Package: lintian-brush Version: 0.167 Severity: normal X-Debbugs-Cc: [email protected]
Hi, please check $ gbp clone salsa:med-team/murasaki $ lintian-brush It does several unwanted changes 1. git show 4475fbd1886c5189d234a154520ef8d07eab0bf1q commit 4475fbd1886c5189d234a154520ef8d07eab0bf1 Author: Andreas Tille <[email protected]> Date: Sat Feb 21 21:06:35 2026 +0100 Drop use of autotools-dev debhelper. Changes-By: lintian-brush Fixes: lintian: debhelper-tools-from-autotools-dev-are-deprecated See-also: https://lintian.debian.org/tags/debhelper-tools-from-autotools-dev-are-deprecated.html Fixes: lintian: debhelper-tools-from-autotools-dev-are-deprecated See-also: https://lintian.debian.org/tags/debhelper-tools-from-autotools-dev-are-deprecated.html Fixes: lintian: debhelper-tools-from-autotools-dev-are-deprecated See-also: https://lintian.debian.org/tags/debhelper-tools-from-autotools-dev-are-deprecated.html diff --git a/debian/rules b/debian/rules index 16ebcac..33ccb24 100755 --- a/debian/rules +++ b/debian/rules @@ -16,7 +16,7 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+all override_dh_auto_build: dh_auto_build -- USE_MPI=YES for bin in geneparse mbfa murasaki cgr-* testeco align-* ; do \ - mv $${bin} $${bin}-mpi ; \ + mv $${bin} $${bin}-mpi ; \ done make clean dh_auto_build -- USE_MPI=NO @@ -27,14 +27,14 @@ override_dh_installman-indep: mkdir -p $(CMANDIR) for pscript in $(DEBMEDBIN)/* ; do \ pod2man $${pscript} > $(CMANDIR)/`basename $${pscript}`.1 ; \ - done + pod2man $${pscript} > $(CMANDIR)/`basename $${pscript}`.1 ; \ find $(CMANDIR) -empty -delete override_dh_installman-arch: dh_installman -a mkdir -p $(MMANDIR) for man in $(MANDIR)/*.1 ; do \ - cp -a $${man} $(MMANDIR)/`basename $${man} .1`-mpi.1 ; \ + cp -a $${man} $(MMANDIR)/`basename $${man} .1`-mpi.1 ; \ done override_dh_install-arch: --> The changes have nothing to do with the changelog. Its some reformatting and even worse it contains a breaking change by removing the "done" in the shell for loop. 2. Changing the sequence of paragraphs might be sensible in general - but I think the debian/* section should remain at the end in any case. $ git show f8c5479710ba99f564487c8ee678dc86797cf0d7 commit f8c5479710ba99f564487c8ee678dc86797cf0d7 Author: Andreas Tille <[email protected]> Date: Sat Feb 21 21:06:36 2026 +0100 Reorder Files paragraphs in debian/copyright by directory depth. Changes-By: lintian-brush Fixes: lintian: globbing-patterns-out-of-order See-also: https://lintian.debian.org/tags/globbing-patterns-out-of-order.html diff --git a/debian/copyright b/debian/copyright index e21221a..799dae7 100644 --- a/debian/copyright +++ b/debian/copyright @@ -6,10 +6,6 @@ Files: * Copyright: © 2006-2010 Keio University; Kris Popendorf License: GPL-3+ -Files: perlmodules/Murasaki/K* perlmodules/Murasaki/O* perlmodules/Murasaki/T* -Copyright: © 2006-2010 Keio University; Kris Popendorf -License: GPL-2+ - Files: debian/* Copyright: © 2008-2015 Andreas Tille <[email protected]> License: GPL-3+ @@ -28,6 +24,10 @@ Comment: [1]: https://ftp.ncbi.nlm.nih.gov/genomes/HUMAN_MICROBIOM/Bacteria/Acinetobacter_lwoffii_SH145_uid38343 [2]: