Your message dated Sun, 23 Oct 2022 11:27:38 +0000 with message-id <e1omz8k-0053uh...@fasolo.debian.org> and subject line Bug#1022076: fixed in python-pybedtools 0.9.0-2 has caused the Debian Bug report #1022076, regarding python-pybedtools: Uses deprecated yaml.load (in contrib) 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.) -- 1022076: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1022076 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Source: python-pybedtools Version: 0.9.0-1 Severity: normal X-Debbugs-Cc: gor...@chronitis.net We hope to upgrade python3-yaml (aka pyyaml) to version 6 before the freeze, per #1008262 Your package appears to use `yaml.load()` without specifying a `Loader=` argument, which will become an error in pyyaml version 6. This should have emitted a warning message since version 5.1 (from 2019). In most cases this can be fixed by replacing `yaml.load` with `yaml.safe_load`, unless the ability for yaml to create arbitrary python objects is desirable. The only outstanding case appears to be in contrib: https://sources.debian.org/src/python-pybedtools/0.9.0-1/pybedtools/contrib/plotting.py/?hl=527#L527 (but this file is installed in python3-pybedtools), the test suite uses of yaml appear to be fixed. -- System Information: Debian Release: bookworm/sid APT prefers unstable APT policy: (500, 'unstable'), (1, 'experimental') Architecture: amd64 (x86_64) Kernel: Linux 6.0.0-1-amd64 (SMP w/1 CPU thread; PREEMPT) Locale: LANG=en_GB.UTF-8, LC_CTYPE=en_GB.UTF-8 (charmap=UTF-8), LANGUAGE=en_GB Shell: /bin/sh linked to /usr/bin/dash Init: systemd (via /run/systemd/system) LSM: AppArmor: enabled
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--- Begin Message ---Source: python-pybedtools Source-Version: 0.9.0-2 Done: Nilesh Patra <nil...@debian.org> We believe that the bug you reported is fixed in the latest version of python-pybedtools, 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 1022...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Nilesh Patra <nil...@debian.org> (supplier of updated python-pybedtools 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: Sun, 23 Oct 2022 16:24:34 +0530 Source: python-pybedtools Architecture: source Version: 0.9.0-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Nilesh Patra <nil...@debian.org> Closes: 1018560 1022076 Changes: python-pybedtools (0.9.0-2) unstable; urgency=medium . * Team Upload. * Add patch to replace yaml.load calls with yaml.safe_load (Closes: #1022076) * Change B-D from python3-nose to python3-pytest (Closes: #1018560) * Bump Standards-Version to 4.6.1 (no changes needed) Checksums-Sha1: 356337512ac8fcf20f27f6e41ae568c21408f527 2510 python-pybedtools_0.9.0-2.dsc 7375747318b1cbdc7d89e8a543018802d1e78b7c 29360 python-pybedtools_0.9.0-2.debian.tar.xz a3d01527a106adeffbfba13d874b09c24b3c86be 12492 python-pybedtools_0.9.0-2_amd64.buildinfo Checksums-Sha256: 74c17b2e75335dd332c19a97cbc080b9d0eeb043dea7803becd0dcaed21c4348 2510 python-pybedtools_0.9.0-2.dsc b7c9f7f4c8902404b8d6f7a11fc465fdc9e12b452bda5d1b4a1858e97d1961c8 29360 python-pybedtools_0.9.0-2.debian.tar.xz 12f22c0382ceef5dd19b28d0b59321bff81da5cf267bc2463c9adb13ef37bbd2 12492 python-pybedtools_0.9.0-2_amd64.buildinfo Files: eed15213f047d9c13f3976089c8e1fcb 2510 python optional python-pybedtools_0.9.0-2.dsc efb2b6e854ae867b51be00b5870c3a8d 29360 python optional python-pybedtools_0.9.0-2.debian.tar.xz 6325872e982e29232e6b8386d502490e 12492 python optional python-pybedtools_0.9.0-2_amd64.buildinfo -----BEGIN PGP SIGNATURE----- iQJGBAEBCgAwFiEEPpmlJvXcwMu/HO6mALrnSzQzafEFAmNVH0cSHG5pbGVzaEBk ZWJpYW4ub3JnAAoJEAC650s0M2nxtiMP/302d4X6NlAvxS3t11Vz3gc3/Jwln70n AZIvoJ5ZwyeV2etkhHlGZZr7FfwxNA2kPM+lchfhz+/jpaNMXrGNL2wNjQEyUOYZ AX4ZNZD3PZX1S5WJELNnakhNJAHE6oLBnGMp7/E3cbtdVFHCNS1v/e9lP+2vXJST mFz7tL0lJvfG2UbaJh1mjadL8rNb3kwfnGSRTnJ7oSCrYKMLCL4/vBeyttERoOOW y42kshGuUnAsLdqF5j1aVtKoCGO9sgNphuzUdCgqTCj/BGsuOJ/lp+fpj+dNwwi5 2f1zhVJFmKkRPZUg0MOYZdsayg62ls2fB5OvTuVRbTytfqv8lU1fXi6dY99gZbjX YhkyW5JxanqZsacGeKec9HzUM6hfldrbh7qCcspvah7qBC9VAwmrRYg8EwV0iK25 6Q6Aycb8MqRKA3wd0cTcK2eUcY+q3A0+Yn2Mjbokqde1Eo5Il0nE3WeBZ2NkR7K6 MwcXmkNLtAe+UQY85ZqvA9x5MDFujohl1iSgFC7MyX2K+V2791F2NknOMp6Ovkgs jAvtElS2OUJ+uSrMmfKJqNrGArqjqIvQsPmxjmsvIcHIFAwnxyV6eRlIKHzvy+Jw YacCJc2bXjgCO/4lKKZvhSwcROy0Qyjyd4qH/FCOtKv1FpvWeFAG+ADbeYA4ctiG T74lsbLwKZKf =GoZz -----END PGP SIGNATURE-----
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