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where can I find the crossguid version used ? #10
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Yes, we use an older version (around the 25th of August 2018). That did not yet use std::string_view, I believe this one should work: |
Thanks that seems to fix it. So basically I have to check in every folder of src/ to see the version ? |
The reason we remained at the older version for crossguid / zipper was that at the time we were not ready to use c++17. But i'll discuss with the team as to what can be done. |
that would be awesome thanks. And with nix, you would have a package available everywhere nix is available (ubuntu/arch etc). |
You should be able to compile COPASI with the new version of zipper and grossguid by removing the section: if (CMAKE_MAJOR_VERSION LESS 3 OR CMAKE_MINOR_VERSION LESS 1) in CMakeLists.txt. We keep it to enforce backwards compatibility as Frank said. |
Most linux distributions enforce the use of upstream libraries so using copasi-dependencies is to create a distrib package is out of question (I understand it can be useful for a windows build though).
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When encountering issues like that before, we added the cmake options:
to define the same types as your system lapack. I hope that would resolve it. I was wondering, since Fedora went through probably similar issues, maybe you could look at their build output: https://koji.fedoraproject.org/koji/buildinfo?buildID=1729885 |
I compile on OpenSuse Tumbleweed with lapack 3.9.0-1.1 without encountering the above issue. I also have lapack-devel 3.9.0-1.1 are you missing it? |
setting up DF2C_INTEGER didn't change a thing (I copied the fedora setup). Maybe the compiler is setup with more hardening than on opensuse. Commenting out the line fixes it
After that I get
according to src/libSBML/VERSION.txt it needs sbml 5.19.1 . I've cloned libsbml and yes the file exists but there is no tag for 5.19.1, just for 5.19.0. Thank you all for the prompt answers so far, it has been really helpful and makes me love the copasi community already ;) |
LibSBML does have a number of source archives, with a varying number of additional packages. It would seem you have installed one without the Layout Package. For example from the release page: https://sourceforge.net/projects/sbml/files/libsbml/5.19.0/stable/ if you installed the 'core' file, then you would have libSBML, but no packages. If you installed from |
Thanks I found the
I guess that's because my sbml is now too recent. This repo contains src/libSBML/VERSION.txt with 5.19.1 as a reference but where can I find the exact revision to use ? I am confused as to which source to look at : is the libsbml upstream in this repo, sourceforge or github ? Both libsbml and libnuml seem to build both static and dynamic libraries. Do you know if I can disable static libraries with |
Unfortunately the arrays package does define a duplicated symbol, that one has not been officially approved, so I would compile libSBML using the stable packages only ( LibSBML recently moved its code base from sf to github, however we placed the release binaries on sourceforge, as there were too many of different files built, so the github release page would have been overloaded. And yes, you can disable the static builds if you need via ( |
Thank you your recommendations solved both issues. Something I've noticed that troubles me is that I comple copasi rev 1db9373589ea1e1afc6a36759f7f363cfe84a838 (4.30), yet the CMake tells me
@shoops as you see I am using https://github.com/Reference-LAPACK/lapack/tree/v3.9.0 too. What version of Copasi are you compiling against ? And just for information here is my current copasi package (I've packaged dependencies too elsewhere):
with copasi.patch :
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In your configuration you used cmake to define: so this is where the issue comes from. So this one would appear to have to be as for the version, the actual version information is generated by the use of a script, in the source folder. So please invoke
in the source folder prior to building. We are close to releasing version 4.31 from the respective branch soonish so i would go with that one. (We are in the testing of the final snapshot). |
I am trying to package copasi for www.nixos.org. I've made good progress but I stumble on a libcrossguid error
using crossguid ca1bf4b810e2d188d04cb6286f957008ee1b7681 (from May 2019). I tried to look in this repo what version was used but had a hard time finding it.
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