The autodep8 generator for pkg-r-autopkgtest uses APT lists to determine which R packages from DESCRIPTION exist in Debian. autodep8 is run outside the test runner, not inside it, so this makes the behaviour dependant on the packages available to the test runner host. Here's the code that introduced this approach: https://salsa.debian.org/ci-team/autodep8/-/merge_requests/10 It all works when the autopkgtest runner has approximately the same packages available as the release under test, but that's not always the case. I noticed that the r-bioc-hdf5 package's test misses a dependency on r-cranc-bit64 when the test is run from an older stable release that predates this package. I don't know how else you can solve this particular problem, though... SR
Hi,
any hint from debian-ci list how to solve this?
Kind regards
Andreas.
Am Wed, May 20, 2020 at 09:07:47AM -0700 schrieb Stefano Rivera:
Quoting Paul from https://salsa.debian.org/ci-team/autodep8/-/merge_requests/10#note_279588, I think the right way to solve this is:
On Tue, 2 Jul 2024 16:15:26 +0000 Graham Inggs <ginggs@debian.org> wrote: > Hi Andreas > > > r-cran-spatstat.core was removed from Debian. R-cran-spatstat.geom does > > not depend from this package any more and the autopkgtest in Salsa CI is > > fine[1]. Any hint why it fails in testing would be welcome. > > 82s autopkgtest [21:16:20]: @@@@@@@@@@@@@@@@@@@@ summary > 82s run-unit-test PASS > 82s pkg-r-autopkgtest FAIL badpkg > > It is only the 'pkg-r-autopkgtest' that is failing. The > 'run-unit-test' defined inside the r-cran-spatstat.geom package > succeeds. > > This looks like a bug in autodep8, where pkg-r-autopkgtest is defined. > It could be the same as #961138. Good day, While my MR doesn't fix the issue of querying the wrong distribution metadata, it does fix the overmatching that led to r-cran-spatstat.core (and others) being selected when not requested: https://salsa.debian.org/ci-team/autodep8/-/merge_requests/36 Please consider merging that MR and releasing a new autodep8 so we can re-run the autopkgtests for r-cran-spatstat* and other affected packages (r-cran-stars, r-cran-sf, r-cran-sparr, r-cran-epir, etc..) and get them back into testing. Thank you!
* Antonio Terceiro <terceiro@debian.org> [2021-10-29 09:53]: I would simply add add them all to Suggests. As they are not automatically installed by default it should be fine if not all are installable. Note that this bug is related to #1089197 and makes this package non reproducible on reproduce.debian.net. Also we would like to drop apt and the apt cache from the build chroot so fixing this would be appreciated. Cheers Jochen
Hi Jochen, if you can provide a patch / MR I'm fine to apply it but currently I have no more free spoons to work on this. Thank you Andreas. Am Sat, Mar 01, 2025 at 09:56:15PM +0100 schrieb Jochen Sprickerhof:
Hi Andreas,
* Andreas Tille <tille@debian.org> [2025-03-01 22:39]:
The real question here is how to solve #1089197, i.e. how to encode the
package relationships without depending on the apt cache (grep-aptavail
or rmadison or anything else that is network related). I have no
experience with R packages so I would need some input here. Possible
ways I see are:
1. Don't add relations automatically and let the maintainer do it.
2. Always add all package names from the DISCRIPTION file to Suggest:
From my understanding this would need some mapping from the R package
name to the Debian package name and maybe a rename of the Debian
packages to simplify the mapping.
3. Add the list of R package in Debian to dh-r and use it to convert the
package name. Note that this needs to be updated whenever a R
packages is added or removed in Debian. (This is what dh-python has,
afair).
Cheers Jochen
Hello, Bug #961138 in autodep8 reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below and you can check the diff of the fix at: https://salsa.debian.org/ci-team/autodep8/-/commit/8358d076ff0b9c9153263891d37a580c0f25a20e ------------------------------------------------------------------------ R: don't use APT cache for dependencies The contents of the APT cache is almost not always relevant to the package being tested. For example on ci.debian.net, autodep8 runs on stable, while most testing is done on testing and unstable. Extra test dependencies need to be defined by package maintainers using existing support for packages-specific configuration cf. autodep(1). Closes: #961138 ------------------------------------------------------------------------ (this message was generated automatically) -- Greetings https://bugs.debian.org/961138
Control: forwarded -1 https://salsa.debian.org/ci-team/autodep8/-/merge_requests/39 From my POV, then only option that is viable in autodep8 is 1, so I'm inclined to go with the MR linked above. I understand that at this point in the release cycle this could be too intrusive, so I would do that after trixie is out.
Am Tue, Mar 04, 2025 at 04:39:19PM -0300 schrieb Antonio Terceiro: Thank you for the MR. I'll leave it unapplied until after the release.
