Hi all,
On Wednesday 30 August 2006 23:54, Peter Adrian Meyer wrote:
> Which version of gcc are you using?
gcc (GCC) 4.1.1 20060525 (Red Hat 4.1.1-1)
> A quick check of google for the
> unterminated argument list in macro error makes it look like that could be
> an issues (on my systems, it works for gcc-3.4.5 and 4.0.2; but that's
> using make instead of python distutils). It looks to me like a c
> preprocessor issue, rather than something in Crystal.c; specifically
> dealing with the PRINTF macro in Feedback.h (although it does seem a
> little strange seeing special characters in a logfile...).
Tried doing the make using the Rules.linux . (did not use the ext package)
In the Rule.linux file I changed 2.3 -> 2.4 and added the location of the
python .h file etc:
PYTHON_EXE = /usr/bin/python
PYTHON_INC_DIR = -I$(PYMOL_PATH)/ext/include/python2.4 \
-I$(PYMOL_PATH)/ext/include/python2.4/Numeric
-I/usr/include/python2.4/ \
-I/usr/include/python2.4/Numeric
I copied Rules.linux to Rules.make under the base pymol dir.
It seemed to have compiled ok.
In the pymol file I needed to change line 43 to /usr/bin/python
$PYMOL_PATH/modules/pymol/__init__.py "$@"
so it's poining to the right place for python
However when I run it the following errors are thrown:
Traceback (most recent call last):
File "/home/fauxn/software/pymol-0.99rc6/modules/pymol/__init__.py", line
209, in exec_str
exec s in globals(),globals()
File "<string>", line 1, in ?
File "/home/fauxn/software/pymol-0.99rc6/modules/pymol/__init__.py", line
325, in launch_gui
__import__(invocation.options.gui)
File "/home/fauxn/software/pymol-0.99rc6/modules/pmg_tk/__init__.py", line
22, in ?
from PMGApp import *
File "/home/fauxn/software/pymol-0.99rc6/modules/pmg_tk/PMGApp.py", line 27,
in ?
from Tkinter import *
ImportError: No module named Tkinter
Have I missed something?
The main graphics windows appears. I can load a pdb and view it, but when I
try to select an atom/residue an error is thrown:
*** glibc detected *** /usr/bin/python: double free or corruption (!prev):
0x087de808 ***
Back to square one!!!
>
> You could try 1. checking that you've got all of your development packages
> installed (you probably do, but it never hurts to check);
yum search <for devel packages>
python-devel.i386 2.4.3-8.FC5 installed
python-numeric.i386 23.7-2.2.1 installed
tcl-devel.i386 8.4.13-1.1 installed
freetype-devel.i386 2.1.10-5.2.1 installed
freeglut-devel.i386 2.4.0-4 installed
libpng-devel.i386 2:1.2.8-2.2.1 installed
libgcc.i386 4.1.1-1.fc5 installed
can't find pmw or the zlib-gcc packages through yum.
> 2. upgrading (or downgrading) gcc;
I'm unsure how to downgrade.
> 3. customize setup/rules.generic for your system, and
> build with make (personal preference is for building ext dependencies from
> ext-0_99rc1-src.tgz as well, but this shouldn't make a difference).
Tried to build the ext package but got constant problems:
./build.com tcl
...
checking system version (for dynamic loading)... ./configure: line 7624:
syntax error near unexpected token `)'
./configure: line 7624: ` OSF*)'
make: *** [tcl] Error 2
./build.com tk
...
checking for Tcl configuration... configure:
error: /home/fauxn/software/pymol-0.99rc6/ext/src/build/tcl8.4.11/unix
directory doesn't contain tclConfig.sh
make: *** [tk] Error 1
./build.com zlib-gcc
...
cp: target `/home/fauxn/software/pymol-0.99rc6/ext/include' is not a directory
make: *** [zlib-gcc] Error 1
I'm now at a complete loss as how to get pymol running stability on my
machine. I'm begining to feel that the best and simplest option is to
upgrade my card. Is that really going to fix things if it's a gcc problem?
Many Thanks,
Noel
--
PhD Student
Department of Biochemistry and Molecular Biology
Monash University
Clayton, Victoria
Australia
Ph: +61 3 9905 1418
e-mail: noel.f...@med.monash.edu.au
website: http://vbc.med.monash.edu.au/~fauxn
