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These are all things that *I* can do, and would work for my own
self-compiled programs. But Antimony itself is supposed to be a library,
to be compiled by others for use in their own programs. Ideally, it would
just drop in to whatever system they were already using libsbml or the
cellml api for, and would bring it only the new dependencies. But this
particular issue, if left unresolved, makes that impossible, and requires
particular versions of its dependent libraries.

If this turns out to literally be insoluable, I will have to just tell
people 'either don't use libsbml compiled with libxml, or don't use cellml
support at all', but sheesh. I would think there is a real solution out
there, and not merely a series of complicated workarounds. Since libsbml
manages to use libxml without spoiling it for use in libcellml, I would
think the reverse could be accomplished as well.

-Lucian

* Frank T. Bergmann <fbergman at caltech.edu> [2011-02-19 00:49] writes:
> The next thing to try then is to use static linking of libxml2 (perhaps
> using the CMake project files) for LibSBML if you really need libXML2 at
> this point.
>
> Frank
>
> On Feb 18, 2011, at 4:40 PM, Lucian Smith wrote:
>
> > And indeed, configuring lisbml with expat instead makes the problem go
> > away, as expected.
> >
> > This is a reasonable workaround for now, but I would still like to find a
> > more permanent solution.
> >
> > -Lucian
> >
> > * Frank T. Bergmann <fbergman at caltech.edu> [2011-02-19 00:18] writes:
> >> Perhaps you could try to configure libsbml to work with expat, or
> >> xerces-c.
> >> That will help you to narrow down your suspicion. If the crash persists
> >> then
> >> you know that it is not due to both libraries using libxml.
> >>
> >> Cheers
> >> Frank
> >>
> >>> -----Original Message-----
> >>> From: libsbml-team-bounces at caltech.edu [mailto:libsbml-team-
> >>> bounces at caltech.edu] On Behalf Of Lucian Smith
> >>> Sent: Friday, February 18, 2011 4:12 PM
> >>> To: A list for the developers of CellML tools
> >>> Cc: libSBML Team
> >>> Subject: [libsbml-team] Changing state in libxml
> >>>
> >>> When trying to code up a translator which would convert between CellML,
> >>> Antimony, and SBML, I ran into the following problem.
> >>>
> >>> Right now, I have libsbml configured to use libxml, the same XML parser
> >> that
> >>> CellML uses. I can read a document in with libsbml, and everything is
> >> fine. I
> >>> can then read a document with the CellML API, and everything is fine.
> >>> However, if I then read that same document with libsbml, I get a
> >>> segfault
> >>> error, and if I run it though valgrind, I'm actually getting an invalid
> >> read.
> >>>
> >>> Attached is a smallish program that demonstrates this issue. It seems
> >>> to
> >> me
> >>> that CellML is changing the state of libxml in some way, and this messes
> >> up the
> >>> subsequent libsbml call, causing the segfault.
> >>>
> >>> So my question is: how does CellML change the state of libxml, and how
> >>> do
> >> I
> >>> undo this? Or is there something else going on?
> >>>
> >>> -Lucian
> >>
> >>
>

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• [cellml-dev] Changing state in libxml, Lucian Smith, 02/19/2011
  • Message not available
    • [cellml-dev] [libsbml-team] Changing state in libxml, Lucian Smith, 02/19/2011
      • Message not available
        • [cellml-dev] [libsbml-team] Changing state in libxml, Lucian Smith, 02/19/2011

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