From noreply at release.debian.org Thu Jul 3 05:39:09 2025 From: noreply at release.debian.org (Debian testing autoremoval watch) Date: Thu, 03 Jul 2025 04:39:09 +0000 Subject: [Debichem-devel] mdanalysis is marked for autoremoval from testing Message-ID: mdanalysis 2.9.0-8 is marked for autoremoval from testing on 2025-08-07 It is affected by these RC bugs: 1108309: mdanalysis: FTBFS randomly: autobuilder hangs https://bugs.debian.org/1108309 It (build-)depends on packages with these RC bugs: 1108255: rdflib: autopkgtest regression in testing https://bugs.debian.org/1108255 For more information on the autoremoval process, including hints to prevent autoremoval can be found on the wiki: https://wiki.debian.org/Autoremoval This mail is generated by: https://salsa.debian.org/release-team/release-tools/-/blob/master/mailer/mail_autoremovals.pl Autoremoval data is generated by: https://salsa.debian.org/qa/udd/-/blob/master/udd/testing_autoremovals_gatherer.pl From noreply at release.debian.org Thu Jul 3 05:39:18 2025 From: noreply at release.debian.org (Debian testing autoremoval watch) Date: Thu, 03 Jul 2025 04:39:18 +0000 Subject: [Debichem-devel] python-mp-api is marked for autoremoval from testing Message-ID: python-mp-api 0.45.3-4 is marked for autoremoval from testing on 2025-08-07 It (build-)depends on packages with these RC bugs: 1108255: rdflib: autopkgtest regression in testing https://bugs.debian.org/1108255 1108309: mdanalysis: FTBFS randomly: autobuilder hangs https://bugs.debian.org/1108309 For more information on the autoremoval process, including hints to prevent autoremoval can be found on the wiki: https://wiki.debian.org/Autoremoval This mail is generated by: https://salsa.debian.org/release-team/release-tools/-/blob/master/mailer/mail_autoremovals.pl Autoremoval data is generated by: https://salsa.debian.org/qa/udd/-/blob/master/udd/testing_autoremovals_gatherer.pl From noreply at release.debian.org Thu Jul 3 05:39:18 2025 From: noreply at release.debian.org (Debian testing autoremoval watch) Date: Thu, 03 Jul 2025 04:39:18 +0000 Subject: [Debichem-devel] python-emmet-core is marked for autoremoval from testing Message-ID: python-emmet-core 0.84.2-2 is marked for autoremoval from testing on 2025-08-07 It (build-)depends on packages with these RC bugs: 1108255: rdflib: autopkgtest regression in testing https://bugs.debian.org/1108255 1108309: mdanalysis: FTBFS randomly: autobuilder hangs https://bugs.debian.org/1108309 For more information on the autoremoval process, including hints to prevent autoremoval can be found on the wiki: https://wiki.debian.org/Autoremoval This mail is generated by: https://salsa.debian.org/release-team/release-tools/-/blob/master/mailer/mail_autoremovals.pl Autoremoval data is generated by: https://salsa.debian.org/qa/udd/-/blob/master/udd/testing_autoremovals_gatherer.pl From dparsons at debian.org Thu Jul 3 13:08:59 2025 From: dparsons at debian.org (Drew Parsons) Date: Thu, 03 Jul 2025 14:08:59 +0200 Subject: [Debichem-devel] Bug#1108309: mdanalysis: FTBFS randomly: autobuilder hangs References: Message-ID: <175154453913.1039254.8169045833828121247.reportbug@sandy> Source: mdanalysis Followup-For: Bug #1108309 Control: tags -1 ftbfs Yeah, mdanalysis is generally flakey. Not a whole lot we can do about it except run the tests again till they pass, or keep skipping tests until the probability of failure is sufficiently reduced. From owner at bugs.debian.org Thu Jul 3 13:11:02 2025 From: owner at bugs.debian.org (Debian Bug Tracking System) Date: Thu, 03 Jul 2025 12:11:02 +0000 Subject: [Debichem-devel] Processed: Re: mdanalysis: FTBFS randomly: autobuilder hangs References: <175154453913.1039254.8169045833828121247.reportbug@sandy> Message-ID: Processing control commands: > tags -1 ftbfs Bug #1108309 [src:mdanalysis] mdanalysis: FTBFS randomly: autobuilder hangs Ignoring request to alter tags of bug #1108309 to the same tags previously set -- 1108309: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1108309 Debian Bug Tracking System Contact owner at bugs.debian.org with problems From zeha at debian.org Thu Jul 3 16:08:51 2025 From: zeha at debian.org (Chris Hofstaedtler) Date: Thu, 3 Jul 2025 17:08:51 +0200 Subject: [Debichem-devel] Bug#1014740: Bug#1014740: pdb-tools: mangled manual pages: errors, duplicate text In-Reply-To: <440d7acb26c894a5f7d4b500b5513cc2ff007508.camel@debian.org> References: <440d7acb26c894a5f7d4b500b5513cc2ff007508.camel@debian.org> Message-ID: user reproducible-builds at lists.alioth.debian.org usertag -1 + randomness thanks Hi, On Tue, Jul 12, 2022 at 09:42:47PM +0800, Paul Wise wrote: > On Tue, 2022-07-12 at 13:36 +0300, Andrius Merkys wrote: > > > This was caused by '--version' option not being supported by some of the > > programs. Fixed in 2.5.0-2 upload. > > Looks like there are some more errors for --help, see this command: > > $?zgrep -iE -- '-help|not valid' /usr/share/man/man1/pdb_*.1.gz > > Also a lot of the manual pages are even more broken now, some of them > contain just an error message from the program and no help text but > that help text was present in the 2.5.0-1 upload. I used diffoscope to > compare the 2.5.0-1 and 2.5.0-2 binaries to notice this. The builds also do not seem deterministic now. Rebuilds on reproduce.debian.net show such a diff: ??? data.tar.xz ? ??? data.tar ? ? ??? ./usr/share/man/man1/pdb_wc.1.gz ? ? ? ??? pdb_wc.1 ? ? ? ? @@ -1,6 +1,6 @@ ? ? ? ? .