Dear Bioinformaticians.
Can TopHat be installed on a 32bit Ubuntu (Linux ubuntu 2.6.31-14-generic #48-Ubuntu SMP Fri Oct 16 14:04:26 UTC 2009 i686 GNU/Linux) installation? I tried and get the following:
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/features.h:378,
from /usr/include/assert.h:37,
from /usr/include/c++/4.4/cassert:45,
from reads.cpp:14:
/usr/include/gnu/stubs.h:9:27: error: gnu/stubs-64.h: No such file or directory
It looks like the configure script is expecting the system to be 64bit. I tried make clean, edited all files to change -m64 to -m32 but when I run configure, it always ends up with:
-- 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 4.4.1-4ubuntu9) 4.4.1
Host System type: i686-pc-linux-gnu
Install prefix: /home/john/Documents/software/tophat-1.0.13
Install eprefix: ${prefix}
Both the gcc and g++ have the -m64 flag. Does anyone know how I can fix this? I saw another 2 threads about similar problems installing MAQ but the fixes don't work for TopHat.
Thanks a lot for any help.
Kind regards,
P
Can TopHat be installed on a 32bit Ubuntu (Linux ubuntu 2.6.31-14-generic #48-Ubuntu SMP Fri Oct 16 14:04:26 UTC 2009 i686 GNU/Linux) installation? I tried and get the following:
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/features.h:378,
from /usr/include/assert.h:37,
from /usr/include/c++/4.4/cassert:45,
from reads.cpp:14:
/usr/include/gnu/stubs.h:9:27: error: gnu/stubs-64.h: No such file or directory
It looks like the configure script is expecting the system to be 64bit. I tried make clean, edited all files to change -m64 to -m32 but when I run configure, it always ends up with:
-- 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 4.4.1-4ubuntu9) 4.4.1
Host System type: i686-pc-linux-gnu
Install prefix: /home/john/Documents/software/tophat-1.0.13
Install eprefix: ${prefix}
Both the gcc and g++ have the -m64 flag. Does anyone know how I can fix this? I saw another 2 threads about similar problems installing MAQ but the fixes don't work for TopHat.
Thanks a lot for any help.
Kind regards,
P
Comment