Broken output from homebrew build

gistfile1.txt

laserson@hobbes:~$ brew install -v exonerate
==> Build Environment
CC: /usr/bin/cc => /usr/bin/gcc-4.2
CXX: /usr/bin/c++ => /usr/bin/c++-4.2
LD: /usr/bin/cc => /usr/bin/gcc-4.2
CFLAGS: -O3 -march=core2 -w -pipe
CXXFLAGS: -O3 -march=core2 -w -pipe
MACOSX_DEPLOYMENT_TARGET: 10.6
MAKEFLAGS: -j2
==> Downloading http://www.ebi.ac.uk/~guy/exonerate/exonerate-2.2.0.tar.gz
File already downloaded and cached to /Users/laserson/Library/Caches/Homebrew
/usr/bin/tar xf /Users/laserson/Library/Caches/Homebrew/exonerate-2.2.0.tar.gz
==> ./configure --disable-debug --disable-dependency-tracking --prefix=/usr/local/Cellar/exonerate/2.2.0
./configure --disable-debug --disable-dependency-tracking --prefix=/usr/local/Cellar/exonerate/2.2.0
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking whether make sets $(MAKE)... yes
checking for working aclocal-1.4... missing
checking for working autoconf... found
checking for working automake-1.4... missing
checking for working autoheader... found
checking for working makeinfo... found
checking for gcc... /usr/bin/cc
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 /usr/bin/cc accepts -g... yes
checking for /usr/bin/cc option to accept ISO C89... none needed
checking for a BSD-compatible install... /usr/bin/install -c
checking whether make sets $(MAKE)... (cached) yes
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking how to run the C preprocessor... /usr/bin/cc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -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 limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking errno.h usability... yes
checking errno.h presence... yes
checking for errno.h... yes
checking math.h usability... yes
checking math.h presence... yes
checking for math.h... yes
checking for strings.h... (cached) yes
checking ctype.h usability... yes
checking ctype.h presence... yes
checking for ctype.h... yes
checking for sys/stat.h... (cached) yes
checking for sys/types.h... (cached) yes
checking time.h usability... yes
checking time.h presence... yes
checking for time.h... yes
checking for unistd.h... (cached) yes
checking build system type... i386-apple-darwin10.5.0
checking host system type... i386-apple-darwin10.5.0
Set host to i386-apple-darwin10.5.0
i386-apple-darwin10.5.0
Customising build for OSX
Set source_root_dir to /private/tmp/homebrew-exonerate-2.2.0-bpG3/exonerate-2.2.0
----------------------------------------------------------------
checking for socklen_t... yes
checking for pkg-config... /usr/local/bin/pkg-config
Using GLIB-2
Turning assertions off
Turning paranoid options off
Not using options for profiling with gprof
Not using options for analysis with gcov
Adding support for LARGE FILES (>2Gb) for a 32 bit system
Using COMPILED C4 MODELS
Installing UTILITIES
Using PTHREADS
----------------------------------------------------------------
configure: creating ./config.status
config.status: creating Makefile
config.status: creating doc/Makefile
config.status: creating doc/man/Makefile
config.status: creating doc/man/man1/Makefile
config.status: creating src/Makefile
config.status: creating src/general/Makefile
config.status: creating src/sequence/Makefile
config.status: creating src/database/Makefile
config.status: creating src/struct/Makefile
config.status: creating src/comparison/Makefile
config.status: creating src/c4/Makefile
config.status: creating src/bsdp/Makefile
config.status: creating src/sdp/Makefile
config.status: creating src/hub/Makefile
config.status: creating src/model/Makefile
config.status: creating src/program/Makefile
config.status: creating src/util/Makefile
config.status: creating test/Makefile
config.status: creating test/util/Makefile
config.status: creating test/ipcress/Makefile
config.status: creating test/exonerate/Makefile
config.status: creating test/data/Makefile
config.status: creating test/data/cdna/Makefile
config.status: creating test/data/protein/Makefile
==> make
make 
Making all in doc
Making all in man
Making all in man1
make[3]: Nothing to be done for `all'.
make[3]: Nothing to be done for `all-am'.
make[2]: Nothing to be done for `all-am'.
Making all in src
Making all in struct
/usr/bin/cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"exonerate\" -DVERSION=\"2.2.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -DHAVE_ERRNO_H=1 -DHAVE_MATH_H=1 -DHAVE_STRINGS_H=1 -DHAVE_CTYPE_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_TIME_H=1 -DHAVE_UNISTD_H=1 -I. -I.      -O3 -march=core2 -w -pipe -I/usr/local/Cellar/glib/2.24.2/include/glib-2.0 -I/usr/local/Cellar/glib/2.24.2/lib/glib-2.0/include -I/usr/local/Cellar/gettext/0.17/include   -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -c fsm.test.c

[...snip out tons of compiler stuff...]


