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Hi Ben,

I just tried to install libsbml-2.3-2 on Mac OS X 10.3 and upon
installing the python bindings, I got the following error message:

cp libsbml.py build/libsbml
/sw/bin/python setup.py install --skip-build
--prefix=/sw/apps/libsbml-2.3.2
running install
error: $MACOSX_DEPLOYMENT_TARGET mismatch: now "" but "10.3" during
configure
make[3]: *** [install] Error 1
make[3]: Leaving directory
`/Users/ralph/Download/libsbml-2.3.2/src/bindings/python'
make[2]: *** [python-recursive] Error 2
make[2]: Leaving directory
`/Users/ralph/Download/libsbml-2.3.2/src/bindings'
make[1]: *** [bindings-recursive] Error 2
make[1]: Leaving directory `/Users/ralph/Download/libsbml-2.3.2/src'
make: *** [src-recursive] Error 2


This happens when I use a fink installed version of python. If I try it
with the python that comes with OS X, get get a list of undefined
symbols.

g++
-L/System/Library/Frameworks/Python.framework/Versions/2.3/lib/
python2.3/lib-dynload -bundle_loader /usr//bin/python -L/sw//lib
-bundle -o _libsbml.so libsbml_wrap.o -L../.. -lsbml -lexpat -lm
ld: Undefined symbols:
_PyArg_ParseTuple
_PyCFunction_Type
_PyCObject_FromVoidPtr
_PyCObject_Import
_PyDict_SetItemString
_PyErr_Clear
_PyErr_Fetch
_PyErr_Format
_PyErr_Occurred
_PyErr_SetString
_PyExc_NameError
_PyExc_NotImplementedError
_PyExc_OverflowError
_PyExc_TypeError
_PyFloat_FromDouble
_PyFloat_Type
_PyInt_FromLong
_PyInt_Type
_PyLong_AsDouble
_PyLong_AsLong
_PyLong_AsUnsignedLong
_PyLong_FromUnsignedLong
_PyLong_Type
_PyModule_AddObject
_PyModule_GetDict
_PyOS_snprintf
_PyObject_CallObject
_PyObject_Free
_PyObject_GetAttr
_PyObject_Init
_PyObject_Malloc
_PyObject_SetAttrString
_PyObject_Size
_PyObject_Str
_PyString_AsString
_PyString_FromFormat
_PyString_FromString
_PyString_FromStringAndSize
_PyString_Type
_PyTuple_GetItem
_PyType_IsSubtype
_PyType_Type
_Py_BuildValue
_Py_InitModule4
__Py_NoneStruct
__Py_TrueStruct
__Py_ZeroStruct
make[3]: *** [_libsbml.so] Error 1
make[3]: Leaving directory
`/Users/ralph/Download/libsbml-2.3.2/src/bindings/python'
make[2]: *** [python-recursive] Error 2
make[2]: Leaving directory
`/Users/ralph/Download/libsbml-2.3.2/src/bindings'
make[1]: *** [bindings-recursive] Error 2
make[1]: Leaving directory `/Users/ralph/Download/libsbml-2.3.2/src'


Has anyone sucessfully installed the python bindings on Mac OS X?

Thanks

Ralph

I had the same list of missing symbols when I tried to build the
previous libSBML on Mac. You should have the details in a separate
note.

-Ed


On Thu, Jun 02, 2005 at 08:45:18AM -0700, Ben Bornstein wrote:
> Hi Ralph,
>
> I tested the installation of the Python bindings on my Mac last night
> before the release and all went well. I'm running Mac OS X 10.3.9 with
> Python 2.3.4 built from source and installed in /usr/local.
>
> Can someone else test the Python bindings under Mac and report back?
>
> Thanks.
>
> Ben
>
>
> On Jun 2, 2005, at 8:05 AM, Ralph Gauges wrote:
>
> >I just tried to install libsbml-2.3-2 on Mac OS X 10.3 and upon
> >installing the python bindings, I got the following error message:
> >
> >Has anyone sucessfully installed the python bindings on Mac OS X?
>

--
Ed Frank 630-252-4548 (-5986, fax)
Division of Math & Computer Science Argonne National Laboratory

Hi Ralph, Ed,

Ralph, thanks for the fix. Mike and/or I will look into this further.

Ed, thanks for the reminder. Unfortunately, your original message is
probably caught in my (now small) post-Hackathon backlog. Let me know
if Ralph's workaround doesn't work for some reason.

Ben


On Jun 2, 2005, at 9:45 AM, Ralph Gauges wrote:

> I could solve the missing symbols problem by adding -framework python
> to the LD_FLAGS in the Makefile. No clue why they are missing. I also
> have no clue, why the distutils from python won't work with this
> release, never had a problem before.


