beagle failed to build on 10.8.2 followup

gistfile1.txt

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-mDzX
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 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... /usr/local/opt/doxygen/bin/doxygen
checking for perl... /usr/bin/perl
checking for dot... no
configure: WARNING: dot not found - will not generate graphics for doxygen documentation
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-mDzX -I/private/tmp/beagle-mDzX
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-mDzX -I/private/tmp/beagle-mDzX) || 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-mDzX -I/private/tmp/beagle-mDzX
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-mDzX -I/private/tmp/beagle-mDzX) || 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-mDzX -I/private/tmp/beagle-mDzX -I/System/Library/Frameworks/JavaVM.framework/Versions/Current/Headers -DDLS_MACOS -m64 -DCUDA -I/Developer/NVIDIA/CUDA-5.0/bin/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
libtool: compile:  c++ -DHAVE_CONFIG_H -I. -I../../libhmsbeagle -I/private/tmp/beagle-mDzX -I/private/tmp/beagle-mDzX -I/System/Library/Frameworks/JavaVM.framework/Versions/Current/Headers -DDLS_MACOS -m64 -DCUDA -I/Developer/NVIDIA/CUDA-5.0/bin/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
brew: superenv removed: -m64 -O3
mv -f .deps/libhmsbeagle_cuda_la-GPUImplHelper.Tpo .deps/libhmsbeagle_cuda_la-GPUImplHelper.Plo
/bin/sh ../../libtool  --tag=CXX   --mode=compile c++ -DHAVE_CONFIG_H -I. -I../../libhmsbeagle  -I/private/tmp/beagle-mDzX -I/private/tmp/beagle-mDzX -I/System/Library/Frameworks/JavaVM.framework/Versions/Current/Headers -DDLS_MACOS -m64 -DCUDA -I/Developer/NVIDIA/CUDA-5.0/bin/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
libtool: compile:  c++ -DHAVE_CONFIG_H -I. -I../../libhmsbeagle -I/private/tmp/beagle-mDzX -I/private/tmp/beagle-mDzX -I/System/Library/Frameworks/JavaVM.framework/Versions/Current/Headers -DDLS_MACOS -m64 -DCUDA -I/Developer/NVIDIA/CUDA-5.0/bin/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
brew: superenv removed: -m64 -O3
GPUInterfaceCUDA.cpp:36:10: fatal error: 'cuda.h' file not found
#include <cuda.h>
         ^
1 error generated.
make[4]: *** [libhmsbeagle_cuda_la-GPUInterfaceCUDA.lo] Error 1
make[3]: *** [all-recursive] Error 1
make[2]: *** [all-recursive] Error 1
make[1]: *** [all] Error 2
make: *** [all-recursive] Error 1
==> Configuration
HOMEBREW_VERSION: 0.9.3
HEAD: c5bf6f2313c415ed662f7922a24b86440e288c66
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++
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/doxygen/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/perl5/perlbrew/bin:/Users/crd1859/perl5/perlbrew/perls/perl-5.16.0/bin:/Users/crd1859:/usr/local/texlive/2012/bin/x86_64-darwin:/usr/local/share/python

Error: beagle did not build