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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

---

• [[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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