\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.49.3. ? ? ? ? .TH PDB_WC "1" "September 2024" "pdb_wc 2.5.1" "User Commands" ? ? ? ? .SH NAME ? ? ? ? pdb_wc \- manual page for pdb_wc 2.5.1 ? ? ? ? .SH DESCRIPTION ? ? ? ? -pdb_wc The following options are not valid: 'pel\-' ? ? ? ? +pdb_wc The following options are not valid: 'epl\-' I don't quite understand what goes wrong with sed et al, but that seems bad. Please either fix it or if the manpages are useless anyway, drop help2man? Chris From ftpmaster at ftp-master.debian.org Fri Jul 4 09:39:30 2025 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Fri, 04 Jul 2025 08:39:30 +0000 Subject: [Debichem-devel] Processing of mdanalysis_2.9.0-9_source.changes Message-ID: mdanalysis_2.9.0-9_source.changes uploaded successfully to localhost along with the files: mdanalysis_2.9.0-9.dsc mdanalysis_2.9.0-9.debian.tar.xz mdanalysis_2.9.0-9_source.buildinfo Greetings, Your Debian queue daemon (running on host usper.debian.org) From ftpmaster at ftp-master.debian.org Fri Jul 4 09:49:13 2025 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Fri, 04 Jul 2025 08:49:13 +0000 Subject: [Debichem-devel] mdanalysis_2.9.0-9_source.changes ACCEPTED into unstable Message-ID: Thank you for your contribution to Debian. Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Fri, 04 Jul 2025 10:23:27 +0200 Source: mdanalysis Architecture: source Version: 2.9.0-9 Distribution: unstable Urgency: medium Maintainer: Debichem Team Changed-By: Drew Parsons Closes: 1108309 Changes: mdanalysis (2.9.0-9) unstable; urgency=medium . * debian/tests/control: mark mdanalysis with Restrictions: flaky. mdanalysis tests are generally unreliable and fail often and randomly. Closes: #1108309 * debian/tests: skip tests observed failing in debci migration-reference runs: test_dihedral_attr_warning test_AnalysisFromFunction test_villin_unfolded test_rmsd_frames test_file_guess_hydrogens test_gnm_run_step test_all_backends_give_correct_results test_startframe test_hbond_analysis Checksums-Sha1: 526f51e7d7445edb17593caf3928431f65ea0c92 2970 mdanalysis_2.9.0-9.dsc 50a1f259c15fa6dcd490b709690d582c621c4d0b 13516 mdanalysis_2.9.0-9.debian.tar.xz 8e3e8bd85e0e76b4acadd9b14c5a9b26b9e47c5e 15888 mdanalysis_2.9.0-9_source.buildinfo Checksums-Sha256: b5918fca126b45935a410d26c9cac39bf260744e3d8370dde4895af9eb411333 2970 mdanalysis_2.9.0-9.dsc c0b576ca475ab44db5891ece72a8b568d9f5311cd5a9d9205f086d0c70292d8f 13516 mdanalysis_2.9.0-9.debian.tar.xz a850ae31e616839ab403a09bf9b2f07bdbf17b855e2d4404149c01dd2dbfb895 15888 mdanalysis_2.9.0-9_source.buildinfo Files: 6cddd819103ce391de2fa5d38dd545f9 2970 python optional mdanalysis_2.9.0-9.dsc ef11611b1ccd68d2b0fa6b9de87f6592 13516 python optional mdanalysis_2.9.0-9.debian.tar.xz 4b1097b2cb30f60ad0675b999c7b8773 15888 python optional mdanalysis_2.9.0-9_source.buildinfo -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEI8mpPlhYGekSbQo2Vz7x5L1aAfoFAmhnj8gUHGRwYXJzb25z QGRlYmlhbi5vcmcACgkQVz7x5L1aAfrm5w//ZpuiDnVEarEmo6y8PtTHe8C1U3DX 11AkG1k5D2Xhxpb8iS/gcFYVjCtPzZ2Db+SEFeqk14zZ/jT9Q275/bgx5Z9VZ75u Oj5vCBXWUBaYHM/jycKJPDNB2Yhg5oXl04te/8iBZuARqoJHfEBLsdrsKPb6MbXv PQfWASMDpaWjfyH8AVnwWRFWiKDfnMHxqvUTJZ+QpENw2OxMQ99JdgVO291hM0kt arqqIPpZvBRNOetQfScJeNBfxt22mlldmhqUWgsmbHMkGJPbY5RD1GQQhti/oAi1 FZB9/pzzBQujC4FoqprQqQJgzi3QklFEiGIkJDFeieNVj9v6zzaqNYuluRwIrNic R1q/zjvozhhb6kQI5L1V8TuqjI+tYyOFlUR00E9mhUbOqpfVMDs3MusKB19z6MQG sJItnB3TEAfjeTVvQz70XkyZIszdgSYjwqdbMYlbwv0GNQ4oIjzgwgATaspxPyfG 5Y9SMgoZqi9EAtp4gN7L070/TDARnuWj3uCj96vJWn4BpOp5v6OQktzfSo+u+pIT s6TAxwx0ZfmmyFsz8kPiAQQeXTpSj0s4zkM95BaoR/AsPr2nj5IdVhXGzB5mA2FR MjeEwa2UOZ5gnbIT/EFWxz1GT7oIRtx4yrEfa0hOtUsXjHtUUHsM+tVN/eTw1BGd cRk+x5bYpvzQ4Gg= =O59d -----END PGP SIGNATURE----- -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/pgp-signature Size: 228 bytes Desc: not available URL: From owner at bugs.debian.org Fri Jul 4 09:51:02 2025 From: owner at bugs.debian.org (Debian Bug Tracking System) Date: Fri, 04 Jul 2025 08:51:02 +0000 Subject: [Debichem-devel] Bug#1108309: marked as done (mdanalysis: FTBFS randomly: autobuilder hangs) References: Message-ID: Your message dated Fri, 04 Jul 2025 08:49:13 +0000 with message-id and subject line Bug#1108309: fixed in mdanalysis 2.9.0-9 has caused the Debian Bug report #1108309, regarding mdanalysis: FTBFS randomly: autobuilder hangs 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 owner at bugs.debian.org immediately.) -- 1108309: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1108309 Debian Bug Tracking System Contact owner at bugs.debian.org with problems -------------- next part -------------- An embedded message was scrubbed... From: Santiago