Karsten Schöke pushed to branch master at Debian Med / lefse
Commits: 842d9862 by Karsten Schöke at 2026-08-18T12:14:33+02:00 d/control: restricted architecture to amd64, arm64, loong64, ppc64el, and riscv64 The reason is the restriction of R packages via r-pkg-team-core-architecture; for instance, the r-cran-coin dependency cannot be installed on s390x, and the tests fail. - - - - - 6067d857 by Karsten Schöke at 2026-08-18T12:15:21+02:00 Packaging update (routine-update) - - - - - 1b3b08aa by Karsten Schöke at 2026-08-18T12:15:21+02:00 Standards-Version: 4.7.4 (routine-update) - - - - - f67d980e by Karsten Schöke at 2026-08-18T12:15:33+02:00 Changes made by cme - - - - - caf8cdaa by Karsten Schöke at 2026-08-18T12:19:24+02:00 Drop 'Rules-Requires-Root: no' from d/control (routine-update) - - - - - bafc789f by Karsten Schöke at 2026-08-18T12:22:53+02:00 Packaging update (routine-update) - - - - - 223abbd4 by Karsten Schöke at 2026-08-18T12:54:49+02:00 Fix autopkgtest for lefse_format_input.py Update the autopkgtest to check the exit status of lefse_format_input.py -h instead of matching the exact usage string. The command supports additional options, so its usage output differs from the pattern expected by the test. This caused the test to fail even though the command itself works correctly. - - - - - 3 changed files: - debian/changelog - debian/control - debian/tests/run-unit-test Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,16 @@ +lefse (1.1.2-3) UNRELEASED; urgency=medium + + * Team upload. + * Standards-Version: 4.7.4 (routine-update) + * Reflow Uploaders field (cme) + * Remove Priority field (cme) + * Drop 'Rules-Requires-Root: no' from d/control (routine-update) + * d/control: restricted architecture to + amd64, arm64, loong64, ppc64el, and riscv64 + * Fix autopkgtest for lefse_format_input.py + + -- Karsten Schöke <[email protected]> Tue, 18 Aug 2026 12:36:45 +0200 + lefse (1.1.2-2) unstable; urgency=medium * Correct patch header metadata ===================================== debian/control ===================================== @@ -1,25 +1,26 @@ Source: lefse +Standards-Version: 4.7.4 Maintainer: Debian Med Packaging Team <[email protected]> -Uploaders: Andreas Tille <[email protected]> +Uploaders: + Andreas Tille <[email protected]>, Section: science -Priority: optional -Build-Depends: debhelper-compat (= 13), - dh-python, - python3-all, - python3-setuptools -Standards-Version: 4.7.0 +Build-Depends: + debhelper-compat (= 14), + dh-python, + python3-all, + python3-setuptools, Vcs-Browser: https://salsa.debian.org/med-team/lefse Vcs-Git: https://salsa.debian.org/med-team/lefse.git Homepage: https://github.com/SegataLab/lefse -Rules-Requires-Root: no Package: lefse -Architecture: all -Depends: ${python3:Depends}, - ${misc:Depends}, - python3-rpy2, - r-cran-coin, - python3-matplotlib +Architecture: amd64 arm64 loong64 ppc64el riscv64 +Depends: + ${python3:Depends}, + ${misc:Depends}, + python3-rpy2, + r-cran-coin, + python3-matplotlib, Description: determine features of organisms, clades, taxonomic units, genes LEfSe (Linear discriminant analysis Effect Size) determines the features (organisms, clades, operational taxonomic units, genes, or functions) ===================================== debian/tests/run-unit-test ===================================== @@ -58,7 +58,7 @@ else fi # lefse_format_input.py -if [[ $(lefse_format_input.py -h 2>&1) = "usage: lefse_format_input.py [-h]"* ]]; then +if lefse_format_input.py -h >/dev/null 2>&1; then echo "lefse_format_input.py comparative pass" else echo "lefse_format_input.py comparative fail. Instead, I get:" View it on GitLab: https://salsa.debian.org/med-team/lefse/-/compare/f4fd09e22fab756f4954a82102b77a78a95664f0...223abbd4267985a4d1957603541e37caebda57b1 -- View it on GitLab: https://salsa.debian.org/med-team/lefse/-/compare/f4fd09e22fab756f4954a82102b77a78a95664f0...223abbd4267985a4d1957603541e37caebda57b1 You're receiving this email because of your account on salsa.debian.org. Manage all notifications: https://salsa.debian.org/-/profile/notifications | Help: https://salsa.debian.org/help
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