cufflinks

[liweixie]

Try to put cufflinks-2.1.1 on my mac mini. I use brew install cufflinks to install, however, it give errors
make[2]: *** [differential.o] Error 1
20 errors generated.
make[2]: *** [assemble.o] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2

So, I download the source code to install to the directory of boost and eigen,
it gives
./abundances.h:21:10: fatal error: 'Eigen/Dense' file not found
#include <Eigen/Dense>
^
1 error generated.
make[2]: *** [clustering.o] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2
I try to search past post for this error. Nothing works. Who knows how to deal with this question.
Thank you!

[dpryan]

Is there a reason you're not just using the binary?

The error message just means that you need to specify an -I (and probably an -L) option when compiling so that everything can be found.

[liweixie]

Is there a reason you're not just using the binary?

The error message just means that you need to specify an -I (and probably an -L) option when compiling so that everything can be found.

this is cufflinks configure command
./configure --prefix=/usr/local/cellar/cufflinks --with-boost=/usr/local/cellar/boost --with-eigen=/usr/local/cellar/eigen
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 g++... g++
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 g++ accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of g++... gcc3
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ANSI C... none needed
checking dependency style of gcc... gcc3
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/local/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 >= 1.47.0... yes
checking for bamlib... yes
checking build system type... i686-apple-darwin13.0.0
checking whether the Boost::System library is available... yes
checking whether the Boost::Thread library is available... yes
checking how to run the C preprocessor... 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 eigenlib... 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-darwin13.0.0
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 gcc... (cached) gcc3
checking dependency style of g++... (cached) gcc3
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating config.h
config.status: config.h is unchanged
config.status: executing depfiles commands

-- cufflinks 2.1.1 Configuration Results --
C++ compiler: g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -arch x86_64 -O3 -DNDEBUG -pthread -I/usr/local/cellar/boost/include -I/usr/local/include -I/usr/local/cellar/eigen/include
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
GCC version: Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)
Host System type: i686-apple-darwin13.0.0
Install prefix: /usr/local/cellar/cufflinks
Install eprefix: ${prefix}

See config.h for further configuration information.
Email <[email protected]> with questions and bug reports.
and then make install
/Applications/Xcode.app/Contents/Developer/usr/bin/make all-recursive
Making all in src
if g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -arch x86_64 -O3 -DNDEBUG -pthread -I/usr/local/cellar/boost/include -I/usr/local/include -I/usr/local/cellar/eigen/include -MT clustering.o -MD -MP -MF ".deps/clustering.Tpo" -c -o clustering.o clustering.cpp; \
then mv -f ".deps/clustering.Tpo" ".deps/clustering.Po"; else rm -f ".deps/clustering.Tpo"; exit 1; fi
In file included from clustering.cpp:10:
In file included from ./clustering.h:38:
./abundances.h:21:10: fatal error: 'Eigen/Dense' file not found
#include <Eigen/Dense>
^
1 error generated.
make[2]: *** [clustering.o] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2