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Hi Matthias,



I tried to build the CellML API by also enabling TeLICeMS and I can confirm
the build issue you are reporting. In fact, that issue is the direct result
of a warning generated before due to TeLICeMS/sources/TeLICeMParse.yy using
the now deprecated %name_prefix construct. Anyway, I have fixed it (see
here), as well as fixed a small warning issue (see here). So, get those
changes and you should be fine. (Note that sometimes I had to regenerate some
header files ‘by hand’ using: make CXX_HEADERS_FOR_INTERFACES).



Cheers, Alan.



On 19/10/2016, 16:41, "Matthias König"
<cellml-tools-developers-request AT lists.cellml.org
on behalf of
konigmatt AT googlemail.com>
wrote:



Thanks for the info.

I got the library build from the git repositoy with the subset of packages
enabled in your description.

Unfortunately, I also need

TELICEMS_LIB

for antimony.

So I installed the additional dependencies

- bison

- flex

and set

-DENABLE_TELICEMS



But than the build fails with


Scanning dependencies of target telicems
[ 78%] Building CXX object
CMakeFiles/telicems.dir/TeLICeMS/sources/TeLICeMSImpl.cpp.o
In file included from
/home/mkoenig/git/cellml-api/TeLICeMS/sources/TeLICeMSImpl.hxx:5:0,
from
/home/mkoenig/git/cellml-api/TeLICeMS/sources/TeLICeMSImpl.cpp:2:
/home/mkoenig/git/cellml-api/TeLICeMS/sources/TeLICeMService.hpp:9:29: fatal
error: IfaceTeLICeMS.hxx: No such file or directory
compilation terminated.
CMakeFiles/telicems.dir/build.make:78: recipe for target
'CMakeFiles/telicems.dir/TeLICeMS/sources/TeLICeMSImpl.cpp.o' failed
make[2]: *** [CMakeFiles/telicems.dir/TeLICeMS/sources/TeLICeMSImpl.cpp.o]
Error 1
CMakeFiles/Makefile2:441: recipe for target 'CMakeFiles/telicems.dir/all'
failed
make[1]: *** [CMakeFiles/telicems.dir/all] Error 2

What do I have to do to build with TELICEMS ?

M





On Wed, Oct 19, 2016 at 10:25 AM, Alan Garny
<alan.garny AT inria.fr>
wrote:

Hi Matthias/Lucian,



FWIW, I am using the CellML API on both Ubuntu 14.04 LTS and Ubuntu 16.04
LTS, and it’s all working fine. The binaries you mention are somewhat old and
a few things have since been fixed in the API (see here). This is the reason
I am building the CellML API myself. Note, however, that I am not building
all of the CellML API, just the bits that are needed by OpenCOR. Anyway, and
just in case it may help you (and maybe others), here is some information on
how I build the CellML API on Windows, Linux and macOS.



HTH, Alan.



On 19/10/2016, 10:05, "Matthias König"
<cellml-tools-developers-request AT lists.cellml.org
on behalf of
konigmatt AT googlemail.com>
wrote:



More information for the issue below.

Messages were rejected before



---------- Forwarded message ----------
From: SYMPA
<sympa AT lists.cellml.org>
Date: Wed, Oct 19, 2016 at 9:51 AM
Subject: cellml-tools-developers Message distribution failed: Authorization
denied
To:
konigmatt AT googlemail.com


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---------- Forwarded message ----------
From: "Matthias König"
<konigmatt AT googlemail.com>
To: Lucian Smith
<lucianoelsmitho AT gmail.com>
Cc: A list for the developers of CellML tools
<cellml-tools-developers AT cellml.org>
Date: Wed, 19 Oct 2016 09:50:56 +0200
Subject: Re: The CellML API on Ubuntu 16.04

I already tried to build the SDK from source but never could manage to make
this work (dependency nightmare). I have no idea what are the third party
dependencies are and there are so many of them.



For instance trying to just build the barbone SDK via
cmake -DCMAKE_RUNTIME_OUTPUT_DIRECTORY=${CELLML_BUILD} ../${API_VERSION}
make all

results in:


Scanning dependencies of target cellml
[ 1%] Building CXX object CMakeFiles/cellml.dir/sources/Utilities.cpp.o
In file included from
/home/mkoenig/tmp/cellml-api-1.13/sources/Utilities.cpp:1:0:
/home/mkoenig/tmp/cellml-api-1.13/sources/Utilities.hxx:41:26: fatal error:
Ifacexpcom.hxx: No such file or directory
compilation terminated.
CMakeFiles/cellml.dir/build.make:62: recipe for target
'CMakeFiles/cellml.dir/sources/Utilities.cpp.o' failed
make[2]: *** [CMakeFiles/cellml.dir/sources/Utilities.cpp.o] Error 1
CMakeFiles/Makefile2:1176: recipe for target 'CMakeFiles/cellml.dir/all'
failed

despite cmake-gui not showing any problems.