On Jun 2, 2005, at 9:08 AM, Ed Frank wrote:

> I had the same list of missing symbols when I tried to build the
> previous libSBML on Mac. You should have the details in a separate
> note.

Hi Mike,

For the Mac OS X python, my configure command line was:

./configure --prefix=/sw/apps/libsbml-2.3.2 --enable-layout --with-java
--with-swig=/sw/apps/swig-1.3.24/ --with-expat=/sw/ --with-python=/usr/

I also tried

./configure --prefix=/sw/apps/libsbml-2.3.2 --enable-layout --with-java
--with-swig=/sw/apps/swig-1.3.24/ --with-expat=/sw/
--with-python=/System/Library/Frameworks/Python.framework/Versions/
Current/

with the same result. The -framework option was not added to the linker
flags and I got the missing symbols again.

I will try the whole thing on another Mac later on. I will let you know
if I have the same problems on the other machine.

Ralph


On 02.06.2005, at 21:54, Michael Hucka wrote:

>>>>>> On 2 Jun 2005, Ralph Gauges <ralph.gauges@eml-r.villa-bosch.de>
>>>>>> wrote:
> RG> I could solve the missing symbols problem by adding
> RG> -framework python to the LD_FLAGS in the Makefile. No
> RG> clue why they are missing. I also have no clue, why
> RG> the distutils from python won't work with this
> RG> release, never had a problem before.
>
> Hi Ralph,
>
> The -framework argument is automatically added by the
> configure command (the specific code is in config/python.m4)
> when it detects that the user is configuring on a darwin
> system and using a python executable located in /usr/bin.
>
> What was your configuration command line?
>
> Like Ben, I test the installation on a Mac (OS 10.3.9 with
> Fink python 2.3.3 in my case) and have not experienced this,
> but I have to admit my testing of different configurations
> is not at all extensive.
>
> MH
>
>

Yes, you are right. If I don't specify a path for the python binary and
the Mac OS X one is the default, it actually works.

Ralph


On 03.06.2005, at 09:06, Michael Hucka wrote:

> RG> ./configure --prefix=/sw/apps/libsbml-2.3.2
> RG> --enable-layout --with-java
> RG> --with-swig=/sw/apps/swig-1.3.24/ --with-expat=/sw/
> RG> --with-python=/usr/
>
> Hi Ralph,
>
> That looks like it ought to work. Have you tried
> using --with-python *without* giving a path? If your path
> is such that the fink version of python is gotten first
> (e.g., if you type "which python" and you get something in
> /sw), could you try temporarily changing your command search
> path such that it does not search /sw/bin ahead of /usr/bin?
> I'm wondering whether --with-python without any path
> arguments will work for you when it finds the MacOS python.
>
> MH
>
>

Hello,

Some answers finally to an old problem on MacOSX.

Ralph, you reported problems with installing on MacOSX
10.3. These turn out to be 2 separate problems.

Problem #1
----------

>>>>> On 2 Jun 2005, Ralph Gauges <ralph.gauges@eml-r.villa-bosch.de> wrote:
RG> Hi Ben, I just tried to install libsbml-2.3-2 on Mac
RG> OS X 10.3 and upon installing the python bindings, I
RG> got the following error message:
RG>
RG> cp libsbml.py build/libsbml /sw/bin/python setup.py
RG> install --skip-build --prefix=/sw/apps/libsbml-2.3.2
RG> running install error: $MACOSX_DEPLOYMENT_TARGET
RG> mismatch: now "" but "10.3" during configure make[3]:

This MACOSX_DEPLOYMENT_TARGET thing is actually due to a bug
in the MacOSX Python Distutils prior to versions 2.3.5 and
2.4.1. See item #5.7 at

http://www.pythonmac.org/wiki/FAQ

Now, the curious thing is: why was this happening to you,
when your command above references the Fink version of
python in /sw/bin and not the Apple version in /usr/bin? My
guess is that your shell's command $path was set to search
/usr/bin before /sw/bin, and somewhere in the commands
invoked by python setup.py during the 'make install'
process, it's calling "python" without an explicit path and
getting /usr/bin/python instead of /sw/bin/python. This
might explain why you're getting this error about
MACOSX_DEPLOYMENT_TARGET, an error that shouldn't occur if
everything was invoking the non-Apple /sw version of python.