Vila Subject: mdanalysis: FTBFS randomly: autobuilder hangs Date: Wed, 25 Jun 2025 17:20:52 +0000 Size: 6270 URL: -------------- next part -------------- An embedded message was scrubbed... From: Debian FTP Masters Subject: Bug#1108309: fixed in mdanalysis 2.9.0-9 Date: Fri, 04 Jul 2025 08:49:13 +0000 Size: 7293 URL: From sanvila at debian.org Fri Jul 4 18:25:07 2025 From: sanvila at debian.org (Santiago Vila) Date: Fri, 4 Jul 2025 19:25:07 +0200 Subject: [Debichem-devel] Bug#1108309: mdanalysis: FTBFS randomly: autobuilder hangs References: Message-ID: found 1108309 2.9.0-9 tags 1108309 patch thanks Hi. My autobuilders still hang when trying to build this package. All the time, as in "tried 50 times and failed 50 times". I've put recent build logs here: https://people.debian.org/~sanvila/build-logs/202507/ Those build logs were produced using machines with 2 CPUs. When using machines with one CPU, the failure rate is only 10%. Some of the existing PRs here: https://github.com/MDAnalysis/mdanalysis/pulls read like "enable parallelization on XXX" or "enable parallelization on YYY". Also, in page 2 of Issues: https://github.com/MDAnalysis/mdanalysis/issues?page=2 there is a number of them saying "Implement parallelization or mark as unparallelizable". I think this is an upstream bug. Maybe the tests are buggy in a way that they need a minimum number of CPUs to run (probably in an unintended way), and such number is unfortunately strictly greater than 2. If that's the case, we (Debian) should be honest and skip those tests when we know for sure that they will fail (as in the (untested) attached patch). But maybe I'm over-diagnosing this, and many of the functions that have been modified "so that they run in parallel" do not really work ok in parallel. Can you please forward this upstream? (Or give me some hint about how I should word the issue myself, as I have a github account). Thanks. -------------- next part -------------- --- a/debian/rules +++ b/debian/rules @@ -120,13 +120,13 @@ execute_after_dh_auto_clean: ifeq (yes,$(findstring yes,$(RUNTEST))) override_dh_auto_test: set -e; \ - for py in $(shell py3versions -rv); do \ + if [ $(nproc) -gt 2 ]; then for py in $(shell py3versions -rv); do \ echo "=== testing with python$$py ==="; \ pydir=`pybuild -p $$py --system=distutils --print {build_dir}`; \ MPLBACKEND=agg PYTHONPATH=$$pydir python$$py -mpytest -v -k "$(SKIP_TESTS)" --disable-pytest-warnings testsuite; \ rm -rf $$pydir/MDAnalysis/.hypothesis; \ rm -rf $$pydir/MDAnalysis/.duecredit.p; \ - done + done; fi endif execute_after_dh_python3: From owner at bugs.debian.org Fri Jul 4 18:27:02 2025 From: owner at bugs.debian.org (Debian Bug Tracking System) Date: Fri, 04 Jul 2025 17:27:02 +0000 Subject: [Debichem-devel] Processed: mdanalysis: FTBFS randomly: autobuilder hangs References: Message-ID: Processing commands for control at bugs.debian.org: > found 1108309 2.9.0-9 Bug #1108309 {Done: Drew Parsons } [src:mdanalysis] mdanalysis: FTBFS randomly: autobuilder hangs Marked as found in versions mdanalysis/2.9.0-9; no longer marked as fixed in versions mdanalysis/2.9.0-9 and reopened. > tags 1108309 patch Bug #1108309 [src:mdanalysis] mdanalysis: FTBFS randomly: autobuilder hangs Added tag(s) patch. > thanks Stopping processing here. Please contact me if you need assistance. -- 1108309: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1108309 Debian Bug Tracking System Contact owner at bugs.debian.org with problems From sanvila at debian.org Fri Jul 4 19:09:55 2025 From: sanvila at debian.org (Santiago Vila) Date: Fri, 4 Jul 2025 20:09:55 +0200 Subject: [Debichem-devel] Bug#1108309: mdanalysis: FTBFS randomly: autobuilder hangs In-Reply-To: References: Message-ID: On Fri, Jul 04, 2025 at 07:25:07PM +0200, Santiago Vila wrote: > - for py in $(shell py3versions -rv); do \ > + if [ $(nproc) -gt 2 ]; then for py in $(shell py3versions -rv); do \ Note: Should be really if [ $(shell nproc) -gt 2 ]; then etc Thanks. From elbrus at debian.org Sun Jul 6 11:01:04 2025 From: elbrus at debian.org (Paul Gevers) Date: Sun, 6 Jul 2025 12:01:04 +0200 Subject: [Debichem-devel] Bug#1108852: cclib: autopkgtest regression: No such file or directory Message-ID: <60394be1-1ac6-46e4-abaf-9d9bece44863@debian.org> Source: cclib Version: 1.8-1 Severity: serious User: debian-ci at lists.debian.org Usertags: regression Tags: trixie-ignore Dear maintainer(s), Your package has an autopkgtest, great. However, it fails since January 2024. Can you please investigate the situation and fix it? I copied some of the output at the bottom of this report. The release team has announced [1] that failing autopkgtest on amd64 and arm64 are considered RC in testing. More information about this bug and the reason for filing it can be found on https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation With my Release Team member hat on I have tagged this as trixie-ignore as it's so late in the freeze and it's not worth removing the package from trixie because of this at this moment. Having said that, if a