Your message dated Sat, 18 Nov 2023 16:19:07 +0000 with message-id <e1r4o2f-000i4m...@fasolo.debian.org> and subject line Bug#1055414: fixed in bedtools 2.31.0+dfsg-2 has caused the Debian Bug report #1055414, regarding bedtools: FTBFS on i386: "intersect" tool failure 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.) -- 1055414: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1055414 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Source: bedtools Version: 2.31.0+dfsg-1 Severity: serious Tags: ftbfs Justification: ftbfs Dear Maintainer, While making a routine metadata update on a Debian patch against bedtools, Salsa CI caught a build failure on i386[1] which I could reproduce multiple times in sid and in testing with the unmodified version of the package. [1]: https://salsa.debian.org/med-team/bedtools/-/jobs/4891166 The relevant part of the build log shows the following differences in the test suite of the "intersect" tool: intersect.t22.p...0a1 > chr1 0 30 one_block_one_exon_30bp 40 - 0 30 0,0,0 1 30, 0, chr1 0 100 exon1 1 + 30 fail intersect.t22.q...1a2 > chr1 80 110 one_block_one_exon_20bp 40 - 80 110 0,0,0 1 30, 0, chr1 0 100 exon1 1 + 20 fail The tests are started from test/intersect/test-intersect.sh. I'm not sure what change caused the build failure to appear. The issue is not affecting amd64, nor armhf, which suggest something very i386 specific. I have not checked closely the other CPU architectures yet. The relevant upstream change that introduced this code begins to date back from quite some time ago[2] and the package builds with -ffloat-store for a while, so this may be caused by a dependency, or a compiler change. [2]: https://github.com/arq5x/bedtools2/commit/9d22ccb24f258553b0eff31e689b09563227331b Hope this helps pinpointing what's up, Étienne. -- System Information: Debian Release: trixie/sid APT prefers unstable APT policy: (500, 'unstable') Architecture: amd64 (x86_64) Foreign Architectures: i386 Kernel: Linux 6.5.0-3-amd64 (SMP w/12 CPU threads; PREEMPT) Locale: LANG=C.UTF-8, LC_CTYPE=C.UTF-8 (charmap=UTF-8), LANGUAGE not set Shell: /bin/sh linked to /usr/bin/dash Init: systemd (via /run/systemd/system) LSM: AppArmor: enabled -- .''`. Étienne Mollier <emoll...@debian.org> : :' : gpg: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da `. `' sent from /dev/pts/7, please excuse my verbosity `- on air: Condition Red - Let It All Come Out
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--- Begin Message ---Source: bedtools Source-Version: 2.31.0+dfsg-2 Done: Étienne Mollier <emoll...@debian.org> We believe that the bug you reported is fixed in the latest version of bedtools, 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 1055...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Étienne Mollier <emoll...@debian.org> (supplier of updated bedtools 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: Sat, 18 Nov 2023 16:34:59 +0100 Source: bedtools Architecture: source Version: 2.31.0+dfsg-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Étienne Mollier <emoll...@debian.org> Closes: 1055414 Changes: bedtools (2.31.0+dfsg-2) unstable; urgency=medium . * gcc-13.patch: fixed upstream by different change. The Applied-Upstream field is set accordingly to point to PR 1067. * d/rules: use sse for floating point calculations. This fixes bedtools "intersect" test failures during build time. This change is brought for consistency with htslib's own settings. While this is an architecture baseline violation, the alternative is no htslib support at all for the i386 distribution, since it fails its own test suite with anything else than sse for floating point calculations. (Closes: #1055414) * d/control: depend on python3:any per M-A hint. Checksums-Sha1: b69869f9eb17040a63e6a4fd3d61cf5416a0db80 2230 bedtools_2.31.0+dfsg-2.dsc ffc64ee2b9dc7aad78ab729e21dc245bb2bc330c 14612 bedtools_2.31.0+dfsg-2.debian.tar.xz 7a670314ea9bc8241bab29a0ba3f7d65a659b4b9 7085 bedtools_2.31.0+dfsg-2_amd64.buildinfo Checksums-Sha256: 51f056d80db2e0e80acfcd3b998b967ed813f7b70c0512174f7709769cfdfb55 2230 bedtools_2.31.0+dfsg-2.dsc a11c7ff99c891175178ce7f79b3a5efd2e71885565d8a931ec09c82f3e924c50 14612 bedtools_2.31.0+dfsg-2.debian.tar.xz 2514f71a9ee14948b3ac72b4cd180678c87b514b047664524b4d7603623e5017 7085 bedtools_2.31.0+dfsg-2_amd64.buildinfo Files: fb3db78a27670dadc7302c3e9fb77d61 2230 science optional bedtools_2.31.0+dfsg-2.dsc 9e47e14001ed5d267fd182cf1a56890a 14612 science optional bedtools_2.31.0+dfsg-2.debian.tar.xz 30b406eb7a0e8e4a4987eae3c8e0a719 7085 science optional bedtools_2.31.0+dfsg-2_amd64.buildinfo -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmVY3/QUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdppGBAAstjOxT/StG6tGXxGXZAbUVZF1pyQ i7r/q4kCywKsupPlFU7TV1Qt40bMdVrolPQc01JlD1GiPQAO2AvxoSS8URpu481Z BByJP99e2KKDPorA3g8IHW3QYSdBkXpSYo9baKeV7tdF+LLhhHwzazkV8rrNNL8z +jULcoX9ptaoyldXt+A3v8NsNdsGNXs8wQEZWLgQ7wdks37QRflYlrusWhMBexmN mR2sZoQfgZIjoHqCIRMWgZ1eESssr94lrL6b6CFXQI3/2MPCAUJyLXC50Ov7filI pcNkt6iiIFF8gOnZFMEO1Q2YXAdLobg7LQZC2fEaIA1ZqeBMi8okkx9SQp24/qvm HxSy3yzTy5v3zpTPW+eHw8QzHSiqjpOM2aib446dIGIcyPUDvdR5iU5PdVWRkcIp 6WXVZ9ulS1l5G0HzDQf5nB9x8K3PSbKnZ6ej7gAUJKJkgjaj/M1qX3RGWIDs/q9g dU7sbB7X+CmyOc8xiWhPreMST8n6HFmDUuGDJXzvCt9xZCZCzONKIi7vJLsfPBVw 49zJdVcBQAymPuFcYClNHzu11fp9LOUJIT7wniAf4QgV8DZ1nCqM6+uq07Bz6R4E uv19HHM7+Ow7T8HuS0uWEj50uWlAEu4dMSTO8DYDLwLr8DnMg5Bqi+6B60cw0p+l 3weQ7FcyJxExP4U= =4Jhd -----END PGP SIGNATURE-----
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