[Debichem-devel] Bug#1009079: mdtraj: autopkgtest timeout on arm64 (downloading pdb file?)

[Stuart Prescott]

Source: mdtraj
Version: 1.9.7-2
Severity: important
X-Debbugs-Cc: stuart at debian.org

Dear Maintainer,

The autopkgtest tets for mdtraj attempts to download a pdb file and then use
that in calculations. This is failing (either all the time or intermittently)
with a timeout:

https://ci.debian.net/data/autopkgtest/unstable/arm64/m/mdtraj/20581005/log.gz

           except Empty:
>               raise Exception(
                    'Timeout (%.1f) when executing the following %s cell: "%s"' %
                    (TIMEOUT, cell.cell_type, cell.source.strip()))
E               Exception: Timeout (60.0) when executing the following code cell: "# pull a random protein from the PDB
E               # (The unitcell info happens to be wrong)
E               traj = md.load_pdb('http://www.rcsb.org/pdb/files/2MI7.pdb')
E               
E               # just for example, use the first frame as the 'native' conformation
E               q = best_hummer_q(traj, traj[0])"

rscb.org is not fast to serve up the pdb files, but I'm not sure if that is
the cause, whether the download is failing entirely, or whether the computation
that follows is just slow.

If this is an isolated use of a single pdb file in the tests, perhaps the
Debian package could carry that pdb file as some test data and patch the test
to use the local file instead.

An internest using test should also be marked as "needs-internet".

regards
Stuart