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  • cufflinks

    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!

  • #2
    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.

    Comment


    • #3
      Originally posted by dpryan View Post
      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

      Comment

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