fix is possible without fully removing the autopkgtest and without making the test superficial, it's still welcome, but it would need to happen soon. Paul [1] https://lists.debian.org/debian-devel-announce/2019/07/msg00002.html https://ci.debian.net/data/autopkgtest/testing/amd64/c/cclib/61846681/log.gz 91s =================================== FAILURES =================================== 91s _______________________________ test_regressions _______________________________ 91s 91s which = [], opt_traceback = True 91s regdir = '/tmp/autopkgtest-lxc.6gtorn54/downtmp/build.BtZ/src/test/../data/regression/' 91s loglevel = 40 91s 91s def test_regressions(which=[], opt_traceback=True, regdir=__regression_dir__, loglevel=logging.ERROR): 91s 91s # Build a list of regression files that can be found. If there is a directory 91s # on the third level, then treat all files within it as one job. 91s try: 91s filenames = {} 91s for p in parser_names: 91s filenames[p] = [] 91s pdir = os.path.join(regdir, get_program_dir(p)) 91s for version in os.scandir(pdir): 91s if version.is_file(): 91s continue 91s 91s for job in os.listdir(version.path): 91s path = os.path.join(version.path, job) 91s if os.path.isdir(path): 91s filenames[p].append(os.path.join(path, "*")) 91s else: 91s filenames[p].append(path) 91s except OSError as e: 91s print(e) 91s print("\nERROR: At least one program direcory is missing.") 91s print("Run 'git pull' or regression_download.sh in cclib to update.") 91s sys.exit(1) 91s 91s # This file should contain the paths to all regresssion test files we have gathered 91s # over the years. It is not really necessary, since we can discover them on the disk, 91s # but we keep it as a legacy and a way to track the regression tests. 91s > regfile = open(os.path.join(regdir, "regressionfiles.txt"), "r") 91s E FileNotFoundError: [Errno 2] No such file or directory: '/tmp/autopkgtest-lxc.6gtorn54/downtmp/build.BtZ/src/test/../data/regression/regressionfiles.txt' 91s 91s test/regression.py:3652: FileNotFoundError -------------- next part -------------- A non-text attachment was scrubbed... Name: OpenPGP_signature.asc Type: application/pgp-signature Size: 585 bytes Desc: OpenPGP digital signature URL: From dparsons at debian.org Sun Jul 6 12:08:57 2025 From: dparsons at debian.org (Drew Parsons) Date: Sun, 06 Jul 2025 13:08:57 +0200 Subject: [Debichem-devel] Bug#1108309: mdanalysis: 1 References: Message-ID: <175180013799.1235354.4971523977250189390.reportbug@sandy> Source: mdanalysis Followup-For: Bug #1108309 Upstream has no* special requirements for their bug reports, so please do file with them directly at https://github.com/MDAnalysis/mdanalysis/issues It's actually a good idea to do that, because they'll be able to discuss directly what their intentions are for multiprocessor testing, compared to the conditions that you (and debci) are using in our testing. They are proud of their code and they want their tests to pass reliably, so it can be a constructive dialogue with them. * the only catch is that they release regularly, so our debian version is a little behind the latest upstream release. There may be improvements they've already made they we haven't caught yet. But the problems with their tests are longstanding, so I think it's still worth filing the issue with them. In regards to the severity of this bug, the faiing tests will no longer block migration to testing after marking them with Restriction: flakey. So in that regard this issue is Severity: important not Severity: serious, unless you prefer to mean severity "serious" in the sense that trixie shouldn't be providing the package even with tests marked flakey. From sanvila at debian.org Sun Jul 6 14:31:45 2025 From: sanvila at debian.org (Santiago Vila) Date: Sun, 6 Jul 2025 15:31:45 +0200 Subject: [Debichem-devel] Bug#1108309: mdanalysis: 1 In-Reply-To: <175180013799.1235354.4971523977250189390.reportbug@sandy> References: <175180013799.1235354.4971523977250189390.reportbug@sandy> Message-ID: On Sun, Jul 06, 2025 at 01:08:57PM +0200, Drew Parsons wrote: > Source: mdanalysis > Followup-For: Bug #1108309 > > Upstream has no* special requirements for their bug reports, so please > do file with them directly at > https://github.com/MDAnalysis/mdanalysis/issues > > It's actually a good idea to do that, because they'll be able to > discuss directly what their intentions are for multiprocessor testing, > compared to the conditions that you (and debci) are using in our testing. > They are proud of their code and they want their tests to pass > reliably, so it can be a constructive dialogue with them. Ok, I'm going to try that route. > * the only catch is that they release regularly, so our debian version > is a little behind the latest upstream release. There may be > improvements they've already made they we haven't caught yet. > But the problems with their tests are longstanding, so I think it's > still worth filing the issue with them. Ok, even if we are a little bit behind, we can always try to backport whatever fixes they