Bug#1103579: coot: autopkgtest regression: ImportError

[Andrius Merkys]

Hi,

On 2025-04-19 14:09, Chris Hofstaedtler wrote:
> coot's autopkgtests fail with rdkit 202503.1-2:
> 
> https://ci.debian.net/packages/c/coot/testing/amd64/60162582/
> 
>   76s Traceback (most recent call last):
>   76s   File "<frozen runpy>", line 198, in _run_module_as_main
>   76s   File "<frozen runpy>", line 88, in _run_code
>   76s   File "/usr/lib/python3/dist-packages/coot/pyrogen.py", line 38,
> in <module>
>   76s     import pyrogen_swig as pysw # relies on above rdkit.Chem import
>   AllChem (but ideally should not)
>   76s     ^^^^^^^^^^^^^^^^^^^^^^^^^^^
>   76s   File "/usr/lib/python3/dist-packages/coot/pyrogen_swig.py", line
> 12, in <module>
>   76s     import _pyrogen_swig
>   76s ImportError:
> /usr/lib/x86_64-linux-gnu/coot/libcoot-lidia-core.so.0: undefined
> symbol: _ZN5RDKit6MolOps5addHsERKNS_5ROMolEbbPKSt6vectorIjSaIjEEb

coot/1.1.15+dfsg-1+b1 (in unstable) was a rebuild against 
rdkit/202503.1-2 (in unstable). coot/1.1.15+dfsg-1 (in testing) is built 
to work with rdkit/202409.6-2 (in testing). Mixing versions from stable 
and unstable results in autopkgtest failures. I do not know how to do 
this, but coot+rdkit has to migrate to testing together.

Best,
Andrius