Hi,
See below:
On 21 February 2010 20:59, Sébastien Morin <sebastien.morin.1@xxxxxxxxx>
wrote:
Hi,
I just installed relax on a Mac using fink.
relax-py26 1.3.4-2 Protein dynamics by NMR relax. data analysis
I also installed the dependencies using fink.
minfx-py26 1.0.2-1 The minfx optimisation library
numpy-py26 [virtual package]
python26 1:2.6.4-101 Interpreted, object-oriented language
scientificpython-py26 2.8-1 Python modules for scientific
computing
scons 0.98.3-1 Python-based build tool
I created a link in the relax directory pointing to the minfx directory:
minfx@ -> /sw/lib/python2.6/site-packages/minfx/
This should not be necessary. If there are any strange optimisation
issues, this should be the first place to look.
I compiled the relaxation curve fitting modules using scons but got the
following deprecation warnings:
========
scons: Reading SConscript files ...
/sw/lib/scons-0.98.3/SCons/Platform/posix.py:38: DeprecationWarning: The
popen2 module is deprecated. Use the subprocess module.
import popen2
/sw/lib/scons-0.98.3/SCons/Tool/msvs.py:37: DeprecationWarning: the md5
module is deprecated; use hashlib instead
========
These are ok. Like most mac software ported for other Unix systems,
the versions are ancient and from the dark ages. Scons released
version 1.2 in december, not of last year, but 2 years ago! See
http://www.scons.org/. Hence the warnings. This is no problem
though.
After, I launched relax but got the following warning:
========
ImportError: dlopen(/sw/lib/relax-py26/maths_fns/relax_fit.so, 2): no
suitable image found. Did find:
/sw/lib/relax-py26/maths_fns/relax_fit.so: mach-o, but wrong
architecture
Relaxation curve fitting is unavailable, try compiling the C modules.
========
Try "scons clean_all" followed by "scons". Does the file
/sw/lib/relax-py26/maths_fns/relax_fit.so exist? This will be a
problem for curve-fitting!
Concerning the test-suite, there were nultiple errors:
System tests
4 failures + 20 errors
Unit tests
12 errors
The unit tests errors were all the same:
======
Traceback (most recent call last):
File
"/sw/lib/relax-py26/test_suite/unit_tests/_generic_fns/_structure/test_scientific.py",
line 54, in setUp
self.data = Scientific_data()
File "/sw/lib/relax-py26/generic_fns/structure/scientific.py", line
60, in __init__
raise RelaxError, "The Scientific python PDB module
Scientific.IO.PDB could not be imported."
RelaxError: RelaxError: The Scientific python PDB module
Scientific.IO.PDB could not be imported.
======
...
I guess all these errors are not normal...
Any idea to help me debug this issue ?
Thank you !!!
This is normal as Scientific python is not installed. Maybe it would
be good to add a new section to the test suite listing the installed
and missing modules, and then disabling the relevant system and unit
tests (scientific-python, relax curve-fitting C modules, etc.) if
missing. This will be a bit of work though, hence why I haven't done
it yet! I would guess that all the failures are due to these 2
missing pieces, but it's hard to tell.
Regards,
Edward
Re: relax on Mac with fink