Edward,
I'll try these tonight as I don't have my laptop with me
today. I do notice that if I compare the linkage of the two
pythons....
[prrg4:~] howarth% otool -L /sw/bin/python2.5
/sw/bin/python2.5:
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current
version 111.1.3)
/usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version
1.0.0)
[prrg4:~] howarth% otool -L /sw/bin/python2.6
/sw/bin/python2.6:
/sw/lib/python2.6/config/libpython2.6.dylib (compatibility version
2.6.0, current version 2.6.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current
version 111.1.4)
/usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version
1.0.0)
It would appear that...
gcc -o maths_fns/relax_fit.so -bundle -bundle_loader /sw/bin/python2.6 -dynamic
maths_fns/c_chi2.os maths_fns/exponential.os maths_fns/relax_fit.os
...isn't picking up /sw/lib/python2.6/config/libpython2.6.dylib for linkage.
Jack
On Mon, Aug 17, 2009 at 06:34:33PM +0200, Edward d'Auvergne wrote:
> Hi,
>
> Does one of the following commands compile the module (with the
> test-suite passing as well)?
>
> $ gcc -o maths_fns/relax_fit.so /sw/bin/python2.6 maths_fns/c_chi2.os
> maths_fns/exponential.os maths_fns/relax_fit.os
> $ gcc -o maths_fns/relax_fit.so /sw/bin/python2.6 -dynamic
> maths_fns/c_chi2.os maths_fns/exponential.os maths_fns/relax_fit.os
> $ gcc -o maths_fns/relax_fit.so -bundle_loader /sw/bin/python2.6
> -dynamic maths_fns/c_chi2.os maths_fns/exponential.os
> maths_fns/relax_fit.os
> $ gcc -o maths_fns/relax_fit.so -bundle /sw/bin/python2.6 -dynamic
> maths_fns/c_chi2.os maths_fns/exponential.os maths_fns/relax_fit.os
> $ gcc -o maths_fns/relax_fit.so -module -bundle -bundle_loader
> /sw/bin/python2.6 maths_fns/c_chi2.os maths_fns/exponential.os
> maths_fns/relax_fit.os
> $ gcc -o maths_fns/relax_fit.so -module -bundle -bundle_loader
> /sw/bin/python2.6 -dynamic maths_fns/c_chi2.os
> maths_fns/exponential.os maths_fns/relax_fit.os
>
> Cheers,
>
> Edward
>
>
> 2009/8/17 Edward d'Auvergne <[email protected]>:
> > Hi,
> >
> > The way we can solve this issue is to first type the gcc linking
> > command by hand, rather than using scons. Then once all is
> > functional, I can fix the Scons script. Here is what Douglas Kojetin
> > did to make this work
> > (https://mail.gna.org/public/relax-devel/2006-11/msg00092.html), and
> > then I tailored the scons script to match. If you cut an past this
> > gcc command, can you compile the modules and run the system test
> > without failures? Also, once this is all functional, I would like to
> > get your changes (well, modified to be compatible with all other
> > operating systems) into the repository so that it is easier for you
> > next time.
> >
> > Cheers,
> >
> > Edward
> >
> >
> >
> > 2009/8/17 Jack Howarth <[email protected]>:
> >> Edward,
> >> I'll have to look into that as I'm not very familar with scons.
> >> Currently for 1.3.3, it is sufficient to use...
> >>
> >> --- relax-1.3.0.orig/relax 2007-02-19 00:36:06.000000000 -0500
> >> +++ relax-1.3.0/relax 2008-08-11 02:13:30.000000000 -0400
> >> @@ -1,4 +1,4 @@
> >> -#! /usr/bin/env python
> >> +#! /usr/bin/env python2.X
> >>
> >> ###############################################################################
> >> #
> >> #
> >> --- relax-1.3.0/scons/install.py.sav 2008-08-10 15:31:01.000000000 -0400
> >> +++ relax-1.3.0/scons/install.py 2008-08-10 16:01:22.000000000 -0400
> >> @@ -112,8 +112,8 @@
> >> ###############
> >>
> >> # Run relax to create the *.pyc files.
> >> - print "\nRunning relax to create the byte-compiled *.pyc files."
> >> - system(env['SYMLINK'] + " --test")
> >> + # print "\nRunning relax to create the byte-compiled *.pyc files."
> >> + # system(env['SYMLINK'] + " --test")
> >>
> >> # Final print out.