Looking at the SDK-build/lib directory suggests that there are around 50
library dependencies I somehow have to get installed for building.

I already fought to build the cellml SDK 2 years ago and gave up than. And
after 1h now I am at the same point.



In summary: It would be nice to have a SDK build which works on Ubuntu 16.04
or at least a way that one can build the SDK easily.





On Wed, Oct 19, 2016 at 8:35 AM, Matthias König
<konigmatt AT googlemail.com>
wrote:

Just for information:

I can reproduce this problem on all my Ubuntu 16.04 machines & in docker
images based on Ubuntu 16.04

I tried linking against 1.11, 1.12 and 1.13 from here

wget
https://sourceforge.net/projects/cellml-api/files/CellML-API-Nightly/1.12/20121031/linux-x86_64/${VERSION}.tar.bz2/download
wget
https://sourceforge.net/projects/cellml-api/files/CellML-API-Nightly/1.11/20120418/linux-x86_64/${VERSION}.tar.bz2/download
wget
https://sourceforge.net/projects/cellml-api/files/CellML-API-Nightly/1.13/20130716/linux-x86_64/${VERSION}.tar.bz2/download
but none of the SDK versions works on Ubuntu 16.04.

I have no problems in 14.04, but it is no longer supported . The current Long
term support version is 16.04 LTS and cellml SDK should work on it.

Matthias





On Tue, Oct 18, 2016 at 11:12 PM, Lucian Smith
<lucianoelsmitho AT gmail.com>
wrote:

So, it turns out that in Antimony, using the now-old CellML API, calls to the
CellML library error out with a SIGABRT if compiled on Ubuntu 16.04, but not
when compiled on Ubuntu 14.04. This is presumably an issue with the CellML
SDK.



While a new CellML library would certainly be nice, I'm unlikely to have the
time to update Antimony to use it any time soon, so if someone wouldn't mind
looking into creating a CellML SDK for these more recent versions of Ubuntu,
that'd be great.



SDKs for more recent versions of Visual Studio would also be nice, though I
haven't actually checked to see if they already exist ;-)



Thank you!



-Lucian




--

Matthias König
Junior Group Leader LiSym - Systems Medicine of the Liver
Humboldt-University Berlin, Institute for Theoretical Biology
https://www.livermetabolism.com
konigmatt AT googlemail.com
Tel: +49 30 20938450
Tel: +49 176 81168480




--

Matthias König
Junior Group Leader LiSym - Systems Medicine of the Liver
Humboldt-University Berlin, Institute for Theoretical Biology
https://www.livermetabolism.com
konigmatt AT googlemail.com
Tel: +49 30 20938450
Tel: +49 176 81168480






--

Matthias König
Junior Group Leader LiSym - Systems Medicine of the Liver
Humboldt-University Berlin, Institute for Theoretical Biology
https://www.livermetabolism.com
konigmatt AT googlemail.com
Tel: +49 30 20938450
Tel: +49 176 81168480




--

Matthias König
Junior Group Leader LiSym - Systems Medicine of the Liver
Humboldt-University Berlin, Institute for Theoretical Biology
https://www.livermetabolism.com
konigmatt AT googlemail.com
Tel: +49 30 20938450
Tel: +49 176 81168480

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• [[cellml-dev] ] Fwd: cellml-tools-developers Message distribution failed: Authorization denied, Matthias König, 10/19/2016
  • Re: [[cellml-dev] ] Fwd: cellml-tools-developers Message distribution failed: Authorization denied, Alan Garny, 10/19/2016
    • Re: [[cellml-dev] ] Fwd: cellml-tools-developers Message distribution failed: Authorization denied, Matthias König, 10/20/2016
      • Re: [[cellml-dev] ] Fwd: cellml-tools-developers Message distribution failed: Authorization denied, Alan Garny, 10/20/2016
        • Re: [[cellml-dev] ] Fwd: cellml-tools-developers Message distribution failed: Authorization denied, Matthias König, 10/20/2016
          • Re: [[cellml-dev] ] Fwd: cellml-tools-developers Message distribution failed: Authorization denied, Alan Garny, 10/21/2016
            • Re: [[cellml-dev] ] Fwd: cellml-tools-developers Message distribution failed: Authorization denied, Matthias König, 10/21/2016

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