implement. > In regards to the severity of this bug, the failing tests will no longer > block migration to testing after marking them with Restriction: flakey. > So in that regard this issue is Severity: important not Severity: serious, > unless you prefer to mean severity "serious" in the sense that trixie > shouldn't be providing the package even with tests marked flakey. Well, I did not file this bug because of flaky tests in ci.debian.net, but because the end user who wants to build the package from source may easily find that the autobuilder hangs (because of timeout) and the package does not build from source. That's worse than having flaky tests and I think it should never happen in a stable release. I see that Paul Gevers (from RT) is already filing some bugs with trixie-ignore tag, and I think it is likely that he will apply trixie-ignore to this bug as well, usually with the meaning of "this bug will not delay the release nor will make the package to be autoremoved, but please keep trying to fix it in trixie if you can". I think that's what we should do. If we can't fix it before the release, I would be willing to prepare an upload for proposed-updates once that we have a proper fix in unstable. Thanks. From dparsons at debian.org Sun Jul 6 15:09:58 2025 From: dparsons at debian.org (Drew Parsons) Date: Sun, 06 Jul 2025 16:09:58 +0200 Subject: [Debichem-devel] Bug#1108309: mdanalysis: FTBFS randomly: autobuilder hangs References: Message-ID: <175181099868.1238953.2822472834435538889.reportbug@sandy> Source: mdanalysis Followup-For: Bug #1108309 Thanks Santiago, I appreciate your help improving the package. Certainly good for everyone if we can find how to stop these random timeouts. Drew From owner at bugs.debian.org Tue Jul 8 02:19:02 2025 From: owner at bugs.debian.org (Debian Bug Tracking System) Date: Tue, 08 Jul 2025 01:19:02 +0000 Subject: [Debichem-devel] Processed: mdanalysis: FTBFS randomly: autobuilder hangs References: Message-ID: Processing commands for control at bugs.debian.org: > forwarded 1108309 https://github.com/MDAnalysis/mdanalysis/issues/5078 Bug #1108309 [src:mdanalysis] mdanalysis: FTBFS randomly: autobuilder hangs Set Bug forwarded-to-address to 'https://github.com/MDAnalysis/mdanalysis/issues/5078'. > thanks Stopping processing here. Please contact me if you need assistance. -- 1108309: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1108309 Debian Bug Tracking System Contact owner at bugs.debian.org with problems From sanvila at debian.org Tue Jul 8 02:17:51 2025 From: sanvila at debian.org (Santiago Vila) Date: Tue, 8 Jul 2025 03:17:51 +0200 Subject: [Debichem-devel] Bug#1108309: mdanalysis: FTBFS randomly: autobuilder hangs References: Message-ID: forwarded 1108309 https://github.com/MDAnalysis/mdanalysis/issues/5078 thanks Hi. I've forwarded this to the above URL. Thanks. From dparsons at debian.org Wed Jul 9 10:15:52 2025 From: dparsons at debian.org (Drew Parsons) Date: Wed, 09 Jul 2025 11:15:52 +0200 Subject: [Debichem-devel] Bug#1108997: unblock: mdanalysis/2.9.0-9 Message-ID: <175205255210.1254471.1370432878592188856.reportbug@sandy> Package: release.debian.org Severity: normal X-Debbugs-Cc: mdanalysis at packages.debian.org Control: affects -1 + src:mdanalysis User: release.debian.org at packages.debian.org Usertags: unblock Please unblock package mdanalysis [ Reason ] mdanalysis tests are generally flakey, randomly timing out. In response to Bug#1108309, mdanalysis/2.9.0-9 adds Restrictions: flaky to debian/tests and skips a few more tests in order to reduce the level of nuisance from the flakey tests in trixie-stable. Tests are currently halted on riscv64 so 2.9.0-9 will not automatically migrate. Hence filing this unblock request to consider if we're happy to provide mdanalysis/2.9.0-9 in trixie. [ Impact ] Without this update, random timeouts in debci will be registed as "Failed" rather than "Flakey", making the state of mdanalysis seem worse than its actual "known flakey" state. [ Tests ] debian/tests runs the upstream test-suite, which is actually the cause of the problem. Would it be better to stop running mdanalysis tests altogether? [ Risks ] No risk in 2.9.0-9 compared to 2.9.0-8. It skips more tests so in principle reduces the risk of test failure. [ Checklist ] [x ] all changes are documented in the d/changelog [x ] I reviewed all changes and I approve them [x ] attach debdiff against the package in testing [ Other info ] This update does not fix the random timeouts, but rather marks them as flaky in debci to keep them from blocking the package. Santiago Vila has requested to keep Bug#1108309 open for communication with upstream to find a more fundamental fix. We are suggesting this bug be tagged not-trixie, to let mdanalysis/2.9.0-9 into trixie. unblock mdanalysis/2.9.0-9 From ftpmaster at ftp-master.debian.org Wed Jul 9 14:26:00 2025 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Wed, 09 Jul 2025 13:26:00 +0000 Subject: [Debichem-devel] Processing of mdanalysis_2.9.0-10_source.changes Message-ID: mdanalysis_2.9.0-10_source.changes uploaded successfully to localhost along with the files: mdanalysis_2.9.0-10.dsc mdanalysis_2.9.0-10.debian.tar.xz mdanalysis_2.9.0-10_source.buildinfo Greetings, Your Debian queue daemon (running on host usper.debian.org) From ftpmaster at ftp-master.debian.org Wed Jul 9 14:35:07 2025 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Wed, 09 Jul 2025 13:35:07 +0000 Subject: [Debichem-devel] mdanalysis_2.9.0-10_source.changes ACCEPTED into unstable Message-ID: Thank you for your contribution to Debian. Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Wed, 09 Jul 2025 15:12:21 +0200 Source: mdanalysis Architecture: source Version: 2.9.0-10 Distribution: unstable Urgency: medium Maintainer: Debichem Team Changed-By: Drew Parsons Changes: mdanalysis (2.9.0-10) unstable; urgency=medium . * apply suggestion from Bug#1108309 to skip tests (build and runtime) if less than 2 CPUs are available * do not run build-time tests on hurd-i386 or when nocheck is set in DEB_BUILD_OPTIONS Checksums-Sha1: 7bead9177d075238f1d4f7810b8107b409e20c40 2974 mdanalysis_2.9.0-10.dsc 6438a12fe3b25685ac6275ea12e6d310aba7f0d3 13828 mdanalysis_2.9.0-10.debian.tar.xz e51eba5c42cf9a7917d3f6a8f32d27c4b6d99f6a 15889 mdanalysis_2.9.0-10_source.buildinfo Checksums-Sha256: 6e4dd23d185b6bda96d7c8705e75bbabc41c17f84eed5ab1cf95d68b097a8a7b 2974 mdanalysis_2.9.0-10.dsc 993052805d549d268f71b39a8218c6d107cb673ce326b2c2a7b335dba289407c 13828 mdanalysis_2.9.0-10.debian.tar.xz 50069a55d43c345c17abc2a774eb1fc79619fcb9896eaa422a34cce93478a44a 15889 mdanalysis_2.9.0-10_source.buildinfo Files: 78aafb31eaf50305f7eb22b56af751f7 2974 python optional mdanalysis_2.9.0-10.dsc 4ebd6d7c9f363d61548f1b83d62fbe98 13828 python optional mdanalysis_2.9.0-10.debian.tar.xz 8813b5f7d4d943cd2de0ff95aa4137e2 15889 python optional mdanalysis_2.9.0-10_source.buildinfo -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEI8mpPlhYGekSbQo2Vz7x5L1aAfoFAmhua4YUHGRwYXJzb25z QGRlYmlhbi5vcmcACgkQVz7x5L1aAfqkPQ//R0xX1zQGgirIDw+rBVw4ecof1ZGa uhL9ry46+Zy1KPE4u9/9ipGxZl6if9VJp3DxyFdx7rqKv25OhkS8ZNeMnLIc1aRE VmHmm93NMF9X1wy24aDVZnunWBMUYKZKxRtq+a/RBsWbBjZCoRuaEu23rCcNbAaY 9BnkVIp/NuuTEqBSY6D24PVicCPPUFV6xRa7WAWTpDzKOh1QughsSXnwfuNOWss+ WZvLb8gYjvPRVIqb3uyjAP6QBKiLW2Fv40TkAsfmCBbnVjuSkz9TZqy/xR1tOQLs V+e4cyw3Y0fTK6SNiOixhjhL7G5BF05FY3iZYYJJe4N7YAXm3Ouhd/DvHiBkYnBC 9TECTATXG5s80S2CM/qxVjU1UQjt3AzWcP7SDOPQ3sNHXOEal23DmsFFTFR3tC7a hHVLXYHHKFPwyJ21hs7up/YlBhK+xM7ZIklfmzchnN0VudLre8u/ZKkxiUJ3DHWn nQzn3Z/gJJOhaLnSAEV1G2QEHp+UKoVV3MHISphJs8pn6nXiidfsp3vhNvOoXZ85 Ib5CH6q6XPdRtH1YL/SLSjsqbR6SnHw7P0/O3BZBRkuWL+MmeHxVW/Jvhrsfk5a5 PNG8SEASV2x/ZLPiIELlPUMbhYNxZtsCGddF8Fr+volSHLs9+6IQuI5Iqocuyo+N rw0X+HOSy0OxDEY= =q1UX -----END PGP SIGNATURE----- -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/pgp-signature Size: 228 bytes Desc: not available URL: From ftpmaster at ftp-master.debian.org Wed Jul 9 18:57:18 2025 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Wed, 09 Jul 2025 17:57:18 +0000 Subject: [Debichem-devel] Processing of mdanalysis_2.9.0-11_source.changes Message-ID: mdanalysis_2.9.0-11_source.changes uploaded successfully to localhost along with the files: mdanalysis_2.9.0-11.dsc mdanalysis_2.9.0-11.debian.tar.xz mdanalysis_2.9.0-11_source.buildinfo Greetings, Your Debian queue daemon (running on host usper.debian.org) From ftpmaster at ftp-master.debian.org Wed Jul 9 19:04:33 2025 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Wed, 09 Jul 2025 18:04:33 +0000 Subject: [Debichem-devel] mdanalysis_2.9.0-11_source.changes ACCEPTED into unstable Message-ID: Thank you for your contribution to Debian. Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Wed, 09 Jul 2025 19:16:36 +0200 Source: mdanalysis Architecture: source Version: 2.9.0-11 Distribution: unstable Urgency: medium Maintainer: Debichem Team Changed-By: Drew Parsons Changes: mdanalysis (2.9.0-11) unstable; urgency=medium . * fix order of conditional control of build-time tests Checksums-Sha1: 22be95d17e548ccdb883d706313b790a203764ab 2974 mdanalysis_2.9.0-11.dsc 09d05a804ffddd577b55d57c4bf36e04dcd9b4e4 13848 mdanalysis_2.9.0-11.debian.tar.xz 4a16150951400541f79f81ec81d7e2768e2c3325 15889 mdanalysis_2.9.0-11_source.buildinfo Checksums-Sha256: 3a15d33dd4cc4acf4b56bc1021578b3933d8f261764b2be426be80d6b9dcbcef 2974 mdanalysis_2.9.0-11.dsc 6b2dc6c384818f6c86715cc24260cf4786ef1a5a4f17d97718767b407d1d4f99 13848 mdanalysis_2.9.0-11.debian.tar.xz eaca0d6ba4015f025a0b858b5dab7941e476cad52a01764b5922f0d60138a452 15889 mdanalysis_2.9.0-11_source.buildinfo Files: 85634ecf8956b53aab26df7b627f4f23 2974 python optional mdanalysis_2.9.0-11.dsc f2f782e6542833b3bee92be187bd8863 13848 python optional mdanalysis_2.9.0-11.debian.tar.xz 8092e0206dfa8c7f13bceb59ffc5d58f 15889 python optional mdanalysis_2.9.0-11_source.buildinfo -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEI8mpPlhYGekSbQo2Vz7x5L1aAfoFAmhuqrkUHGRwYXJzb25z QGRlYmlhbi5vcmcACgkQVz7x5L1aAfp8tQ//W02nCp/U2DpganuA6yQ6J/NW6Xvt yzMVlfZWPsNJV05iFi4LjD01dkoLnt3BB0mtOJH0ysDqFKy3cXHuHETemZjw6Akx