:%x:%x:%x\n", eax, ebx, ecx, edx);
| fclose(f);
| return 0;
|
| ;
| return 0;
| }
configure:15943: result: unknown
configure:15962: checking for x86 cpuid 0x00000001 output
configure:15991: cc -o conftest -g -O2 conftest.c -lltdl >&5
configure:15991: $? = 0
configure:15991: ./conftest
configure:15991: $? = 0
configure:16001: result: 20655:100800:29ae3ff:bfebfbff
configure:16013: checking whether mmx is supported
configure:16025: result: yes
configure:16028: checking whether sse is supported
configure:16040: result: yes
configure:16043: checking whether sse2 is supported
configure:16063: result: yes
configure:16066: checking whether sse3 is supported
configure:16078: result: yes
configure:16081: checking whether ssse3 is supported
configure:16093: result: yes
configure:16096: checking whether sse4.1 is supported
configure:16108: result: yes
configure:16111: checking whether sse4.2 is supported
configure:16123: result: yes
configure:16126: checking whether avx is supported
configure:16138: result: no
configure:16145: checking whether C compiler accepts -mmmx
configure:16164: cc -c -g -O2 -mmmx conftest.c >&5
configure:16164: $? = 0
configure:16172: result: yes
configure:16186: checking whether C compiler accepts -msse
configure:16205: cc -c -g -O2 -msse conftest.c >&5
configure:16205: $? = 0
configure:16213: result: yes
configure:16227: checking whether C compiler accepts -msse2
configure:16246: cc -c -g -O2 -msse2 conftest.c >&5
configure:16246: $? = 0
configure:16254: result: yes
configure:16268: checking whether C compiler accepts -msse3
configure:16287: cc -c -g -O2 -msse3 conftest.c >&5
configure:16287: $? = 0
configure:16295: result: yes
configure:16309: checking whether C compiler accepts -mssse3
configure:16328: cc -c -g -O2 -mssse3 conftest.c >&5
configure:16328: $? = 0
configure:16336: result: yes
configure:16350: checking whether C compiler accepts -msse4.1
configure:16369: cc -c -g -O2 -msse4.1 conftest.c >&5
configure:16369: $? = 0
configure:16377: result: yes
configure:16391: checking whether C compiler accepts -msse4.2
configure:16410: cc -c -g -O2 -msse4.2 conftest.c >&5
configure:16410: $? = 0
configure:16418: result: yes
configure:16473: checking cpuid.h usability
configure:16473: cc -c -g -O2 conftest.c >&5
configure:16473: $? = 0
configure:16473: result: yes
configure:16473: checking cpuid.h presence
configure:16473: cc -E conftest.c
configure:16473: $? = 0
configure:16473: result: yes
configure:16473: checking for cpuid.h
configure:16473: result: yes
configure:16606: checking for javac
configure:16622: found /usr/bin/javac
