Hi, Do these changes fix the problem? For the INSTALL_PATH, I think we have to be careful here. You have changed it to the default fink installation path for its relax versions. But this is not where relax defaults to for non-fink installs. I'm not even sure this is used at all in this case? The change to RELAX_PATH should not be made as this breaks all relax installs and is not specific to Mac OS X - it changes the path for all operating systems. As for the -m32 C compiler flag, this could be quite dangerous to add as then 64-bit systems will fail. Is this flag necessary? I would guess that all these issues are due to 2 python versions being present on the system anyway so that these changes are not necessary. See my post at https://mail.gna.org/public/relax-users/2010-02/msg00009.html for more details.
Cheers, Edward On 22 February 2010 16:28, Sébastien Morin <[email protected]> wrote: > Hi, > > I forgot to mention something... > > It probably arises from fink, but there is a file called "sconstruct.orig". > The date goes back from my installation. This file is somewhat different > from the new "sconstruct" file: > > ==================== > diff -u sconstruct.orig sconstruct > --- sconstruct.orig 2009-08-12 13:52:35.000000000 -0400 > +++ sconstruct 2010-02-05 00:11:32.000000000 -0500 > @@ -98,7 +98,7 @@ > SYS = SYSTEM > > # Mac OS X installation path. > - INSTALL_PATH = sys.prefix + sep + 'local' > + INSTALL_PATH = '/sw' + sep + 'lib' > > > # All other operating systems. > @@ -115,16 +115,15 @@ > ############### > > # Relax installation directory. > -RELAX_PATH = INSTALL_PATH + sep + 'relax' > +RELAX_PATH = INSTALL_PATH + sep + 'relax-py26' > > # Installation path for binaries. > -BIN_PATH = INSTALL_PATH + sep + 'bin' > +BIN_PATH = '/sw' + sep + 'bin' > > # Symbolic link installation path. > SYMLINK = BIN_PATH + sep + 'relax' > > > - > # The distribution files. > ######################### > > @@ -485,7 +484,7 @@ > if SYSTEM == 'Windows': > cflags = '/nologo /I\"' + py_include_minpath + '\" /I\"' + > numpy_path + '\"' > else: > - cflags = '-I' + py_include_fullpath + ' -I' + numpy_path > + cflags = '-m32 -I' + py_include_fullpath + ' -I' + numpy_path > > # Relaxation curve fitting build environment. > env = Environment() > @@ -500,7 +499,7 @@ > > # Catch Mac OS X and send the correct command line options to the > linker (these may become redundant as SCons improves). > if env['PLATFORM'] == 'darwin': > - env.Append(LINKFLAGS = ['-bundle', '-bundle_loader', sys.prefix > + path.sep + 'bin' + path.sep + 'python', '-dynamic']) > + env.Append(LINKFLAGS = ['-m32', '-bundle', '-bundle_loader', > sys.prefix + path.sep + 'bin' + path.sep + 'python2.6', '-dynamic', > '-undefined', 'dynamic_lookup']) > env['SHLINKFLAGS'] = SCons.Util.CLVar('$LINKFLAGS') > > # Shared library prefix and suffix. > ==================== > > This (especially the "cflags" and "env" lines) might explain the compilation > problem..? > > > Séb > > > > On 10-02-22 10:23 AM, Sébastien Morin wrote: >> >> 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<[email protected]> >>> 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 [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
