Your message dated Wed, 17 Mar 2021 09:03:26 +0000 with message-id <e1lms5o-000ifg...@fasolo.debian.org> and subject line Bug#985284: fixed in hyphy 2.5.28+dfsg-3 has caused the Debian Bug report #985284, regarding hyphy-common: unhandled symlink to directory conversion: /usr/lib/hyphy -> ../share/hyphy 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.) -- 985284: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=985284 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Package: hyphy-common Version: 2.5.28+dfsg-2 Severity: serious User: debian...@lists.debian.org Usertags: piuparts Hi, an upgrade test with piuparts revealed that your package installs files over existing symlinks and possibly overwrites files owned by other packages. This usually means an old version of the package shipped a symlink but that was later replaced by a real (and non-empty) directory. This kind of overwriting another package's files cannot be detected by dpkg. This was observed on the following upgrade paths: buster -> bullseye For /usr/share/doc/PACKAGE this may not be problematic as long as both packages are installed, ship byte-for-byte identical files and are upgraded in lockstep. But once one of the involved packages gets removed, the other one will lose its documentation files, too, including the copyright file, which is a violation of Policy 12.5: https://www.debian.org/doc/debian-policy/ch-docs.html#copyright-information For other overwritten locations anything interesting may happen. Note that dpkg intentionally does not replace directories with symlinks and vice versa, you need the maintainer scripts to do this. See in particular the end of point 4 in https://www.debian.org/doc/debian-policy/ch-maintainerscripts.html#details-of-unpack-phase-of-installation-or-upgrade It is recommended to use the dpkg-maintscript-helper commands 'dir_to_symlink' and 'symlink_to_dir' (available since dpkg 1.17.14) to perform the conversion, ideally using d/$PACKAGE.maintscript. See dpkg-maintscript-helper(1) and dh_installdeb(1) for details. >From the attached log (scroll to the bottom...): 0m33.7s ERROR: installs objects over existing directory symlinks: /usr/lib/hyphy/bin (hyphy-common) != /usr/share/hyphy/bin (?) /usr/lib/hyphy -> ../share/hyphy /usr/lib/hyphy/bin/simd-dispatch (hyphy-common) != /usr/share/hyphy/bin/simd-dispatch (?) /usr/lib/hyphy -> ../share/hyphy cheers, Andreas
hyphy-common_2.5.28+dfsg-2.log.gz
Description: application/gzip
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--- Begin Message ---Source: hyphy Source-Version: 2.5.28+dfsg-3 Done: Étienne Mollier <etienne.moll...@mailoo.org> We believe that the bug you reported is fixed in the latest version of hyphy, 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 985...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Étienne Mollier <etienne.moll...@mailoo.org> (supplier of updated hyphy 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: Tue, 16 Mar 2021 21:52:00 +0100 Source: hyphy Architecture: source Version: 2.5.28+dfsg-3 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Étienne Mollier <etienne.moll...@mailoo.org> Closes: 985284 Changes: hyphy (2.5.28+dfsg-3) unstable; urgency=medium . * d/*.maintscript: handle symbolic link removal in hyphy 2.5.18+dfsg-1. Closes: #985284 Checksums-Sha1: 3dec71916c68fd86b087d7ca5ad346aea1854181 2245 hyphy_2.5.28+dfsg-3.dsc a1f4aff9ac5c40ea74edf523789d3340dec90cab 17328 hyphy_2.5.28+dfsg-3.debian.tar.xz c4061eb0e9bafe28546cde028b807c183c0cc884 9284 hyphy_2.5.28+dfsg-3_amd64.buildinfo Checksums-Sha256: 4f0811135d9b87aeac3700a0a3e751dd0679df4d6688515c9299c11f707c150f 2245 hyphy_2.5.28+dfsg-3.dsc 85e2272de56508804b4a26633b04354ebf012eb83026d154b7a7444332c3887a 17328 hyphy_2.5.28+dfsg-3.debian.tar.xz 6dd9e8ebcf0623593580d50a474c64d51e85f6cff6c98b3888e751d4debd18ec 9284 hyphy_2.5.28+dfsg-3_amd64.buildinfo Files: 9c0c0687e60fff5f78b7e20c66159a55 2245 science optional hyphy_2.5.28+dfsg-3.dsc 969f8646fc01df5ec1f5400be59237ef 17328 science optional hyphy_2.5.28+dfsg-3.debian.tar.xz 53cbd29699c295e06dc941699d7ef583 9284 science optional hyphy_2.5.28+dfsg-3_amd64.buildinfo -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmBRwMQACgkQeTz2fo8N Edq19A/+Iqy1M4LdfEXuGlBUqn+0vIr9XaIFJVHBk6+FHF+o/jrr04yORnqIzmG+ zP0lvt2+ftNvCoAQ+XHQYF08PMmEl+AokBWd3TZc+faDU0L9WRQpizGxdHxFxAWy G/qwUgmOaEOQP/7wPrurSQq4L6I0mr5xG+66WInQkY1HzPXJnaIANxD6Ht2XDjjr E6fb+NhThfD1u2YxgefpBocCo1USBCJ8WAQNO4GCdfVI0npZ6O50cnX4OeayGLiF 33GsJFlKDywslGwK4G/rLp3YxbxF/1X1Y9tNQPAdBOAjH/HFLXStXlyWu/fIXkaR WUdxbpOQK6JH2GwcJAbNW8PIPEhBFROUIoxvC52vbC+4pyCwMeCb3QAk4odLJI8d Zzyni1IMKH7n+XgirpSeYDUWpgghc+vwhqwEBTg7tcEJQKIXUJ+DL+5CVIf4x3Bl RpQ3xxy0rYWUbXxos3ETF+mwfBYIxDQpwIJMUih42Fb+8KfWarsA2+ODEp2krT6Y 3MWwm/NRuebJvNiCEPngINmwZsnDQlqxQQWmulZcncZzvuUeYHfH1sDfSObycSa6 Q2ndZQWuXPVLDxeVYJA9aNB4mkNn/BcEctHs2ZQ4Ztn0rmB7RPvA6oxEFZYALc9J y794o4wJtVscc+oC/ISg6tgLWilfHsBMdRSx/af52rHkDQHWCYI= =YyRH -----END PGP SIGNATURE-----
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