configure:16633: result: javac
configure:16703: checking for javac
configure:16721: found /usr/bin/javac
configure:16734: result: /usr/bin/javac
configure:16792: checking symlink for /usr/bin/javac
configure:16800: result: /System/Library/Frameworks/JavaVM.framework/Versions/Current/Commands/javac
configure:16994: checking for doxygen
configure:17027: result: no
configure:17047: WARNING: doxygen not found - will not generate any doxygen documentation
configure:17100: checking for perl
configure:17118: found /usr/bin/perl
configure:17130: result: /usr/bin/perl
configure:18953: checking that generated files are newer than configure
configure:18959: result: done
configure:19114: creating ./config.status
## ---------------------- ##
## Running config.status. ##
## ---------------------- ##
This file was extended by libhmsbeagle config.status 1.0.0, which was
generated by GNU Autoconf 2.69. Invocation command line was
CONFIG_FILES =
CONFIG_HEADERS =
CONFIG_LINKS =
CONFIG_COMMANDS =
$ ./config.status
on Peter-Fieldss-MacBook-Pro.local
config.status:1238: creating Makefile
config.status:1238: creating hmsbeagle-1.pc
config.status:1238: creating libhmsbeagle/Makefile
config.status:1238: creating libhmsbeagle/GPU/Makefile
config.status:1238: creating libhmsbeagle/GPU/kernels/Makefile
config.status:1238: creating libhmsbeagle/CPU/Makefile
config.status:1238: creating libhmsbeagle/plugin/Makefile
config.status:1238: creating examples/Makefile
config.status:1238: creating examples/tinytest/Makefile
config.status:1238: creating examples/complextest/Makefile
config.status:1238: creating examples/oddstatetest/Makefile
config.status:1238: creating examples/fourtaxon/Makefile
config.status:1238: creating examples/genomictest/Makefile
config.status:1238: creating examples/matrixtest/Makefile
config.status:1238: creating libhmsbeagle/config.h
config.status:1467: executing depfiles commands
config.status:1467: executing libtool commands
## ---------------- ##
## Cache variables. ##
## ---------------- ##
ac_cv_build=x86_64-apple-darwin12.2.0
ac_cv_c_compiler_gnu=yes
ac_cv_cxx_compiler_gnu=yes
ac_cv_env_CCC_set=
ac_cv_env_CCC_value=
ac_cv_env_CC_set=set
ac_cv_env_CC_value=cc
ac_cv_env_CFLAGS_set=
ac_cv_env_CFLAGS_value=
ac_cv_env_CPPFLAGS_set=
ac_cv_env_CPPFLAGS_value=
ac_cv_env_CPP_set=
ac_cv_env_CPP_value=
ac_cv_env_CXXCPP_set=
ac_cv_env_CXXCPP_value=
ac_cv_env_CXXFLAGS_set=
ac_cv_env_CXXFLAGS_value=
ac_cv_env_CXX_set=set
ac_cv_env_CXX_value=c++
ac_cv_env_DOXYGEN_PAPER_SIZE_set=
ac_cv_env_DOXYGEN_PAPER_SIZE_value=
ac_cv_env_LDFLAGS_set=
ac_cv_env_LDFLAGS_value=
ac_cv_env_LIBS_set=
