Hi Ed, Please see below...
On 10-02-22 2:49 AM, Edward d'Auvergne wrote: > Hi, > > See below: > > > On 21 February 2010 20:59, Sébastien Morin<sebastien.mori...@ulaval.ca> > 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. > > In fact, if the link is not present, relax complains about minfx not being installed... > >> 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. > > > Ok... >> 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...) > > >> 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 ! Séb > 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 relax-users@gna.org 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
