Hi Edward,
Here is the output:
% ./relax
ImportError: relaxation curve fitting is unavailible, try compiling
the C modules.
relax repository checkout
Protein dynamics by NMR relaxation data
analysis
Copyright (C) 2001-2006 Edward d'Auvergne
This is free software which you are welcome to modify and
redistribute under the conditions of the
GNU General Public License (GPL). This program, including all
modules, is licensed under the GPL
and comes with absolutely no warranty. For details type 'GPL'.
Assistance in using this program
can be accessed by typing 'help'.
relax> from maths_fns.relax_fit import setup, func, dfunc, d2func,
back_calc_I
Traceback (most recent call last):
File "<console>", line 1, in ?
ImportError: No module named relax_fit
relax>
Does this provide any hints?
Doug
On Nov 8, 2006, at 11:07 AM, Edward d'Auvergne wrote:
I wonder if it is the file 'maths_fns/relax_fit.dylib' which should
have a different extension? As relax hides the importing error
messages and prints 'ImportError: relaxation curve fitting is
unavailable, try compiling the C modules.' instead, you can get the
true error message by typing the following at the relax prompt:
from maths_fns.relax_fit import setup, func, dfunc, d2func,
back_calc_I
Does typing this give any useful messages?
Edward
On 11/9/06, Douglas Kojetin <douglas.kojetin@xxxxxxxxx> wrote:
Hi Edward-
The following worked without error:
gcc -bundle -bundle_loader /sw/bin/python -dynamic -o
maths_fns/relax_fit.dylib maths_fns/c_chi2.os maths_fns/
exponential.os
maths_fns/relax_fit.os
but invoking relax afterwards suggests the relaxation curve fitting
is still not available:
% ./relax --test
ImportError: relaxation curve fitting is unavailible, try compiling
the C modules.
Is there anything else I need to do or should try?
Thanks,
Doug
On Nov 8, 2006, at 9:30 AM, Edward d'Auvergne wrote:
> Hi,
>
> I have to warn you first that the 'tensor_pdb' branch is very
unstable
> code at the moment and I'm constantly breaking things as the code
> shapes up. There may be times when it won't even run. These
aren't
> related to this bug though.
>
> I've had a look at the 'sconstruct' script in the base relax
directory
> and one thing which is apparent is the '-dynamiclib' flag being
passed
> into 'gcc'. The script has been specifically modified for OS X to
> compile the shared objects to be loaded by python, hence the
> '-bundle', etc. flags. However '-dynamiclib' is not one of the
> options in the script so it must be SCons adding that. If you type
> the following gcc line at the prompt, do get the same
> 'powerpc-apple-darwin8-gcc-4.0.1' error message or does the code
> compile?
>
> gcc -bundle -bundle_loader /sw/bin/python -dynamic -o
> maths_fns/relax_fit.dylib maths_fns/c_chi2.os maths_fns/
exponential.os
> maths_fns/relax_fit.os
>
> If we can work out how to compile the C modules on the command
line,
> then the SCons script can be subsequently updated to pass the
correct
> options to gcc.
>
> Cheers,
>
> Edward
>
>
> On 11/8/06, anonymous <NO-REPLY.INVALID-ADDRESS@xxxxxxx> wrote:
>>
>> URL:
>> <http://gna.org/bugs/?7670>
>>
>> Summary: scons compile issue
>> Project: relax
>> Submitted by: None
>> Submitted on: Wednesday 11/08/2006 at 13:52 CET
>> Category: Scons build system
>> Priority: 5 - Normal
>> Severity: 4 - Important
>> Status: None
>> Privacy: Public
>> Assigned to: None
>> Originator Name: doug
>> Originator Email:
>> Open/Closed: Open
>> Release: 1.2.7
>> Operating System: Mac OS X
>>
>> _______________________________________________________
>>
>> Details:
>>
>> I'm using the tensor_pdb version (svn co
>> svn://svn.gna.org/svn/relax/branches/tensor_pdb) and running Mac
>> OS X 10.4.8
>> w/ gcc version 4.0.1 (PowerPC version).
>>
>> I tried to install relax using the directions in the relax.pdf
>> section 1.2.1
>> using the 'scons' program under OS X. I am seeing the following
>> error (even
>> after trying to execute 'scons' a few times, which is shown
below):
>>
>> % scons clean
>> scons: Reading SConscript files ...
>> scons: done reading SConscript files.
>> scons: Building targets ...
>> clean_temp_files(["clean_temp"], [])
>>
>> ###############################
>> # Cleaning up temporary files #
>> ###############################
>>
>>
>>
>> Removing the files ending in ['pyc', 'bak', 'o', 'os', 'obj',
>> 'exp', 'lib'].
>>
>>
>>
>>
>>
>> clean_manual_files(["manual_clean"], [])
>>
>> ##########################################
>> # Cleaning up the temporary manual files #
>> ##########################################
>>
>>
>>
>>
>>
>>
>> clean_files(["clean"], [])
>>
>> ###############
>> # Cleaning up #
>> ###############
>>
>>
>>
>> Removing the files ending in ['so', 'sconsign', 'dll'].