ac_cv_env_LIBS_value=
ac_cv_env_build_alias_set=
ac_cv_env_build_alias_value=
ac_cv_env_host_alias_set=
ac_cv_env_host_alias_value=
ac_cv_env_target_alias_set=
ac_cv_env_target_alias_value=
ac_cv_file__usr_local_cuda_=yes
ac_cv_file__usr_local_cuda_include=yes
ac_cv_file__usr_local_cuda_lib=yes
ac_cv_header_cpuid_h=yes
ac_cv_header_dlfcn_h=yes
ac_cv_header_inttypes_h=yes
ac_cv_header_memory_h=yes
ac_cv_header_stdc=yes
ac_cv_header_stdint_h=yes
ac_cv_header_stdlib_h=yes
ac_cv_header_string_h=yes
ac_cv_header_strings_h=yes
ac_cv_header_sys_stat_h=yes
ac_cv_header_sys_types_h=yes
ac_cv_header_unistd_h=yes
ac_cv_host=x86_64-apple-darwin12.2.0
ac_cv_objext=o
ac_cv_path_EGREP='/usr/bin/grep -E'
ac_cv_path_FGREP='/usr/bin/grep -F'
ac_cv_path_GREP=/usr/bin/grep
ac_cv_path_NVCC=/Developer/NVIDIA/CUDA-5.0/bin/nvcc
ac_cv_path_SED=/usr/local/Library/ENV/4.3/sed
ac_cv_path__ACJNI_JAVAC=/usr/bin/javac
ac_cv_path_ac_pt_DX_PERL=/usr/bin/perl
ac_cv_path_install='/usr/bin/install -c'
ac_cv_prog_AWK=awk
ac_cv_prog_CPP='cc -E'
ac_cv_prog_CXXCPP='c++ -E'
ac_cv_prog_JAVAC=javac
ac_cv_prog_ac_ct_AR=ar
ac_cv_prog_ac_ct_CC=cc
ac_cv_prog_ac_ct_DSYMUTIL=dsymutil
ac_cv_prog_ac_ct_LIPO=lipo
ac_cv_prog_ac_ct_NMEDIT=nmedit
ac_cv_prog_ac_ct_OTOOL=otool
ac_cv_prog_ac_ct_RANLIB=ranlib
ac_cv_prog_ac_ct_STRIP=strip
ac_cv_prog_cc_c89=
ac_cv_prog_cc_g=yes
ac_cv_prog_cxx_g=yes
ac_cv_prog_make_make_set=yes
ac_cv_search_lt_dlinit=-lltdl
am_cv_CC_dependencies_compiler_type=gcc3
am_cv_CXX_dependencies_compiler_type=gcc3
am_cv_make_support_nested_variables=yes
ax_cv_check_cflags___mmmx=yes
ax_cv_check_cflags___msse2=yes
ax_cv_check_cflags___msse3=yes
ax_cv_check_cflags___msse4_1=yes
ax_cv_check_cflags___msse4_2=yes
ax_cv_check_cflags___msse=yes
ax_cv_check_cflags___mssse3=yes
ax_cv_gcc_version=4.2.1
ax_cv_gcc_x86_cpuid_0x00000001=20655:100800:29ae3ff:bfebfbff
ax_cv_gcc_x86_cpuid_=unknown
ax_cv_have_avx_ext=no
ax_cv_have_mmx_ext=yes
ax_cv_have_sse2_ext=yes
ax_cv_have_sse3_ext=yes
ax_cv_have_sse41_ext=yes
ax_cv_have_sse42_ext=yes
ax_cv_have_sse_ext=yes
ax_cv_have_ssse3_ext=yes
lt_cv_apple_cc_single_mod=yes
lt_cv_ar_at_file=no
lt_cv_deplibs_check_method=pass_all
lt_cv_file_magic_cmd='$MAGIC_CMD'
lt_cv_file_magic_test_file=
lt_cv_ld_exported_symbols_list=yes
lt_cv_ld_force_load=yes
lt_cv_ld_reload_flag=-r
lt_cv_nm_interface='BSD nm'
lt_cv_objdir=.libs
lt_cv_path_LD=/usr/bin/ld
lt_cv_path_LDCXX=/usr/bin/ld
lt_cv_path_NM=/usr/bin/nm
lt_cv_path_mainfest_tool=no
lt_cv_prog_compiler_c_o=yes
lt_cv_prog_compiler_c_o_CXX=yes
lt_cv_prog_compiler_pic='-fno-common -DPIC'
lt_cv_prog_compiler_pic_CXX='-fno-common -DPIC'
