Hi,
Unless fink is a requirement, you can install relax 1.3.4 using
macports and its GUI porticus. Last time I tried, it worked nicely, though
there were some failures in the test-suite.
It will install relax in /opt/local/lib/relax/,( with a link from
/opt/local/bin/relax for the binary). Then you can update it by yourself with a
svn trunk version if you wish to.
Of course, it will install its own python2.6, which you might not want
to.
Hope it helps,
Cheers,
Olivier Serve
Le 23 févr. 2010 à 22:57, Edward d'Auvergne a écrit :
> 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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