> >> print "\n\n\n"
> >> --- relax-1.3.0.orig/sconstruct 2007-02-19 00:36:06.000000000 -0500
> >> +++ relax-1.3.0/sconstruct 2008-08-11 02:02:56.000000000 -0400
> >> @@ -94,7 +94,7 @@
> >> SYS = SYSTEM
> >>
> >> # Mac OS X installation path.
> >> - INSTALL_PATH = sys.prefix + sep + 'local'
> >> + INSTALL_PATH = 'FINK_INSTALL_DIR' + sep + 'lib'
> >>
> >>
> >> # All other operating systems.
> >> @@ -111,16 +111,15 @@
> >> ###############
> >>
> >> # Relax installation directory.
> >> -RELAX_PATH = INSTALL_PATH + sep + 'relax'
> >> +RELAX_PATH = INSTALL_PATH + sep + 'relax-py2X'
> >>
> >> # Installation path for binaries.
> >> -BIN_PATH = INSTALL_PATH + sep + 'bin'
> >> +BIN_PATH = 'FINK_INSTALL_DIR' + sep + 'bin'
> >>
> >> # Symbolic link installation path.
> >> SYMLINK = BIN_PATH + sep + 'relax'
> >>
> >>
> >> -
> >> # The distribution files.
> >> #########################
> >>
> >> @@ -486,7 +485,7 @@
> >>
> >> # 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 = ['-bundle', '-bundle_loader',
> >> sys.prefix + path.sep + 'bin' + path.sep + 'python2.X', '-dynamic'])
> >> env['SHLINKFLAGS'] = SCons.Util.CLVar('$LINKFLAGS')
> >> env['SHLIBSUFFIX'] = '.so'
> >>
> >>
> >> to build against the fink python24 and python25 packages.
> >> Jack
> >>
> >> On Mon, Aug 17, 2009 at 03:55:06PM +0200, Edward d'Auvergne wrote:
> >>> Hi,
> >>>
> >>> It could be, that Python 2.6 dynamically linked libraries are now
> >>> compiled differently to earlier Python versions. I'll have to look
> >>> that up as well. Would you know the linker options now required?
> >>>
> >>> Cheers,
> >>>
> >>> Edward
> >>>
> >>>
> >>> 2009/8/17 Jack Howarth <[email protected]>:
> >>> > Edward,
> >>> > I think I see the problem. The link line is missing a linkage on
> >>> > either
> >>> > /sw/lib/python2.6/config/libpython2.6.a or
> >>> > /sw/lib/python2.6/config/libpython2.6,dylib.
> >>> > What do you have for the linkage of maths_fns/relax_fit.so on linux?
> >>> > Does
> >>> > that build explicitly link in the python library?
> >>> > Jack
> >>> >
> >>> >
> >>> > On Mon, Aug 17, 2009 at 11:50:10AM +0200, Edward d'Auvergne wrote:
> >>> >> Hi,
> >>> >>
> >>> >> Thank you for building these packages (or at least attempting for now
> >>> >> ;). I'm still looking into the problem, but it's looking like the
> >>> >> Python header files are missing or are from an old version. Do you
> >>> >> know if this could be the issue, that the Python development packages
> >>> >> are out of date or are missing?
> >>> >>
> >>> >> Cheers,
> >>> >>
> >>> >> Edward
> >>> >>
> >>> >>
> >>> >>
> >>> >> On Sun, Aug 16, 2009 at 4:08 AM, Jack
> >>> >> Howarth<[email protected]> wrote:
> >>> >> > Edward,
> >>> >> > I am trying to build updated relax-py packaging
> >>> >> > for fink using the 1.3.4 release on x86_64 fink
> >>> >> > with python2.6. Although your web page indicates
> >>> >> > that the binaries available are built against
> >>> >> > python 2.5 and 2.6, I am seeing build failures
> >>> >> > when I try here with scons 1.2.0...
> >>> >> >
> >>> >> > /sw/bin/python2.6 /sw/bin/scons
> >>> >> > scons: Reading SConscript files ...
> >>> >> > scons: done reading SConscript files.
> >>> >> > scons: Building targets ...
