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RE: [[cellml-dev] ] Mac OS X CellML API 1.12


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  • From: "Alan Garny" <alan.garny AT inria.fr>
  • To: <cellml-tools-developers AT lists.cellml.org>
  • Subject: RE: [[cellml-dev] ] Mac OS X CellML API 1.12
  • Date: Tue, 6 May 2014 09:42:47 +0200
  • Organization: INRIA
Hi Ivo,

David mentioned the use of the CellML API in OpenCOR, but FWIW OpenCOR
doesn't use all of the CellML API, only the bits that are relevant to
OpenCOR. Anyway, and just in case, here is some information on the CellML API
is built for use in OpenCOR:
https://github.com/opencor/opencor/tree/master/src/plugins/api/CellMLAPI.

HTH, Alan.

> -----Original Message-----
> From:
> cellml-tools-developers-request AT lists.cellml.org
> [mailto:cellml-tools-
> developers-request AT lists.cellml.org]
> On Behalf Of Ivo Siekmann
> Sent: 06 May 2014 02:47
> To:
> cellml-tools-developers AT lists.cellml.org
> Subject: Re: [[cellml-dev] ] Mac OS X CellML API 1.12
>
> Hi Andre,
>
> thanks a lot for your quick reply... I hope all is fine in Auckland!
> Sorry that I missed the bug tracker otherwise I'd have asked my question
> there.
> I'll have a look there and I'll try using the binaries from the various
> sources that
> you mentioned!
>
> Cheers from Melbourne,
> Ivo
>
> On 6/05/14 10:29 am, David Nickerson wrote:
> > Hi Ivo,
> >
> > See https://tracker.physiomeproject.org/show_bug.cgi?id=3673,
> > https://tracker.physiomeproject.org/show_bug.cgi?id=3671, and
> > https://tracker.physiomeproject.org/show_bug.cgi?id=3670 for some
> > recent tracker items regarding building the CellML API under OS X
> > 10.9.
> >
> > The upshot is that you should be able to build the current trunk code
> > (which has some fixes that are not in the 1.12 release, so I would
> > recommend using that), but you will not be able to build all the
> > tests. I have been able to build CellML2C (the code generation test)
> > but haven't tried the other test codes. I use clang for all
> > compilation/linking on OS X:
> > $ clang --version
> > Apple LLVM version 5.1 (clang-503.0.40) (based on LLVM 3.4svn)
> > Target: x86_64-apple-darwin13.1.0
> > Thread model: posix
> >
> > The 1.12 binaries should work - not sure why you're getting that
> > error. I know I have linked my own code agains the 1.12 binaries
> > (using clang), but generally use my own build of the current trunk
> > code nowadays.
> >
> > If needed, Alan Garny has the OpenCOR development environment all
> > nicely set up so you can probably extract the required binaries from
> > that source.
> >
> >
> > Cheers,
> > Andre.
> >
> > On Mon, May 5, 2014 at 5:12 PM, Ivo Siekmann
> > <ivo.siekmann AT unimelb.edu.au>
> > wrote:
> >> Hi CellMLers,
> >>
> >> I'm trying to get the CellML API running on Mac and I ran into some
> >> difficulties.
> >>
> >> 1) Compiling from source code:
> >> a) This fails with clang (Apple LLVM version 5.1 (clang-503.0.40)),
> >> apparently due to a forward declaration of the << operator in
> >> TestAssert.h when attempting to build DOMTEST.cpp.o (I don't know
> >> much about this but from some googling it seems to me that clang is
> >> stricter about the standard than some other compilers. So it may see
> >> errors where other compilers don't).
> >>
> >> b) Compiling with gcc 4.8.2 goes through and passes the tests of
> >> 'CheckCodeGenerator' and 'CheckVACSS' but fails for 'RunTestBin'. I
> >> didn't find out a lot more about how/why it failed.
> >>
> >> 2) Binaries:
> >> I've downloaded the binaries and Mac OS X complains that the package
> >> can't be opened "because it may be damaged or incomplete". Well, I
> >> can open the package and look at its contents, so it may be possible
> >> to link the libraries but I haven't tried.
> >>
> >> Any help would be greatly appreciated.
> >> Cheers
> >> Ivo


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