** Message: Compiling codegen:
/usr/bin/cc -O3 -march=core2 -w -pipe -I/usr/local/Cellar/glib/2.24.2/include/glib-2.0 -I/usr/local/Cellar/glib/2.24.2/lib/glib-2.0/include -I/usr/local/Cellar/gettext/0.17/include   -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS  -I/private/tmp/homebrew-exonerate-2.2.0-bpG3/exonerate-2.2.0/src/c4 -I/private/tmp/homebrew-exonerate-2.2.0-bpG3/exonerate-2.2.0/src/struct -I/private/tmp/homebrew-exonerate-2.2.0-bpG3/exonerate-2.2.0/src/general -I/private/tmp/homebrew-exonerate-2.2.0-bpG3/exonerate-2.2.0/src/sequence -I/usr/local/Cellar/glib/2.24.2/include/glib-2.0 -I/usr/local/Cellar/glib/2.24.2/lib/glib-2.0/include -I/usr/local/Cellar/gettext/0.17/include   -I/private/tmp/homebrew-exonerate-2.2.0-bpG3/exonerate-2.2.0/src/model -I/private/tmp/homebrew-exonerate-2.2.0-bpG3/exonerate-2.2.0/src/comparison -I/private/tmp/homebrew-exonerate-2.2.0-bpG3/exonerate-2.2.0/src/c4 -I/private/tmp/homebrew-exonerate-2.2.0-bpG3/exonerate-2.2.0/src/bsdp -I/private/tmp/homebrew-exonerate-2.2.0-bpG3/exonerate-2.2.0/src/sdp -o /private/tmp/homebrew-exonerate-2.2.0-bpG3/exonerate-2.2.0/codegen/i386_45_apple_45_darwin10_46_5_46_0/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.o -c /private/tmp/homebrew-exonerate-2.2.0-bpG3/exonerate-2.2.0/codegen/i386_45_apple_45_darwin10_46_5_46_0/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.c
** Message: Adding: [/private/tmp/homebrew-exonerate-2.2.0-bpG3/exonerate-2.2.0/codegen/i386_45_apple_45_darwin10_46_5_46_0/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.o]
** Message: Adding object file [/private/tmp/homebrew-exonerate-2.2.0-bpG3/exonerate-2.2.0/codegen/i386_45_apple_45_darwin10_46_5_46_0/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.o] to archive
ar -Sq c4_model_archive.a /private/tmp/homebrew-exonerate-2.2.0-bpG3/exonerate-2.2.0/codegen/i386_45_apple_45_darwin10_46_5_46_0/Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary.o
** Message: Adding function [Scheduler_Cell_process_cdna2genome_58_reverse_58_notraceback_58_boundary]
** Message: Adding: [/private/tmp/homebrew-exonerate-2.2.0-bpG3/exonerate-2.2.0/codegen/i386_45_apple_45_darwin10_46_5_46_0/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.o]
** Message: Adding object file [/private/tmp/homebrew-exonerate-2.2.0-bpG3/exonerate-2.2.0/codegen/i386_45_apple_45_darwin10_46_5_46_0/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.o] to archive
ar -Sq c4_model_archive.a /private/tmp/homebrew-exonerate-2.2.0-bpG3/exonerate-2.2.0/codegen/i386_45_apple_45_darwin10_46_5_46_0/Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary.o
** Message: Adding function [Scheduler_Cell_process_cdna2genome_58_forward_58_traceback_58_boundary]
** Message: Compiling with: [/usr/bin/cc -O3 -march=core2 -w -pipe -I/usr/local/Cellar/glib/2.24.2/include/glib-2.0 -I/usr/local/Cellar/glib/2.24.2/lib/glib-2.0/include -I/usr/local/Cellar/gettext/0.17/include   -DG_DISABLE_ASSERT -O3 -finline-functions -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_PTHREADS -I/private/tmp/homebrew-exonerate-2.2.0-bpG3/exonerate-2.2.0/src/c4 -I/private/tmp/homebrew-exonerate-2.2.0-bpG3/exonerate-2.2.0/src/sequence -I/private/tmp/homebrew-exonerate-2.2.0-bpG3/exonerate-2.2.0/src/general -I/private/tmp/homebrew-exonerate-2.2.0-bpG3/exonerate-2.2.0/src/struct -I/usr/local/Cellar/glib/2.24.2/include/glib-2.0 -I/usr/local/Cellar/glib/2.24.2/lib/glib-2.0/include -I/usr/local/Cellar/gettext/0.17/include   -o c4_model_lookup.o -c c4_model_lookup.c]
** Message: Adding: [c4_model_lookup.o]
** Message: Adding object file [c4_model_lookup.o] to archive
ar -Sq c4_model_archive.a c4_model_lookup.o
** Message: Indexing archive [c4_model_archive.a]
ranlib c4_model_archive.a
** Message: Done
** Message: Finished building bootstrapping components
make[1]: *** [all-recursive] Error 1
make: *** [all-recursive] Error 1
Exit status: 2

http://github.com/mxcl/homebrew/blob/master/Library/Formula/exonerate.rb#L12

==> Environment
HOMEBREW_VERSION: 0.7.1
HEAD: c8aad294f502deef3b18e6e7e7e003f94b326a77
HOMEBREW_PREFIX: /usr/local
HOMEBREW_CELLAR: /usr/local/Cellar
HOMEBREW_REPOSITORY: /usr/local
HOMEBREW_LIBRARY_PATH: /usr/local/Library/Homebrew
Hardware: dual-core 64-bit core2
OS X: 10.6.5
Kernel Architecture: i386
Ruby: 1.8.7-174
/usr/bin/ruby => /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/bin/ruby
Xcode: 3.2.5
GCC-4.0: build 5494 
GCC-4.2: build 5664 
LLVM: build 2333 
MacPorts or Fink? false
X11 installed? true

==> Build Flags
CC: /usr/bin/cc => /usr/bin/gcc-4.2
CXX: /usr/bin/c++ => /usr/bin/c++-4.2
LD: /usr/bin/cc => /usr/bin/gcc-4.2
CFLAGS: -O3 -march=core2 -w -pipe
CXXFLAGS: -O3 -march=core2 -w -pipe
MACOSX_DEPLOYMENT_TARGET: 10.6
MAKEFLAGS: -j2
Error: Failure while executing: make 
Please follow the instructions to report this bug at: 
https://github.com/mxcl/homebrew/wiki/new-issue

Also try:
  `brew doctor` to check your setup for common problems.
  `brew missing` to check installed packages for missing deps.