lt_cv_prog_compiler_pic_works=yes
lt_cv_prog_compiler_pic_works_CXX=yes
lt_cv_prog_compiler_rtti_exceptions=yes
lt_cv_prog_compiler_static_works=no
lt_cv_prog_compiler_static_works_CXX=no
lt_cv_prog_gnu_ld=no
lt_cv_prog_gnu_ldcxx=no
lt_cv_sharedlib_from_linklib_cmd='printf %s\n'
lt_cv_sys_global_symbol_pipe='sed -n -e '\''s/^.*[ ]\([BCDEGRST][BCDEGRST]*\)[ ][ ]*_\([_A-Za-z][_A-Za-z0-9]*\)$/\1 _\2 \2/p'\'' | sed '\''/ __gnu_lto/d'\'''
lt_cv_sys_global_symbol_to_c_name_address='sed -n -e '\''s/^: \([^ ]*\)[ ]*$/ {\"\1\", (void *) 0},/p'\'' -e '\''s/^[BCDEGRST]* \([^ ]*\) \([^ ]*\)$/ {"\2", (void *) \&\2},/p'\'''
lt_cv_sys_global_symbol_to_c_name_address_lib_prefix='sed -n -e '\''s/^: \([^ ]*\)[ ]*$/ {\"\1\", (void *) 0},/p'\'' -e '\''s/^[BCDEGRST]* \([^ ]*\) \(lib[^ ]*\)$/ {"\2", (void *) \&\2},/p'\'' -e '\''s/^[BCDEGRST]* \([^ ]*\) \([^ ]*\)$/ {"lib\2", (void *) \&\2},/p'\'''
lt_cv_sys_global_symbol_to_cdecl='sed -n -e '\''s/^T .* \(.*\)$/extern int \1();/p'\'' -e '\''s/^[BCDEGRST]* .* \(.*\)$/extern char \1;/p'\'''
lt_cv_sys_max_cmd_len=196608
lt_cv_to_host_file_cmd=func_convert_file_noop
lt_cv_to_tool_file_cmd=func_convert_file_noop
## ----------------- ##
## Output variables. ##
## ----------------- ##
ACLOCAL='${SHELL} /private/tmp/beagle-UFvZ/.config/missing aclocal-1.13'
AMDEPBACKSLASH='\'
AMDEP_FALSE='#'
AMDEP_TRUE=''
AMTAR='$${TAR-tar}'
AM_BACKSLASH='\'
AM_CXXFLAGS=' -DDLS_MACOS -m64'
AM_DEFAULT_V='$(AM_DEFAULT_VERBOSITY)'
AM_DEFAULT_VERBOSITY='1'
AM_V='$(V)'
AR='ar'
AUTOCONF='${SHELL} /private/tmp/beagle-UFvZ/.config/missing autoconf'
AUTOHEADER='${SHELL} /private/tmp/beagle-UFvZ/.config/missing autoheader'
AUTOMAKE='${SHELL} /private/tmp/beagle-UFvZ/.config/missing automake-1.13'
AWK='awk'
BUILDCUDA_FALSE='#'
BUILDCUDA_TRUE=''
BUILDJNI_FALSE='#'
BUILDJNI_TRUE=''
BUILDOPENCL_FALSE=''
BUILDOPENCL_TRUE='#'
CC='cc'
CCDEPMODE='depmode=gcc3'
CFLAGS='-g -O2'
CHECK_LIB_PATH='$(top_builddir)/libhmsbeagle/CPU/.libs:$(top_builddir)/libhmsbeagle/GPU/.libs'
CPP='cc -E'
CPPFLAGS=' -I/System/Library/Frameworks/JavaVM.framework/Versions/Current/Headers'
CUDA_CFLAGS=' -DCUDA -I/usr/local/cuda/include'
CUDA_LIBS=' -lcuda -L/usr/local/cuda/lib'
CXX='c++'
CXXCPP='c++ -E'
CXXDEPMODE='depmode=gcc3'
CXXFLAGS=' -O3'
CYGPATH_W='echo'
DEFS='-DHAVE_CONFIG_H'
DEPDIR='.deps'
DLLTOOL='false'
DOXYGEN_PAPER_SIZE=''
DSYMUTIL='dsymutil'
DUMPBIN=''
DX_COND_chi_FALSE=''
DX_COND_chi_TRUE='#'
DX_COND_chm_FALSE=''
DX_COND_chm_TRUE='#'
DX_COND_doc_FALSE=''
DX_COND_doc_TRUE='#'
DX_COND_dot_FALSE=''
DX_COND_dot_TRUE='#'
DX_COND_html_FALSE=''
DX_COND_html_TRUE='#'
DX_COND_latex_FALSE=''
