Edward,
I'll try to find some time to look at these issues over the
weekend with the current 1.3 line code. As far as I recall,
1.3.4 still had some bogus testsuite failures on Darwin intel that
were fixed for the next release of relax 1.3.x.
Jack
On Tue, Feb 23, 2010 at 02:57:23PM +0100, Edward d'Auvergne wrote:
> Hi,
>
> It might be worth talking with Jack Howarth (howarth att bromo dott
> med dott uc dott edu) as he is the maintainer of the relax fink
> packages. You can see our previous discussions about fink at:
>
> http://www.google.com/search?q=fink&btnG=Google+Search&domains=http%3A%2F%2Fnmr-relax.com&sitesearch=https%3A%2F%2Fmail.gna.org%2Fpublic%2Frelax-users
>
> He modified the sconstruct script for this, but I don't think this was
> merged upstream (it's not in the 1.3 line). Maybe all of these
> problems is because one of the other essential components of fink have
> been upgraded (numpy, python, etc.) causing a breakage in the relax C
> modules and in the Scientific python module.
>
> I you have the time and would like to try to get the 1.3 line test
> suite passing 100% and attempt to deposit the newest relax versions
> into fink, this would be appreciated. relax should run without
> problems on Mac OS X, and it shouldn't be too hard to modify relax for
> 100% compatibility. The only problem for me is that I don't have Mac
> hardware.
>
> Cheers,
>
> Edward
>
>
> On 22 February 2010 19:16, Sébastien Morin <[email protected]>
> wrote:
> > Hi Ed,
> >
> > Unfortunately, the problem here arises from the fink version of relax, i.e.
> > 1.3.4.
> > Hence, the '-i' option is unavailable.
> >
> > For python, I indeed have two versions installed...
> > 2.6: standard version
> > 2.5: for rdiff-backup...
> >
> > For the sconstruct file, it was modified by fink. Hence, it seems the fink
> > version of relax might be problematic...
> >
> > ...
> >
> > In order to see if the repository version is also having troubles, I
> > installed it (as well as the minfx repository version) and tested it.
> > The compilation with scons worked fine and relax does not complain anymore
> > about the relax_fit.so file...
> > However, there are still 12 errors from the unit tests and 1 failure and 16
> > errors from the system tests.
> >
> > It is better than with the fink version, although ScientificPython still not
> > works...
> > How should ScientificPython be installed ?
> > Presently, it is installed from fink...
> >
> > ...
> >
> > Here is the output from 'relax -i':
> >
> > ==========
> > Hardware information:
> > Machine: i386
> > Processor: i386
> >
> > System information:
> > System: Darwin
> > Release: 10.2.0
> > Version: Darwin Kernel Version 10.2.0: Tue Nov 3
> > 10:37:10 PST 2009; root:xnu-1486.2.11~1/RELEASE_I386
> > Mac version: 10.6.2 (, , ) i386
> > Distribution:
> > Full platform string: Darwin-10.2.0-i386-64bit
> >
> > Software information:
> > Architecture: 64bit
> > Python version: 2.6.1
> > Python branch: tags/r261
> > Python build: r261:67515, Jul 7 2009 23:51:51
> > Python compiler: GCC 4.2.1 (Apple Inc. build 5646)
> > Python implementation: CPython
> > Python revision: 67515
> > Numpy version: 1.2.1
> > Libc version:
> > Network name: dhcp-160-189.rsvs.ulaval.ca
> > ==========
> >
> > Any idea ?
> >
> >
> > Séb :)
> >
> >
> >
> >
> > On 10-02-22 12:41 PM, Edward d'Auvergne wrote:
> >>
> >> Hi Seb,
> >>
> >> Could you paste the output of 'relax -i'? This will help in working
> >> out what is happening and will be useful to have on record.
> >>
> >> Cheers,
> >>
> >> Edward
> >>
> >>
> >> On 22 February 2010 18:30, Edward d'Auvergne<[email protected]> wrote:
> >>
> >>>>>>
> >>>>>> 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.
> >>>>>
> >>>>>
> >>>>>
> >>>>
> >>>> In fact, if the link is not present, relax complains about minfx not
> >>>> being
> >>>> installed...
> >>>>
> >>>
> >>> Ah, this is an indication that there are 2 python versions present!!!
> >>> I have just added a new command line option to relax to help work out
> >>> what is happening. I'm guessing you have a repository copy from the
> >>> 1.3 line? If so, update this copy (for those who don't know, you
> >>> type):
> >>>
> >>> $ svn up
> >>>
> >>> and then run one of:
> >>>
> >>> $ relax -i
> >>> $ relax --info
> >>>
> >>> This should tell you all you need to know about versions, etc.! I can
> >>> add other useful info later on - i.e. modules installed or missing and
> >>> their versions.
> >>>
> >>>
> >>>
> >>>
> >>>>>>
> >>>>>> 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!
> >>>>>
> >>>>>
> >>>>
> >>>> "scons clean_all" works fine and then, "scons" creates the
> >>>> "relax_fit.so"
> >>>> executable. The file type (obtained from the command "file") is as
> >>>> follows:
> >>>> "Mach-O bundle i386".
> >>>>
> >>>> Is it what it's supposed to be ?
> >>>> (I am really new to Mac...)
> >>>>
> >>>
> >>> I really have no idea either. Maybe someone else on this list knows
> >>> something? It could actually be a version issue again as maybe relax
> >>> is running with an old python version but scons build the module for
> >>> the 2.6 version?
> >>>
> >>>
> >>>
> >>>>>>
> >>>>>> 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.
> >>>>>
> >>>>>
> >>>>
> >>>> Scientific Python is installed...
> >>>> scientificpython-py26 2.8-1 Python modules for scientific
> >>>> computing
> >>>>
> >>>> Maybe, yes, it would be good to simply give a warning for missing
> >>>> dependencies and avoid the tests to be performed...
> >>>>
> >>>> Thanks for your insights !
> >>>>
> >>>
> >>> This could be again related to Python versions, with Scientific Python
> >>> installed for Python 2.6 but relax running with Python 1.5 (Mac Unix
> >>> software versions are painfully old :P). I hope this helps.
> >>>
> >>> Regards,
> >>>
> >>> Edward
> >>>
> >>>
> >
> > --
> > Sébastien Morin
> > PhD Student
> > S. Gagné NMR Laboratory
> > Université Laval& PROTEO
> > Québec, Canada
> >
> >
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