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<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