https://ftp.ncbi.nlm.nih.gov/README.ftp +Files: perlmodules/Murasaki/K* perlmodules/Murasaki/O* perlmodules/Murasaki/T* +Copyright: © 2006-2010 Keio University; Kris Popendorf +License: GPL-2+ + License: GPL-3+ This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License 3. The change Set upstream metadata fields: Archive. is fine. 4. That's another instance of the problem reported in #1128572 $ git show commit baa96c345cf256a19cd1dff2106c32249b292af2 (HEAD -> master) Author: Andreas Tille <[email protected]> Date: Sat Feb 21 21:09:06 2026 +0100 Remove duplicate values for fields Entry, Entry, Name in debian/upstream/metadata. Changes-By: lintian-brush Fixes: lintian: upstream-metadata-yaml-invalid See-also: https://lintian.debian.org/tags/upstream-metadata-yaml-invalid.html diff --git a/debian/upstream/metadata b/debian/upstream/metadata index 129dad8..7e019f4 100644 --- a/debian/upstream/metadata +++ b/debian/upstream/metadata @@ -1,25 +1,22 @@ Archive: SourceForge Reference: Author: > - Kris Popendorf and Hachiya Tsuyoshi and Yasunori Osana and - Yasubumi Sakakibara - Title: > - Murasaki: A Fast, Parallelizable Algorithm to Find Anchors - from Multiple Genomes - Journal: PLOS one - Year: 2010 - Volume: 5 - Number: 9 - Pages: e12651 - DOI: 10.1371/journal.pone.0012651 - PMID: 20885980 - URL: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0012651 - ePrint: "https://www.plosone.org/article/fetchObject.action?uri=info:doi/\ - 10.1371/journal.pone.0012651&representation=PDF" + Kris Popendorf and Hachiya Tsuyoshi and Yasunori Osana and: + Yasubumi Sakakibara: + Title: > + Murasaki: A Fast, Parallelizable Algorithm to Find Anchors + from Multiple Genomes: + Journal: PLOS one + Year: 2010 + Volume: 5 + Number: 9 + Pages: e12651 + DOI: 10.1371/journal.pone.0012651 + PMID: 20885980 + URL: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0012651 + ePrint: https://www.plosone.org/article/fetchObject.action?uri=info:doi/\ + 10.1371/journal.pone.0012651&representation=PDF Registry: - - Name: OMICtools - Entry: OMICS_11714 - - Name: SciCrunch - Entry: NA - - Name: bio.tools - Entry: NA +- Name: OMICtools +Entry: OMICS_11714 +Name: SciCrunch Hope this helps to enhance lintian-brush Andreas. -- System Information: Debian Release: forky/sid APT prefers unstable APT policy: (500, 'unstable'), (500, 'testing'), (50, 'buildd-unstable'), (1, 'experimental') Architecture: amd64 (x86_64) Kernel: Linux 6.18.12+deb14-amd64 (SMP w/8 CPU threads; PREEMPT) Locale: LANG=de_DE.UTF-8, LC_CTYPE=de_DE.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 Versions of packages lintian-brush depends on: ii devscripts 2.26.5 ii libc6 2.42-13 ii libgcc-s1 15.2.0-13 ii libgmp10 2:6.3.0+dfsg-5+b1 ii libhogweed6t64 3.10.2-1 ii liblzma5 5.8.2-2 ii libnettle8t64 3.10.2-1 ii libpython3.13 3.13.12-1 ii libssl3t64 3.5.5-1 ii python3-breezy 3.3.21-1 Versions of packages lintian-brush recommends: ii debhelper 13.30 ii decopy 0.2.4.9-0.1 ii dos2unix 7.5.2-1 ii gpg 2.4.8-5 ii lintian 2.129.0 Versions of packages lintian-brush suggests: ii brz-debian 2.8.80 ii git-buildpackage 0.9.39 ii po-debconf 1.0.22 ii postgresql-common 289 -- no debconf information