Hi, I plan to clean the apt cache by default for forky and implement that already in the trixie sbuild. This would make a number of R packages (via dh-r) and autodep8 FTBFS. For autodep8 there is an open MR linked already and for dh-r a fix has been committed in git: https://salsa.debian.org/r-pkg-team/dh-r/-/commit/144893ae70c2be8ce403b048b095aabaf6865fd8 Please speak up if there is any problem with this plan. You can test the new behaviour with: sbuild --starting-build-commands='apt-get distclean' -d unstable <pkg> Note that you may still want to apply more fixes as outlined in my mail below. Cheers Jochen * Jochen Sprickerhof <jspricke@debian.org> [2025-03-02 08:36]:
Hi, trixie is released so marking this RC. Please upload the fix from git. Cheers Jochen * Jochen Sprickerhof <jspricke@debian.org> [2025-06-01 18:08]:
Hi Andreas, as discussed in Brest, I have written a patch to dh-make/update-R to hard code the dependencies: https://salsa.debian.org/r-pkg-team/dh-r/-/merge_requests/9 Note that I don't have any experience with the tooling and only did some minimal testing so would appreciate feedback. Cheers Jochen * Jochen Sprickerhof <jspricke@debian.org> [2025-03-02 08:36]:
Hi Jochen, thanks for the patch. You might have read that I will not have time next week but I'll put it on high priority in about 10 days. Thanks a lot Andreas. Am Fri, Aug 22, 2025 at 09:19:38PM +0200 schrieb Jochen Sprickerhof:
Hello, Bug #961138 in autodep8 reported by you has been fixed in the Git repository and is awaiting an upload. You can see the commit message below and you can check the diff of the fix at: https://salsa.debian.org/ci-team/autodep8/-/commit/8358d076ff0b9c9153263891d37a580c0f25a20e ------------------------------------------------------------------------ R: don't use APT cache for dependencies The contents of the APT cache is almost not always relevant to the package being tested. For example on ci.debian.net, autodep8 runs on stable, while most testing is done on testing and unstable. Extra test dependencies need to be defined by package maintainers using existing support for packages-specific configuration cf. autodep(1). Closes: #961138 ------------------------------------------------------------------------ (this message was generated automatically) -- Greetings https://bugs.debian.org/961138
We believe that the bug you reported is fixed in the latest version of autodep8, 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 961138@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Paul Gevers <elbrus@debian.org> (supplier of updated autodep8 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 ftpmaster@ftp-master.debian.org) Format: 1.8 Date: Sat, 30 Aug 2025 13:59:46 +0200 Source: autodep8 Architecture: source Version: 0.30 Distribution: unstable Urgency: medium Maintainer: Debian CI team <team+ci@tracker.debian.org> Changed-By: Paul Gevers <elbrus@debian.org> Closes: 961138 Changes: autodep8 (0.30) unstable; urgency=medium . [ Antonio Terceiro ] * R: don't use APT cache for dependencies (Closes: #961138) * Fix all warnings produced by shellcheck Checksums-Sha1: 4231977c47b83a498ba42ab38ff54216cecb6a68 1880 autodep8_0.30.dsc a7ac0d15f907ba692b1ffe9510e83e7ec2b32d05 16940 autodep8_0.30.tar.xz Checksums-Sha256: cb16ff4b324adb4ebf26633b123bb80f41ed740e26dc1373ed49858d3cb36ba3 1880 autodep8_0.30.dsc cf304e0b75ffba384aa23669939c5573b7a56adb25bdc0b04bb67315e243378a 16940 autodep8_0.30.tar.xz Files: 5714ef2a57d7ba27fefece7c3b36efbd 1880 devel optional autodep8_0.30.dsc 6d86d2a652ce0c5e3a428b3955b9866a 16940 devel optional autodep8_0.30.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEG5OTVaxMNcrfvXOcBqMo4AxqzhUFAmizJ9cACgkQBqMo4Axq zhWL5w//Qwq5+34vaQ/JtMz2VtCvbZeQFZCiPdPqN88q+mW+4/s1pKkwMwVuyIzU ePcOpjOwfVrz9kcanXaAdO6CGCb/C8bW4C87KkPccRACbdqHg8l9rAurvvTb3isc UNT26slTX2E40qS+GeJQ0m7aFRtoITptw+vpwfeZfEaA5nBACvkbj345Pgg7nqXL HUKfrxbuiQsnZP7grksXMETxVfErbUf3OiKLTlYDACudT/JmR5Tjl9BEUESxu/gf Ax+PcZhGYamt5KkAn8v8VHClpPU3pr0lKfJcwFyNisKGsu2lBq+0KEOhVAchHu8U VySkd+dOFRIgTnMlJF34r6jZZGle5dp7v87s6cxv/+D3DyyhytqGD6AI6+WP6pFw Jb8bx5ZLsoTbxN5rVsZSKHjDoQxHi9etARcPP12dvoR6B8a+NO0b04dA185tOVhj 7GU1sedGFIPYnVQ95TAn+3e0zDPFf5wfjbOZNuAUcCSnbAFUvOVQqj7muT9lTcWu QaTK4y4qrvhgWlg+yVpIF6eMAveFjG4bqfI3i/t5HSsXDWr2kE4nUw1bJUqg9eBO kV7I+Ruhk8eTex19PSj2DCwKOOWk480opp7hRxWzcKgBvcuuSFsexmg/Wz9mYKaf PPEgeOg5g1Yi4bHI7n9R/SFgoG3aLdKTpn+cieirYBCynkAddrA= =4g1Z -----END PGP SIGNATURE-----