TopHat installation, beginner

[Nicolas902]

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:

checking for ANSI C header files... no

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

[steinmann]

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

[Nicolas902]

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.

[steinmann]

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

instead of:
./configure

[Nicolas902]

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??

[cur]

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"