n2Mp8f3IBdV77f3gQjkaj2wCmUXqj19c/NmCjlv2ger5dvTPqfBzgp41n5jHtR1h cNcMhbZqtKM1sAOFLXpwZIoi4H0XX+QVspAeHxlujmYccxX5MSpDu0hqQH4dhuVG PQTu7+Rpb6X6B45IlprfTaViXWe5Gwbn4Tm9geUGjXxadQ4INU3P7IgLa6cuEd62 RS9rYj3SvAioMloeeI+uWqkG3rVU3/JZbWVcgikPnRe6q3KBMPWsqgv3szlh2uYN ejQI7ofqn22eELzCP8779VC65+HYSw4jSGgJA8rf1b7lVf2fb+XqN2V8gQFDOx4b eml8nNes28b03duXcU9tkkf3un0jEpcFZLU81Vp/6vVbnntMM7hW0wpuZGngtDgm QZ9iHz3rLRLmTROIXYlTi+C3LLTWznnmq46zJu+yJ2Fgrwik9R7c3pVWmLUighhI lZBa7ArPYlTEky5T+GTCZr76VU+3S2s2boYYUVwrRzJDsCM4gpnCOkCY4Fon4Kk6 AnXpvRxoz/qMvJyFPowKK/Sz9/IzkdhIObQ7v8I+hi0sTw4g03uhzOrimMW7QC6a Kt0Wy8IgyWArwPA= =EPXH -----END PGP SIGNATURE----- -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/pgp-signature Size: 228 bytes Desc: not available URL: From sanvila at debian.org Thu Jul 10 02:40:11 2025 From: sanvila at debian.org (Santiago Vila) Date: Thu, 10 Jul 2025 03:40:11 +0200 Subject: [Debichem-devel] Bug#1108309: Accepted mdanalysis 2.9.0-10 (source) into unstable In-Reply-To: References: Message-ID: Hello Drew. I'd like to comment on this: > * apply suggestion from Bug#1108309 to skip tests (build and > runtime) if less than 2 CPUs are available That was really a suggestion for the case where we could say with certainty that the tests need more than 2 CPUs to run successfully. Note that I said "Maybe the tests are buggy in a way [...]", this was really an hypothetical scenario, pending confirmation from upstream. But the build logs from buildd.debian.org which I quoted in my initial report, where the build fails with timeout: https://buildd.debian.org/status/fetch.php?pkg=mdanalysis&arch=all&ver=2.9.0-3&stamp=1744942413&raw=0 https://buildd.debian.org/status/fetch.php?pkg=mdanalysis&arch=amd64&ver=2.9.0-7&stamp=1745409028&raw=0 https://buildd.debian.org/status/fetch.php?pkg=mdanalysis&arch=arm64&ver=2.9.0-6&stamp=1745371276&raw=0 https://buildd.debian.org/status/fetch.php?pkg=mdanalysis&arch=armel&ver=2.9.0-8&stamp=1747011477&raw=0 https://buildd.debian.org/status/fetch.php?pkg=mdanalysis&arch=i386&ver=2.9.0-2&stamp=1744893854&raw=0 https://buildd.debian.org/status/fetch.php?pkg=mdanalysis&arch=mips64el&ver=2.9.0-4&stamp=1745023633&raw=0 happened on machines with more than 2 CPUs, so by skipping the tests if the number of CPUs is <= 2, we are certainly avoiding the problem in some scenarios where we know the tests are quite useless, but not in the buildds. So, to summarize, I don't think it was a good suggestion, and I'm sorry that I realized now. My preferred course of action at this point, in my humble opinion, would be to ask the RT for a trixie-ignore exception, wait for upstream to answer to the github issue, and implement the right fix only when we have it (if they reply soon, before the release of trixie, if they do not reply soon, using proposed-updates, to be included in a point release of trixie). Thanks. From owner at bugs.debian.org Thu Jul 10 09:41:02 2025 From: owner at bugs.debian.org (Debian Bug Tracking System) Date: Thu, 10 Jul 2025 08:41:02 +0000 Subject: [Debichem-devel] Processed: Re: mdanalysis: FTBFS randomly: autobuilder hangs References: <175213673181.1358705.2472190914281477741.reportbug@sandy> Message-ID: Processing control commands: > tags -1 ftbfs Bug #1108309 [src:mdanalysis] mdanalysis: FTBFS randomly: autobuilder hangs Ignoring request to alter tags of bug #1108309 to the same tags previously set -- 1108309: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1108309 Debian Bug Tracking System Contact owner at bugs.debian.org with problems From dparsons at debian.org Thu Jul 10 09:38:51 2025 From: dparsons at debian.org (Drew Parsons) Date: Thu, 10 Jul 2025 10:38:51 +0200 Subject: [Debichem-devel] Bug#1108309: mdanalysis: FTBFS randomly: autobuilder hangs References: Message-ID: <175213673181.1358705.2472190914281477741.reportbug@sandy> Source: mdanalysis Followup-For: Bug #1108309 X-Debbugs-Cc: 1108997 at bugs.debian.org Control: tags -1 ftbfs Santiago Vila wrote: > But the build logs from buildd.debian.org which I quoted in my initial > report, where the build fails with timeout: > ... > happened on machines with more than 2 CPUs, so by skipping the tests > if the number of CPUs is <= 2, we are certainly avoiding the problem > in some scenarios where we know the tests are quite useless, but not > in the buildds. > > So, to summarize, I don't think it was a good suggestion, and I'm sorry > that I realized now. Ok, thanks for clarifying, Santiago. In that case it's better for trixie to just skip all tests. That's gotten done now with a debci ban, but that doesn't let us test any movement from upstream (the ban prevents testing new code in experimental). So I'll upload -12 switching off tests for trixie. Drew From ftpmaster at ftp-master.debian.org Thu Jul 10 10:34:23 2025 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 10 Jul 2025 09:34:23 +0000 Subject: [Debichem-devel] Processing of mdanalysis_2.9.0-12_source.changes Message-ID: mdanalysis_2.9.0-12_source.changes uploaded successfully to localhost along with the files: mdanalysis_2.9.0-12.dsc