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Created August 22, 2012 17:49
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brew install -v cufflinks fails with boost 1.50.0
brew install -v cufflinks
dyld: DYLD_ environment variables being ignored because main executable (/usr/bin/sudo) is setuid or setgid
==> Downloading http://cufflinks.cbcb.umd.edu/downloads/cufflinks-1.3.0.tar.gz
/usr/bin/curl -qf#LA Homebrew 0.9.2 (Ruby 1.8.7-358; Mac OS X 10.8) http://cufflinks.cbcb.umd.edu/downloads/cufflinks-1.3.0.tar.gz -o /Library/Caches/Homebrew/cufflinks-1.3.0.tar.gz --silent
/usr/bin/tar xf /Library/Caches/Homebrew/cufflinks-1.3.0.tar.gz
==> ./configure --disable-debug --disable-dependency-tracking --prefix=/usr/local/Cellar/cufflinks/1.3.0
./configure --disable-debug --disable-dependency-tracking --prefix=/usr/local/Cellar/cufflinks/1.3.0
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking whether make sets $(MAKE)... yes
checking for gawk... (cached) awk
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/llvm-g++ accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of /usr/bin/llvm-g++... none
checking for gcc... /usr/bin/llvm-gcc
checking whether we are using the GNU C compiler... yes
checking whether /usr/bin/llvm-gcc accepts -g... yes
checking for /usr/bin/llvm-gcc option to accept ANSI C... none needed
checking dependency style of /usr/bin/llvm-gcc... none
checking whether make sets $(MAKE)... (cached) yes
checking for ranlib... ranlib
checking for a BSD-compatible install... /usr/bin/install -c
checking for a Python interpreter with version >= 2.4... python
checking for python... /usr/bin/python
checking for python version... 2.7
checking for python platform... darwin
checking for python script directory... ${prefix}/lib/python2.7/site-packages
checking for python extension module directory... ${exec_prefix}/lib/python2.7/site-packages
checking for boostlib >= 1.38.0... yes
checking for bamlib... yes
checking build system type... i686-apple-darwin12.0.0
checking whether the Boost::Thread library is available... yes
checking for exit in -lboost_thread-mt... yes
checking how to run the C preprocessor... /usr/bin/llvm-gcc -E
checking for egrep... 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 if zlib is wanted... yes
checking for inflateEnd in -lz... yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking for inflateEnd in -lz... (cached) yes
checking zlib in /usr... ok
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for unistd.h... (cached) yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for inline... inline
checking for pid_t... yes
checking for size_t... yes
checking for ptrdiff_t... yes
checking host system type... i686-apple-darwin12.0.0
checking for struct sysinfo.totalram... no
checking whether sysctl is declared... yes
checking whether CTL_HW is declared... yes
checking whether HW_PHYSMEM is declared... yes
checking how to create a pax tar archive... gnutar
checking dependency style of /usr/bin/llvm-gcc... (cached) none
checking dependency style of /usr/bin/llvm-g++... (cached) none
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating config.h
config.status: executing depfiles commands
-- cufflinks 1.3.0 Configuration Results --
C++ compiler: /usr/bin/llvm-g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -arch x86_64 -O3 -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -DNDEBUG -pthread -I/usr/local/include -I/usr/local/include
GCC version: i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2336.11.00)
Host System type: i686-apple-darwin12.0.0
Install prefix: /usr/local/Cellar/cufflinks/1.3.0
Install eprefix: ${prefix}
See config.h for further configuration information.
Email <cole@cs.umd.edu> with questions and bug reports.
==> make install
make install
Making install in src
/usr/bin/llvm-g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -isystem /usr/local/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -arch x86_64 -O3 -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -DNDEBUG -pthread -I/usr/local/include -I/usr/local/include -c -o clustering.o clustering.cpp
/usr/bin/llvm-g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -isystem /usr/local/include -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -arch x86_64 -O3 -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4 -DNDEBUG -pthread -I/usr/local/include -I/usr/local/include -c -o differential.o differential.cpp
In file included from /usr/local/include/boost/graph/named_graph.hpp:17,
from /usr/local/include/boost/graph/adjacency_list.hpp:45,
from differential.h:24,
from differential.cpp:18:
/usr/local/include/boost/multi_index/hashed_index.hpp:1254: error: 'boost::BOOST_FOREACH' has not been declared
make[1]: *** [differential.o] Error 1
make: *** [install-recursive] Error 1
==> Exit Status: 2
https://github.com/mxcl/master/blob/master/Library/Formula/cufflinks.rb#L19
==> Build Environment
HOMEBREW_VERSION: 0.9.2
HEAD: a4e3cc304f65e551b92941f2fcca2647c0a4f9d6
CPU: 16-core 64-bit nehalem
OS X: 10.8-x86_64
Xcode: 4.4.1
CLT: 4.4.0.0.1.1249367152
X11: 2.7.2 in /opt/X11
CC: /usr/bin/llvm-gcc => /usr/llvm-gcc-4.2/bin/llvm-gcc-4.2
CXX: /usr/bin/llvm-g++ => /usr/llvm-gcc-4.2/bin/llvm-g++-4.2
LD: /usr/bin/llvm-gcc => /usr/llvm-gcc-4.2/bin/llvm-gcc-4.2
CFLAGS: -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4
CXXFLAGS: -Os -w -pipe -mmacosx-version-min=10.8 -march=core2 -msse4
CPPFLAGS: -isystem /usr/local/include
LDFLAGS: -L/usr/local/lib
MACOSX_DEPLOYMENT_TARGET: 10.8
PKG_CONFIG_PATH: /usr/local/Library/Homebrew/pkgconfig
OBJC: /usr/bin/llvm-gcc
PATH: .:/Users/stu/.rbenv/shims:/usr/local/share/python:/usr/local/bin:/usr/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/Users/stu/bin:/usr/local/Library/Contributions/cmds
Error: Failed executing: make install (cufflinks.rb:19)
This link will help resolve the above errors:
https://github.com/mxcl/homebrew/wiki/bug-fixing-checklist
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