> >>> >> >
> >>> >> >
> >>> >> >
> >>> >> >
> >>> >> > ###########################
> >>> >> > # Compiling the C modules #
> >>> >> > ###########################
> >>> >> >
> >>> >> >
> >>> >> > Building the relaxation curve fitting module 'maths_fns/relax_fit.so'
> >>> >> >
> >>> >> > gcc -o maths_fns/c_chi2.os -c -I/sw/include/python2.6
> >>> >> > -I/sw/lib/python2.6/site-packages/numpy/core/include -fPIC
> >>> >> > maths_fns/c_chi2.c
> >>> >> > gcc -o maths_fns/exponential.os -c -I/sw/include/python2.6
> >>> >> > -I/sw/lib/python2.6/site-packages/numpy/core/include -fPIC
> >>> >> > maths_fns/exponential.c
> >>> >> > gcc -o maths_fns/relax_fit.os -c -I/sw/include/python2.6
> >>> >> > -I/sw/lib/python2.6/site-packages/numpy/core/include -fPIC
> >>> >> > maths_fns/relax_fit.c
> >>> >> > gcc -o maths_fns/relax_fit.so -bundle -bundle_loader
> >>> >> > /sw/bin/python2.6 -dynamic maths_fns/c_chi2.os
> >>> >> > maths_fns/exponential.os maths_fns/relax_fit.os
> >>> >> > Undefined symbols:
> >>> >> > "_PyArg_ParseTupleAndKeywords", referenced from:
> >>> >> > _setup in relax_fit.os
> >>> >> > "_PyErr_Print", referenced from:
> >>> >> > _initrelax_fit in relax_fit.os
> >>> >> > "_Py_InitModule4_64", referenced from:
> >>> >> > _initrelax_fit in relax_fit.os
> >>> >> > "_PyArg_ParseTuple", referenced from:
> >>> >> > _func in relax_fit.os
> >>> >> > _dfunc in relax_fit.os
> >>> >> > "_PyExc_RuntimeError", referenced from:
> >>> >> > __import_array in exponential.os
> >>> >> > __import_array in exponential.os
> >>> >> > __import_array in exponential.os
> >>> >> > __import_array in relax_fit.os
> >>> >> > __import_array in relax_fit.os
> >>> >> > __import_array in relax_fit.os
> >>> >> > "_PyList_New", referenced from:
> >>> >> > _back_calc_I in relax_fit.os
> >>> >> > "__Py_NoneStruct", referenced from:
> >>> >> > _setup in relax_fit.os
> >>> >> > _setup in relax_fit.os
> >>> >> > _setup in relax_fit.os
> >>> >> > "_PyExc_ImportError", referenced from:
> >>> >> > _initrelax_fit in relax_fit.os
> >>> >> > "_PyCObject_AsVoidPtr", referenced from:
> >>> >> > __import_array in exponential.os
> >>> >> > __import_array in relax_fit.os
> >>> >> > "_PyCObject_Type", referenced from:
> >>> >> > __import_array in exponential.os
> >>> >> > __import_array in relax_fit.os
> >>> >> > "_PyImport_ImportModule", referenced from:
> >>> >> > __import_array in exponential.os
> >>> >> > __import_array in relax_fit.os
> >>> >> > "_PyErr_SetString", referenced from:
> >>> >> > _initrelax_fit in relax_fit.os
> >>> >> > "_PyErr_Format", referenced from:
> >>> >> > __import_array in exponential.os
> >>> >> > __import_array in exponential.os
> >>> >> > __import_array in exponential.os
> >>> >> > __import_array in relax_fit.os
> >>> >> > __import_array in relax_fit.os
> >>> >> > __import_array in relax_fit.os
> >>> >> > "_PyList_SetItem", referenced from:
> >>> >> > _back_calc_I in relax_fit.os
> >>> >> > "_PyObject_GetAttrString", referenced from:
> >>> >> > __import_array in exponential.os
> >>> >> > __import_array in relax_fit.os
> >>> >> > "_Py_BuildValue", referenced from:
> >>> >> > _func in relax_fit.os
> >>> >> > _d2func in relax_fit.os
> >>> >> > _back_calc_I in relax_fit.os
> >>> >> > ld: symbol(s) not found
> >>> >> >
> >>> >> > Is the 1.3.4 release really python2.6 compatible or do I need
> >>> >> > additional
> >>> >> > patches? Thanks in advance for any information.
> >>> >> > Jack
> >>> >> > ps I am updating the minfx-py package to the newer 1.0.2 release of
> >>> >> > course for the python 2.6 compatibility changes.
> >>> >> >
> >>> >> > _______________________________________________
> >>> >> > 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
> >>> >> >
> >>> >
> >>
> >
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