DeLano Scientific wrote:
Andreas,
Try removing -D_FORTIFY_SOURCE=2 as a compiler option...
Hi Warren,
I tried running gcc without that option manually - it worked. I did not
find any place in the distutils/setup.py
where this option (or the compiler itself) is set. Now I get this error:
> python setup.py install --prefix=$PWD
running install
running build
running build_py
running build_ext
building 'chempy.champ._champ' extension
gcc -pthread -fno-strict-aliasing -DNDEBUG -O2 -fmessage-length=0 -Wall
-D_FORTIFY_SOURCE=2 -g -fPIC -Icontrib/champ -I/usr/include/python2.4 -c
contrib/champ/feedback2.c -o
build/temp.linux-ia64-2.4/contrib/champ/feedback2.o
contrib/champ/feedback2.c:121:1: error: unterminated argument list
invoking macro "fprintf"
contrib/champ/feedback2.c: In function 'feedback_Push':
contrib/champ/feedback2.c:60: warning: statement with no effect
contrib/champ/feedback2.c:60: error: expected ';' at end of input
error: command 'gcc' failed with exit status 1
Any idea?
Thanks again,
Andreas
Cheers,
Warren
-----Original Message-----
From: [email protected]
[mailto:[email protected]] On Behalf
Of Andreas Henschel
Sent: Friday, April 27, 2007 2:28 PM
To: Michael Kluge
Cc: [email protected]
Subject: Re: [PyMOL] PyMOL compilation from source
Hi,
Michael Kluge wrote:
Hi Andreas,
gcc is not the best compiler on an IA64 machine. We always recommend
using the Intel compilers. Would it be possible to try those?
I have to figure out, where to modify in the setup script/distutils.
Thanks.
Andreas
PS. @Michael
From Martin Hoefling:
i have no idea about your error but i can provide you RPMs
for Opensuse
10.2
i586 and x86_64, if you need them for other SuSE
distributions, I can
try to add them to my repository.
Would that be feasable?
Regards, Michael
Andreas Henschel wrote:
Hi all,
did anyone of you come across the mysterious "internal
compiler error:
Segmentation fault"
while compiling pymol from source?
The offending lines are in contrib/champ/champ.c:2787
PRINTFD(FB_smiles_parsing)
" ChampParseBlockAtom: called.\n"
ENDFD;
Can I get around it somehow? Is it a 64-bit/gcc issue?
Any help would be greatly appreciated.
Some more error/system details:
python setup.py install
...
building 'chempy.champ._champ' extension gcc -pthread
-fno-strict-aliasing -DNDEBUG -O2 -fmessage-length=0 -Wall
-D_FORTIFY_SOURCE=2 -g -fPIC -Icontrib/champ
-I/usr/include/python2.4
-c contrib/champ/champ.c -o
build/temp.linux-ia64-2.4/contrib/champ/champ.o
contrib/champ/champ.c: In function 'ChampParseBlockAtom':
contrib/champ/champ.c:2787: internal compiler error: Segmentation
fault Please submit a full bug report, with preprocessed source if
appropriate.
See <URL:http://www.suse.de/feedback> for instructions.
error: command 'gcc' failed with exit status 1
uname -a
Linux mars 2.6.16.27-0.6-default #1 SMP Wed Dec 13 09:34:50 UTC 2006
ia64 ia64 ia64 GNU/Linux
gcc -v
Using built-in specs.
Target: ia64-suse-linux
Configured with: ../configure --enable-threads=posix --prefix=/usr
--with-local-prefix=/usr/local --infodir=/usr/share/info
--mandir=/usr/share/man --libdir=/usr/lib --libexecdir=/usr/lib
--enable-languages=c,c++,objc,fortran,java,ada
--enable-checking=release
--with-gxx-include-dir=/usr/include/c++/4.1.0 --enable-ssp
--disable-libssp --enable-java-awt=gtk --enable-gtk-cairo
--disable-libjava-multilib --with-slibdir=/lib --with-system-zlib
--enable-shared --enable-__cxa_atexit
--enable-libstdcxx-allocator=new
--with-system-libunwind --host=ia64-suse-linux Thread
model: posix gcc
version 4.1.0 (SUSE Linux)
ia64 GNU/Linux
Cheers,
Andreas
--
Andreas Henschel
Bioinformatics Group
TU Dresden
Tatzberg 47-51
01307 Dresden, Germany
Phone: +49 351 463 40063
EMail: [email protected]
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--
Andreas Henschel
Bioinformatics Group
TU Dresden
Tatzberg 47-51
01307 Dresden, Germany
Phone: +49 351 463 40063
EMail: [email protected]