>>
>>
>>
>>
>>
>> scons: done building targets.
>>
>>
>>
>> % scons
>> scons: Reading SConscript files ...
>> scons: done reading SConscript files.
>> scons: Building targets ...
>>
>>
>>
>>
>> ###########################
>> # Compiling the C modules #
>> ###########################
>>
>>
>> Building the relaxation curve fitting module 'maths_fns/
>> relax_fit.dylib'
>>
>> gcc -I/sw/include/python2.4 -fPIC -c -o maths_fns/c_chi2.os
>> maths_fns/c_chi2.c
>> gcc -I/sw/include/python2.4 -fPIC -c -o maths_fns/exponential.os
>> maths_fns/exponential.c
>> gcc -I/sw/include/python2.4 -fPIC -c -o maths_fns/relax_fit.os
>> maths_fns/relax_fit.c
>> gcc -bundle -bundle_loader /sw/bin/python -dynamic -dynamiclib -o
>> maths_fns/relax_fit.dylib maths_fns/c_chi2.os maths_fns/
>> exponential.os
>> maths_fns/relax_fit.os
>> powerpc-apple-darwin8-gcc-4.0.1: -bundle not allowed with -
dynamiclib
>> scons: *** [maths_fns/relax_fit.dylib] Error 1
>> scons: building terminated because of errors.
>>
>>
>>
>>
>> I blindly tried removing the -bundle and -bundle_loader flags, but
>> that did
>> not help.
>>
>>
>>
>> _______________________________________________________
>>
>> Follow-up Comments:
>>
>>
>> -------------------------------------------------------
>> Date: Wednesday 11/08/2006 at 13:52 CETBy: Anonymous
>> I'm using the tensor_pdb version (svn co
>> svn://svn.gna.org/svn/relax/branches/tensor_pdb) and running Mac
>> OS X 10.4.8
>> w/ gcc version 4.0.1 (PowerPC version).
>>
>> I tried to install relax using the directions in the relax.pdf
>> section 1.2.1
>> using the 'scons' program under OS X. I am seeing the following
>> error (even
>> after trying to execute 'scons' a few times, which is shown
below):
>>
>> % scons clean
>> scons: Reading SConscript files ...
>> scons: done reading SConscript files.
>> scons: Building targets ...
>> clean_temp_files(["clean_temp"], [])
>>
>> ###############################
>> # Cleaning up temporary files #
>> ###############################
>>
>>
>>
>> Removing the files ending in ['pyc', 'bak', 'o', 'os', 'obj',
>> 'exp', 'lib'].
>>
>>
>>
>>
>>
>> clean_manual_files(["manual_clean"], [])
>>
>> ##########################################
>> # Cleaning up the temporary manual files #
>> ##########################################
>>
>>
>>
>>
>>
>>
>> clean_files(["clean"], [])
>>
>> ###############
>> # Cleaning up #
>> ###############
>>
>>
>>
>> Removing the files ending in ['so', 'sconsign', 'dll'].
>>
>>
>>
>>
>>
>> scons: done building targets.
>>
>>
>>
>> % scons
>> scons: Reading SConscript files ...
>> scons: done reading SConscript files.
>> scons: Building targets ...
>>
>>
>>
>>
>> ###########################
>> # Compiling the C modules #
>> ###########################
>>
>>
>> Building the relaxation curve fitting module 'maths_fns/
>> relax_fit.dylib'
>>
>> gcc -I/sw/include/python2.4 -fPIC -c -o maths_fns/c_chi2.os
>> maths_fns/c_chi2.c
>> gcc -I/sw/include/python2.4 -fPIC -c -o maths_fns/exponential.os
>> maths_fns/exponential.c
>> gcc -I/sw/include/python2.4 -fPIC -c -o maths_fns/relax_fit.os
>> maths_fns/relax_fit.c
>> gcc -bundle -bundle_loader /sw/bin/python -dynamic -dynamiclib -o
>> maths_fns/relax_fit.dylib maths_fns/c_chi2.os maths_fns/
>> exponential.os
>> maths_fns/relax_fit.os
>> powerpc-apple-darwin8-gcc-4.0.1: -bundle not allowed with -
dynamiclib
>> scons: *** [maths_fns/relax_fit.dylib] Error 1
>> scons: building terminated because of errors.
>>
>>
>>
>>
>> I blindly tried removing the -bundle and -bundle_loader flags, but
>> that did
>> not help.
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> _______________________________________________________
>>
>> Reply to this item at:
>>
>> <http://gna.org/bugs/?7670>
>>
>> _______________________________________________
>> Message sent via/by Gna!
>> http://gna.org/
>>
>>
>> _______________________________________________
>> relax (http://nmr-relax.com)
>>
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>>
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>>
Re: [bug #7670] scons compile issue