But, the above is pure speculation, because I can't seem to
reproduce the problem locally even if I fiddle with $path
settings and so on. If you are still experiencing the
problem, then please refer to the document above (the Python
wiki) points to a patch for the 10.3 (Panther) version of
Python 2.3.0 that is supposed to address some of the
installation issues. Could you try that, and see if it
resolves the MACOSX_DEPLOYMENT_TARGET error?

Problem #2
----------

RG> If I try it with the python that comes with OS
RG> X, I get a list of undefined symbols.

This was due to a deficiency in config/python.m4; it failed
to recognize the use of --with-python=/System/Library/...
as invoking the Apple version of python. I've checked a fix
into CVS, and it'll be in the next libsbml release.

Sorry about the trouble caused by this. This looks like it
hit several people. Hopefully it's fixed, but I'm very
interested to hear if it's not. If you and others can try
the newly CVS'ed copies of the files in libsbml/config, I'd
appreciate hearing back how it goes.

MH

>>>>> On 2 Jun 2005, Ralph Gauges <ralph.gauges@eml-r.villa-bosch.de> wrote:
RG> Hi Ben, I just tried to install libsbml-2.3-2 on Mac
RG> OS X 10.3 and upon installing the python bindings, I
RG> got the following error message:
RG>
RG> cp libsbml.py build/libsbml /sw/bin/python setup.py
RG> install --skip-build --prefix=/sw/apps/libsbml-2.3.2
RG> running install error: $MACOSX_DEPLOYMENT_TARGET
RG> mismatch: now "" but "10.3" during configure make[3]:
RG> *** [install] Error 1 make[3]: Leaving directory
RG> `/Users/ralph/Download/libsbml-2.3.2/src/bindings/python'
RG> make[2]: *** [python-recursive] Error 2 make[2]:
RG> Leaving directory
RG> `/Users/ralph/Download/libsbml-2.3.2/src/bindings'
RG> make[1]: *** [bindings-recursive] Error 2 make[1]:
RG> Leaving directory
RG> `/Users/ralph/Download/libsbml-2.3.2/src' make: ***
RG> [src-recursive] Error 2
RG>
RG>
RG> This happens when I use a fink installed version of
RG> python. If I try it with the python that comes with OS
RG> X, get get a list of undefined symbols.
RG>
RG> g++
RG> -L/System/Library/Frameworks/Python.framework/Versions/2.3/lib/
RG> python2.3/lib-dynload -bundle_loader /usr//bin/python
RG> -L/sw//lib -bundle -o _libsbml.so libsbml_wrap.o
RG> -L../.. -lsbml -lexpat -lm ld: Undefined symbols:
RG> _PyArg_ParseTuple _PyCFunction_Type
RG> _PyCObject_FromVoidPtr _PyCObject_Import
RG> _PyDict_SetItemString _PyErr_Clear _PyErr_Fetch
RG> _PyErr_Format _PyErr_Occurred _PyErr_SetString
RG> _PyExc_NameError _PyExc_NotImplementedError
RG> _PyExc_OverflowError _PyExc_TypeError
RG> _PyFloat_FromDouble _PyFloat_Type _PyInt_FromLong
RG> _PyInt_Type _PyLong_AsDouble _PyLong_AsLong
RG> _PyLong_AsUnsignedLong _PyLong_FromUnsignedLong
RG> _PyLong_Type _PyModule_AddObject _PyModule_GetDict
RG> _PyOS_snprintf _PyObject_CallObject _PyObject_Free
RG> _PyObject_GetAttr _PyObject_Init _PyObject_Malloc
RG> _PyObject_SetAttrString _PyObject_Size _PyObject_Str
RG> _PyString_AsString _PyString_FromFormat
RG> _PyString_FromString _PyString_FromStringAndSize
RG> _PyString_Type _PyTuple_GetItem _PyType_IsSubtype
RG> _PyType_Type _Py_BuildValue _Py_InitModule4
RG> __Py_NoneStruct __Py_TrueStruct __Py_ZeroStruct
RG> make[3]: *** [_libsbml.so] Error 1 make[3]: Leaving
RG> directory
RG> `/Users/ralph/Download/libsbml-2.3.2/src/bindings/python'
RG> make[2]: *** [python-recursive] Error 2 make[2]:
RG> Leaving directory
RG> `/Users/ralph/Download/libsbml-2.3.2/src/bindings'
RG> make[1]: *** [bindings-recursive] Error 2 make[1]:
RG> Leaving directory
RG> `/Users/ralph/Download/libsbml-2.3.2/src'
RG>
RG>
RG> Has anyone sucessfully installed the python bindings
RG> on Mac OS X?
RG>
RG> Thanks
RG>
RG> Ralph
RG>