Your message dated Thu, 26 May 2022 11:05:13 +0000 with message-id <e1nubin-000ex0...@fasolo.debian.org> and subject line Bug#1009079: fixed in mdtraj 1.9.7-3.1 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
--- End Message ---
--- Begin Message ---Source: mdtraj Source-Version: 1.9.7-3.1 Done: Adrian Bunk <b...@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. Adrian Bunk <b...@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: SHA512 Format: 1.8 Date: Wed, 11 May 2022 23:49:37 +0300 Source: mdtraj Architecture: source Version: 1.9.7-3.1 Distribution: unstable Urgency: medium Maintainer: Debichem Team <debichem-de...@lists.alioth.debian.org> Changed-By: Adrian Bunk <b...@debian.org> Closes: 1009079 Changes: mdtraj (1.9.7-3.1) unstable; urgency=medium . * Non-maintainer upload. * debian/tests/control: Add Restrictions: needs-internet (Closes: #1009079) Checksums-Sha1: ec04c36652df3c0d11550c944a374772dd28ba68 2605 mdtraj_1.9.7-3.1.dsc d3cdd0818b7ce38af7ff367903faecc7d88eee20 298568 mdtraj_1.9.7-3.1.debian.tar.xz Checksums-Sha256: 359d1dda4050b265fa3c00baa9d229129843668a3ffb838de692f8e9cfc61f56 2605 mdtraj_1.9.7-3.1.dsc bdcdd99ca96c7c994f9cf94217c933a3c7ddbc6ebb7f2af93e7004f8d58cebfe 298568 mdtraj_1.9.7-3.1.debian.tar.xz Files: 762304962e2c2e5dec5474e970187ace 2605 python optional mdtraj_1.9.7-3.1.dsc be341981f22c83499e1f129ae54d58c4 298568 python optional mdtraj_1.9.7-3.1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEOvp1f6xuoR0v9F3wiNJCh6LYmLEFAmJ8L+AACgkQiNJCh6LY mLFcKg/8DkK1KBVtkDNycgt+8OM25GNpL7v2ODH8G6Ae74bSLYpDQrEe6+XgYRiI 2yHNvCEAC903d6mdNK4uLgFqFraMZ55d7At1v3mRUPxAWkgEhi7rC5Hx5U/JZQAQ 86miRXeB3GMvBB+HUMJerbaTfzVe2hfIAFbTSOyl4Pn0Sal645smdWm3cdadM06y F3nNXUJN+TaFnAsWjsI7dgH27bIEpMO5ci5tgxt+HSRiDM6kPDFPsl9f3S8UTS3t BKV4dXuqRhW5zwqUwvmI/ZrgGEqA7DT37u1GT3sL0qZ63t2a0tarsZwBZAWRqWCx olnVMCQUWQZsULh8IgdzjbOPQpg1UJOwvIBOFcJ7OrXJlnduuG4WCKgUy9dVGy26 j0l2vPPsJ7cKs9Pp07mPKsjPSEZTM/AHWV44jSMNDx0t3bjzjPhV/any2n9r/v58 rsfyswZd79hAarBJtdUzfuQCDLEbDKSa3H9cSIofUDSSPl5nuJWEBAgAj9OG0ikh oy99a0gSJG46OU9U66ZdPBHXP1Jd4RJu16bietdqyDdfeZDLvvrO5Nmkx8P1xKfb 5Uz8VeAJouQ+qdLorBm4bf6m2dt8lQ6H5s6HTVs7MDf0pKmVAbPn+jfE8UBhzzbr qSah8hv6Nve2nmxwjdhZNZ/Rdi3TdZwddCsf/gDzzi4lVRq+vMM= =bZt2 -----END PGP SIGNATURE-----
--- End Message ---
