Ah, right, now I remember. If there are any remaining failures in the 1.3 line, it would be useful to have these all identified :) Especially if someone has PowerPC Mac hardware as well. I would like to release relax-1.3.5 soon and it would be good to have a 100% pass of the test-suite on both architectures. Do you know what the Scientific python issue Sebastian is seeing could be about?
Cheers! Edward On 24 February 2010 15:30, Jack Howarth <[email protected]> wrote: > 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 >> > >> > > _______________________________________________ relax (http://nmr-relax.com) This is the relax-users mailing list [email protected] To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-users
