Hi, I don't think this is an issue, as the include directories should only contain *.h C header files. Can you find any *.h python files which are not in /sw/include/python2.6? The second include directory is just for the numpy *.h files.
Cheers, Edward 2009/8/17 Jack Howarth <[email protected]>: > 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 >> >>> >> > >> >>> > >> >> >> > > _______________________________________________ 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
