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  • TopHat installation, beginner

    Hello everyone,

    I am a master of research student and my final project is about building an RNA-Seq pipeline. I would like to install TopHat and I am struggling for 1 day and a half without succeeding. I just do not know how to find the right packages and I have this problem of "malloc" which I cannot solve.
    I am a unix beginner (ubuntu 9.10), I tried to install tophat using gcc-4.4 and gcc-4.3 but this does not change a thing. so finally I installed the maximum of packages related to "gcc" via synaptic. Please see below my ./configure, make, and make install.
    I think the problem is coming from there:
    Code:
    checking for ANSI C header files... no
    Code:
    checking for GNU libc compatible malloc... no
    After few hours of research on the web, I found no solution. any ideas?
    Thank you very much for your help.

    ./configure
    checking build system type... i686-pc-linux-gnu
    checking host system type... i686-pc-linux-gnu
    checking for gcc... gcc
    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 gcc accepts -g... yes
    checking for gcc option to accept ISO C89... none needed
    checking for g++... g++
    checking whether we are using the GNU C++ compiler... yes
    checking whether g++ accepts -g... yes
    checking for gawk... gawk
    checking for a BSD-compatible install... /usr/bin/install -c
    checking for ranlib... ranlib
    checking for ar... ar
    checking for perl... /usr/bin/perl
    checking for bash... /bin/bash
    checking for a Python interpreter with version >= 2.4... python
    checking for python... /usr/bin/python
    checking for python version... 2.6
    checking for python platform... linux2
    checking for python script directory... ${prefix}/lib/python2.6/site-packages
    checking for python extension module directory... ${exec_prefix}/lib/python2.6/site-packages
    checking if gcc accepts -m64... yes
    checking for gzread in -lz... yes
    checking how to run the C++ preprocessor... g++ -E
    checking for grep that handles long lines and -e... /bin/grep
    checking for egrep... /bin/grep -E
    checking for ANSI C header files... no
    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 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... no
    checking for an ANSI C-conforming const... yes
    checking for int32_t... yes
    checking for size_t... yes
    checking for uint32_t... yes
    checking for uint64_t... yes
    checking for uint8_t... yes
    checking for special C compiler options needed for large files... no
    checking for _FILE_OFFSET_BITS value needed for large files... no
    checking for stdlib.h... (cached) yes
    checking for GNU libc compatible malloc... no
    checking for memset... yes
    checking for strdup... yes
    checking for strrchr... yes
    checking for strtol... yes
    checking for strsep... yes
    checking whether build environment is sane... yes
    checking for a thread-safe mkdir -p... /bin/mkdir -p
    checking whether make sets $(MAKE)... yes
    checking for style of include used by make... GNU
    checking dependency style of gcc... gcc3
    checking dependency style of g++... gcc3
    configure: creating ./config.status
    config.status: creating Makefile
    config.status: creating src/Makefile
    config.status: creating config.h
    config.status: executing depfiles commands

    -- TopHat 1.0.13 Configuration Results --
    C compiler: gcc -Wall -g -m64 -O3 -DNDEBUG
    C++ compiler: g++ -Wall -g -m64 -O3 -DNDEBUG
    GCC version: gcc (Ubuntu 4.3.4-5ubuntu1) 4.3.4
    Host System type: i686-pc-linux-gnu
    Install prefix: /home/nico/Documents/stage/RNA-Seq-protocol/tophat-1.0.13
    Install eprefix: ${prefix}

    make
    make all-recursive
    make[1]: entrant dans le répertoire « /home/nico/Documents/stage/RNA-Seq-protocol/tophat-1.0.13 »
    Making all in src
    make[2]: entrant dans le répertoire « /home/nico/Documents/stage/RNA-Seq-protocol/tophat-1.0.13/src »
    g++ -DHAVE_CONFIG_H -I. -I.. -Wall -g -m64 -O3 -DNDEBUG -I./SeqAn-1.1 -Wall -g -m64 -O3 -DNDEBUG -MT reads.o -MD -MP -MF .deps/reads.Tpo -c -o reads.o reads.cpp
    In file included from /usr/include/c++/4.3/bits/stl_algo.h:65,
    from /usr/include/c++/4.3/algorithm:67,
    from reads.cpp:16:
    /usr/include/c++/4.3/cstdlib:124: error: ‘::malloc’ has not been declared
    In file included from reads.cpp:20:
    bwt_map.h: In member function ‘bool HitStream::next_read_hits(HitsForRead&)’:
    bwt_map.h:586: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result
    make[2]: *** [reads.o] Erreur 1
    make[2]: quittant le répertoire « /home/nico/Documents/stage/RNA-Seq-protocol/tophat-1.0.13/src »
    make[1]: *** [all-recursive] Erreur 1
    make[1]: quittant le répertoire « /home/nico/Documents/stage/RNA-Seq-protocol/tophat-1.0.13 »
    make: *** [all] Erreur 2

    make install
    Making install in src
    make[1]: entrant dans le répertoire « /home/nico/Documents/stage/RNA-Seq-protocol/tophat-1.0.13/src »
    g++ -DHAVE_CONFIG_H -I. -I.. -Wall -g -m64 -O3 -DNDEBUG -I./SeqAn-1.1 -Wall -g -m64 -O3 -DNDEBUG -MT reads.o -MD -MP -MF .deps/reads.Tpo -c -o reads.o reads.cpp
    In file included from /usr/include/c++/4.3/bits/stl_algo.h:65,
    from /usr/include/c++/4.3/algorithm:67,
    from reads.cpp:16:
    /usr/include/c++/4.3/cstdlib:124: error: ‘::malloc’ has not been declared
    In file included from reads.cpp:20:
    bwt_map.h: In member function ‘bool HitStream::next_read_hits(HitsForRead&)’:
    bwt_map.h:586: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result
    make[1]: *** [reads.o] Erreur 1
    make[1]: quittant le répertoire « /home/nico/Documents/stage/RNA-Seq-protocol/tophat-1.0.13/src »
    make: *** [install-recursive] Erreur 1

  • #2
    Am struggling with the same issues here on Ubuntu 9.10 with Gcc 4.4.1.

    Comment


    • #3
      I confess I installed it on another computer in the lab with a different version of ubuntu and I had no problem for installing.

      I asked only about the malloc error on two different ubuntu forums and I got no answers. I found similar post and the guys (october 2009) never got an answer. I think the only solution is to change of ubuntu version.... :-(

      But if you want to find a solution, I already tried to change the version of gcc, g++, cpp and gfortran. It does nothing to it. By installing other packages (lots of packages), the only errors that remain are ansi headers and malloc. A guy from another lab managed to install tophat with the ansi error, so I think it is not compiling because of the malloc only.

      If you find the solution, you will help lots of people I think.

      Comment


      • #4
        Problem solved. Installed gcc-multilib and ran:
        ./configure CFLAGS="-m32" CXXFLAGS="-m32

        instead of:
        ./configure

        Comment


        • #5
          I officially crown you master of the WWW....

          I looked at the definition of CFLAGS and CXXFLAGS, I did not know this. But what does "-m32" mean??
          Last edited by Nicolas902; 03-03-2010, 06:12 AM.

          Comment


          • #6
            tophat installation on ubuntu 9.10 64 bit

            Thanks, I also had the problem and thanks to your post got the problem solved.
            I Installed gcc-multilib and ran:
            ./configure CFLAGS="-m64" CXXFLAGS="-m64"

            Comment

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