DX_COND_latex_TRUE='#'
DX_COND_man_FALSE=''
DX_COND_man_TRUE='#'
DX_COND_pdf_FALSE=''
DX_COND_pdf_TRUE='#'
DX_COND_ps_FALSE=''
DX_COND_ps_TRUE='#'
DX_COND_rtf_FALSE=''
DX_COND_rtf_TRUE='#'
DX_COND_xml_FALSE=''
DX_COND_xml_TRUE='#'
DX_CONFIG='beagle.dox'
DX_DOCDIR='doc'
DX_DOT=''
DX_DOXYGEN=''
DX_DVIPS=''
DX_EGREP=''
DX_ENV=' SRCDIR='\''.'\'' PROJECT='\''libhmsbeagle'\'' DOCDIR='\''doc'\'' VERSION='\''1.0.0'\'' HAVE_DOT='\''NO'\'' GENERATE_MAN='\''NO'\'' GENERATE_RTF='\''NO'\'' GENERATE_XML='\''NO'\'' GENERATE_HTMLHELP='\''NO'\'' GENERATE_CHI='\''NO'\'' GENERATE_HTML='\''NO'\'' GENERATE_LATEX='\''NO'\'''
DX_FLAG_chi='0'
DX_FLAG_chm='0'
DX_FLAG_doc='0'
DX_FLAG_dot='0'
DX_FLAG_html='0'
DX_FLAG_man='0'
DX_FLAG_pdf='0'
DX_FLAG_ps='0'
DX_FLAG_rtf='0'
DX_FLAG_xml='0'
DX_HHC=''
DX_LATEX=''
DX_MAKEINDEX=''
DX_PDFLATEX=''
DX_PERL='/usr/bin/perl'
DX_PROJECT='libhmsbeagle'
ECHO_C='\c'
ECHO_N=''
ECHO_T=''
EGREP='/usr/bin/grep -E'
EXEEXT=''
FGREP='/usr/bin/grep -F'
GCC_VERSION='4.2.1'
GENERIC_API_VERSION='1'
GENERIC_LIBRARY_NAME='libhmsbeagle'
GENERIC_LIBRARY_VERSION='1:1:0'
GENERIC_VERSION='1.1.0'
GREP='/usr/bin/grep'
HAVE_OPENMP_FALSE=''
HAVE_OPENMP_TRUE='#'
HAVE_SSE2_FALSE='#'
HAVE_SSE2_TRUE=''
INSTALL_DATA='${INSTALL} -m 644'
INSTALL_PROGRAM='${INSTALL}'
INSTALL_SCRIPT='${INSTALL}'
INSTALL_STRIP_PROGRAM='$(install_sh) -c -s'
JAVAC='javac'
JNI_EXTRA_LDFLAGS='-shrext .jnilib'
LD='/usr/bin/ld'
LDFLAGS=''
LIBOBJS=''
LIBS='-lltdl '
LIBTOOL='$(SHELL) $(top_builddir)/libtool'
LIPO='lipo'
LN_S='ln -s'
LTLIBOBJS=''
MAKEINFO='${SHELL} /private/tmp/beagle-UFvZ/.config/missing makeinfo'
MANIFEST_TOOL=':'
MKDIR_P='.config/install-sh -c -d'
NM='/usr/bin/nm'
NMEDIT='nmedit'
NVCC='/Developer/NVIDIA/CUDA-5.0/bin/nvcc'
NVCCFLAGS='-O3 -m64 -D_POSIX_C_SOURCE'
OBJDUMP='false'
OBJEXT='o'
OPENCL_CFLAGS=''
OPENCL_LIBS=''
OPENMP_CFLAGS=''
OPENMP_CXXFLAGS=''
OTOOL64=':'
OTOOL='otool'
PACKAGE='libhmsbeagle'
PACKAGE_BUGREPORT='beagle-dev@googlegroups.com'
PACKAGE_NAME='libhmsbeagle'
PACKAGE_STRING='libhmsbeagle 1.0.0'
PACKAGE_TARNAME='libhmsbeagle'
PACKAGE_URL=''
PACKAGE_VERSION='1.0.0'
PATH_SEPARATOR=':'
RANLIB='ranlib'
SED='/usr/local/Library/ENV/4.3/sed'
SET_MAKE=''
SHELL='/bin/sh'
SIMD_FLAGS=' -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2'
STRIP='strip'
VERSION='1.1.0'
_ACJNI_JAVAC='/usr/bin/javac'
abs_top_builddir=''
abs_top_srcdir=''
ac_ct_AR='ar'
ac_ct_CC='cc'
ac_ct_CXX=''
ac_ct_DUMPBIN=''
am__EXEEXT_FALSE=''
am__EXEEXT_TRUE='#'
am__fastdepCC_FALSE='#'
am__fastdepCC_TRUE=''
am__fastdepCXX_FALSE='#'
am__fastdepCXX_TRUE=''
am__include='include'
am__isrc=''
am__leading_dot='.'
