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
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