Your message dated Wed, 01 Jun 2022 16:49:06 +0000 with message-id <e1nwrws-0002wj...@fasolo.debian.org> and subject line Bug#1009079: fixed in mdtraj 1.9.7-4 has caused the Debian Bug report #1009079, regarding mdtraj: autopkgtest timeout on arm64 (downloading pdb file?) to be marked as done.
This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact ow...@bugs.debian.org immediately.) -- 1009079: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1009079 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Source: mdtraj Version: 1.9.7-2 Severity: important X-Debbugs-Cc: stu...@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
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--- Begin Message ---Source: mdtraj Source-Version: 1.9.7-4 Done: Drew Parsons <dpars...@debian.org> We believe that the bug you reported is fixed in the latest version of mdtraj, which is due to be installed in the Debian FTP archive. A summary of the changes between this version and the previous one is attached. Thank you for reporting the bug, which will now be closed. If you have further comments please address them to 1009...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Drew Parsons <dpars...@debian.org> (supplier of updated mdtraj package) (This message was generated automatically at their request; if you believe that there is a problem with it please contact the archive administrators by mailing ftpmas...@ftp-master.debian.org) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Wed, 01 Jun 2022 18:02:27 +0200 Source: mdtraj Architecture: source Version: 1.9.7-4 Distribution: unstable Urgency: medium Maintainer: Debichem Team <debichem-de...@lists.alioth.debian.org> Changed-By: Drew Parsons <dpars...@debian.org> Closes: 1009079 Changes: mdtraj (1.9.7-4) unstable; urgency=medium . * debian/tests: add Restrictions: needs-internet (test_examples.py pulls a random PDB sample file from www.rcsb.org) * debian patch test_increase_timeout.patch increases TIMEOUT to 180 sec in test_examples.py to allow for poor internet connections. Closes: #1009079. * Standards-Version: 4.6.1 Checksums-Sha1: 559f78858b471735fe17b263e63c3d3291b4a5d6 2597 mdtraj_1.9.7-4.dsc 3094912f23d87f6e99fa412f0161e0054569ff1d 299324 mdtraj_1.9.7-4.debian.tar.xz Checksums-Sha256: c0532349b037525293715448027ef200b15a3f6e1eb633478efeeff125c00f07 2597 mdtraj_1.9.7-4.dsc 1c1d4e8c1cb12f9d39ad26f092fd3130b7f8fe16cd8b816344a7e7699613c5df 299324 mdtraj_1.9.7-4.debian.tar.xz Files: 6d9979f167acfd2745e3b97702e96fa1 2597 python optional mdtraj_1.9.7-4.dsc c9b97788be223353f493d315cb85e19d 299324 python optional mdtraj_1.9.7-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCAAdFiEEI8mpPlhYGekSbQo2Vz7x5L1aAfoFAmKXkvoACgkQVz7x5L1a AfrwPw//afjm5QXTRHn9UgWUZxSfkNYJ3lrIV10I/5m119yBujo868Mtr5+I8bep iBl0iIf19kmiWZPxhmgjas9vLamtHAeZCfUeXgnv4lW9DgFewU2tb/pVWiPIYyFn w+c78dSqYXNwGZlfdNoSUtRDeiKjHWmPiTV5ncJdb5B41+DoIPUCg+F7wYU+3NfQ ci7w0QpQur6P39yzywm/XhDVlGjTQ8vyJm+d/L9rRy98dO7VV83j5jWbADDW72sE Li4uhFey1uAKDPIaKoOW8cP8I3U6T0x6kNX60ucxjwVu71xbEUFiM8FL94jTiAzB mpxQWfvBoP3AKz84D9AHDumjOEQYq/EHLkYU3WQXdeusKpfZcnG1vc8KcGR73Bu+ 9LDbs6cSFVZKpOTKTjQpfTHkP7gcNyQE01HUwot4gHM3NA3h3LMR+B/Ts4y2+2M/ w7jjQ9lG0o3hWSIX9p1ta59CfLjbD6e4i5XS5W8S4mjTlyRJ3Zd46fz84dS2Sibk VQoqmNyI9zqnbBvGrPUd5znQNk5b3/9Zq/HJp/NrBpSwJIhZkF6N7g8MenC1xtgO PrbT1PDJ+/ScNWerRBSOKvbr1WpoFvV43H5t2U8s4NwkXge2aeSuC/LkZ9ZK47MC UzbllT0Ec/IlzuRV6IHJr/Fs6SxbK/hxoQD7tTA5GuPVTDycR4o= =UUYE -----END PGP SIGNATURE-----
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