mdanalysis_2.9.0-12.debian.tar.xz Greetings, Your Debian queue daemon (running on host usper.debian.org) From ftpmaster at ftp-master.debian.org Thu Jul 10 10:50:27 2025 From: ftpmaster at ftp-master.debian.org (Debian FTP Masters) Date: Thu, 10 Jul 2025 09:50:27 +0000 Subject: [Debichem-devel] mdanalysis_2.9.0-12_source.changes ACCEPTED into unstable Message-ID: Thank you for your contribution to Debian. Accepted: -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Thu, 10 Jul 2025 11:07:57 +0200 Source: mdanalysis Architecture: source Version: 2.9.0-12 Distribution: unstable Urgency: medium Maintainer: Debichem Team Changed-By: Drew Parsons Changes: mdanalysis (2.9.0-12) unstable; urgency=medium . * skip all tests, both build-time and run-time. See Bug#1108309. 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Name: not available Type: application/pgp-signature Size: 228 bytes Desc: not available URL: From noreply at release.debian.org Mon Jul 14 05:39:09 2025 From: noreply at release.debian.org (Debian testing autoremoval watch) Date: Mon, 14 Jul 2025 04:39:09 +0000 Subject: [Debichem-devel] minexpert2 is marked for autoremoval from testing Message-ID: minexpert2 9.6.0-1 is marked for autoremoval from testing on 2025-08-18 It (build-)depends on packages with these RC bugs: 1108812: remake: FTBFS randomly: Error running /<>/tests/../make (expected 0; got 14): /<>/tests/../make -f work/features/output-sync.mk -j -Orecurse https://bugs.debian.org/1108812 For more information on the autoremoval process, including hints to prevent autoremoval can be found on the wiki: https://wiki.debian.org/Autoremoval This mail is generated by: https://salsa.debian.org/release-team/release-tools/-/blob/master/mailer/mail_autoremovals.pl Autoremoval data is generated by: https://salsa.debian.org/qa/udd/-/blob/master/udd/testing_autoremovals_gatherer.pl From noreply at release.debian.org Mon Jul 14 05:39:09 2025 From: noreply at release.debian.org (Debian testing autoremoval watch) Date: Mon, 14 Jul 2025 04:39:09 +0000 Subject: [Debichem-devel] massxpert2 is marked for autoremoval from testing Message-ID: massxpert2 8.5.0-2 is marked for autoremoval from testing on 2025-08-18 It (build-)depends on packages with these RC bugs: 1108812: remake: FTBFS randomly: Error running /<>/tests/../make (expected 0; got 14): /<>/tests/../make -f work/features/output-sync.mk -j -Orecurse https://bugs.debian.org/1108812 For more information on the autoremoval process, including hints to prevent autoremoval can be found on the wiki: https://wiki.debian.org/Autoremoval This mail is generated by: https://salsa.debian.org/release-team/release-tools/-/blob/master/mailer/mail_autoremovals.pl Autoremoval data is generated by: https://salsa.debian.org/qa/udd/-/blob/master/udd/testing_autoremovals_gatherer.pl From owner at bugs.debian.org Mon Jul 14 16:13:02 2025 From: owner at bugs.debian.org (Debian Bug Tracking System) Date: Mon, 14 Jul 2025 15:13:02 +0000 Subject: [Debichem-devel] Processed: Re: unblock: mdanalysis/2.9.0-12 References: <175250594126.698516.6223661779822609022.reportbug@sandy> <175205255210.1254471.1370432878592188856.reportbug@sandy> Message-ID: Processing control commands: > severity 1108309 important Bug #1108309 [src:mdanalysis] mdanalysis: FTBFS randomly: autobuilder hangs Severity set to 'important' from 'serious' -- 1108309: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1108309 1108997: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1108997 Debian Bug Tracking System Contact owner at bugs.debian.org with problems From debian-bts-link at lists.debian.org Mon Jul 14 19:03:39 2025 From: debian-bts-link at lists.debian.org (debian-bts-link at lists.debian.org) Date: Mon, 14 Jul 2025 18:03:39 +0000 Subject: [Debichem-devel] [bts-link] source package src:mdanalysis Message-ID: <175251621975.3200119.3457183616591903891.btslink@sonntag.debian.org> # # bts-link upstream status pull for source package src:mdanalysis # see http://lists.debian.org/debian-devel-announce/2006/05/msg00001.html # https://bts-link-team.pages.debian.net/bts-link/ # user debian-bts-link at lists.debian.org # remote status report for #1108309 (http://bugs.debian.org/1108309) # Bug title: mdanalysis: FTBFS randomly: autobuilder hangs # * https://github.com/MDAnalysis/mdanalysis/issues/5078 # * remote status changed: (?) -> open usertags 1108309 + status-open thanks From owner at bugs.debian.org Mon Jul 14 19:35:02 2025 From: owner at bugs.debian.org (Debian Bug Tracking System) Date: Mon, 14 Jul 2025 18:35:02 +0000 Subject: [Debichem-devel] Processed: Re: unblock: mdanalysis/2.9.0-12 References: Message-ID: Processing commands for control at bugs.debian.org: > severity 1108309 normal Bug #1108309 [src:mdanalysis] mdanalysis: FTBFS randomly: autobuilder hangs Severity set to 'normal' from 'important' > thanks Stopping processing here. Please contact me if you need assistance. -- 1108309: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1108309 Debian Bug Tracking System Contact owner at bugs.debian.org with problems