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August 22, 2012 17:49
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brew install -v cufflinks fails with boost 1.50.0
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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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