am__nodep='_no'
am__quote=''
am__tar='$${TAR-tar} chof - "$$tardir"'
am__untar='$${TAR-tar} xf -'
bindir='${exec_prefix}/bin'
build='x86_64-apple-darwin12.2.0'
build_alias=''
build_cpu='x86_64'
build_os='darwin12.2.0'
build_vendor='apple'
datadir='${datarootdir}'
datarootdir='${prefix}/share'
docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'
dvidir='${docdir}'
exec_prefix='${prefix}'
host='x86_64-apple-darwin12.2.0'
host_alias=''
host_cpu='x86_64'
host_os='darwin12.2.0'
host_vendor='apple'
htmldir='${docdir}'
includedir='${prefix}/include'
infodir='${datarootdir}/info'
install_sh='${SHELL} /private/tmp/beagle-UFvZ/.config/install-sh'
libdir='${exec_prefix}/lib'
libexecdir='${exec_prefix}/libexec'
localedir='${datarootdir}/locale'
localstatedir='${prefix}/var'
mandir='${datarootdir}/man'
mkdir_p='$(MKDIR_P)'
oldincludedir='/usr/include'
pdfdir='${docdir}'
prefix='/usr/local/Cellar/beagle/HEAD--with-cuda=/Developer/NVIDIA/CUDA-5.0/bin'
program_transform_name='s,x,x,'
psdir='${docdir}'
sbindir='${exec_prefix}/sbin'
sharedstatedir='${prefix}/com'
sysconfdir='${prefix}/etc'
target_alias=''
## ----------- ##
## confdefs.h. ##
## ----------- ##
/* confdefs.h */
#define PACKAGE_NAME "libhmsbeagle"
#define PACKAGE_TARNAME "libhmsbeagle"
#define PACKAGE_VERSION "1.0.0"
#define PACKAGE_STRING "libhmsbeagle 1.0.0"
#define PACKAGE_BUGREPORT "beagle-dev@googlegroups.com"
#define PACKAGE_URL ""
#define STDC_HEADERS 1
#define HAVE_SYS_TYPES_H 1
#define HAVE_SYS_STAT_H 1
#define HAVE_STDLIB_H 1
#define HAVE_STRING_H 1
#define HAVE_MEMORY_H 1
#define HAVE_STRINGS_H 1
#define HAVE_INTTYPES_H 1
#define HAVE_STDINT_H 1
#define HAVE_UNISTD_H 1
#define HAVE_DLFCN_H 1
#define LT_OBJDIR ".libs/"
#define HAVE_LIBLTDL "1"
#define HAVE_MMX /**/
#define HAVE_SSE /**/
#define HAVE_SSE2 /**/
#define HAVE_SSE3 /**/
#define HAVE_SSSE3 /**/
#define HAVE_SSE41 /**/
#define HAVE_SSE42 1
#define HAVE_CPUID_H 1
configure: exit 0
#################################
######### brew config #############
brew --config
HOMEBREW_VERSION: 0.9.3
HEAD: 9bf47d705a41777275910a5948077073be9dad4d
HOMEBREW_PREFIX: /usr/local
HOMEBREW_CELLAR: /usr/local/Cellar
CPU: quad-core 64-bit arrandale
OS X: 10.8.2-x86_64
Xcode: 4.5.2
CLT: 4.5.0.0.1.1249367152
LLVM-GCC: build 2336
Clang: 4.1 build 421
X11: 2.7.4 => /opt/X11
System Ruby: 1.8.7-358
Perl: /Users/crd1859/perl5/perlbrew/perls/perl-5.16.0/bin/perl
Python: /usr/local/bin/python => /usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/bin/python2.7
Ruby: /Users/crd1859/.rvm/rubies/ruby-1.9.3-p194/bin/ruby
##################################################
######### brew doctor #############
Warning: Unbrewed dylibs were found in /usr/local/lib.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae, and may need to be deleted.
Unexpected dylibs:
/usr/local/lib/libusb-0.1.4.4.4.dylib
/usr/local/lib/libusbpp-0.1.4.4.4.dylib
####################################
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