Étienne Mollier pushed to branch master at Debian Med / bioperl-run
Commits: 0825ac48 by Étienne Mollier at 2026-03-09T20:21:08+01:00 update-kalign-invocation.patch: new. This change adjusts arguments passed to kalign to use stdin as input and stdout as output, per the new command version's usage instructions. Closes: #1129866 - - - - - 690528e2 by Étienne Mollier at 2026-03-09T20:22:34+01:00 d/control: drop redundant Priority: optional. - - - - - 9aec1a0f by Étienne Mollier at 2026-03-09T20:22:51+01:00 d/control: drop redundant Rules-Requires-Root: no. - - - - - bcae4c59 by Étienne Mollier at 2026-03-09T20:23:29+01:00 d/control: declare compliance to standards version 4.7.3. - - - - - 61ce3328 by Étienne Mollier at 2026-03-09T20:42:47+01:00 d/watch: rework to port to Github uscan template. - - - - - b5ffc81a by Étienne Mollier at 2026-03-09T20:43:55+01:00 d/changelog: ready for upload to unstable. - - - - - 5 changed files: - debian/changelog - debian/control - debian/patches/series - + debian/patches/update-kalign-invocation.patch - debian/watch Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,16 @@ +bioperl-run (1.7.3-14) unstable; urgency=medium + + * update-kalign-invocation.patch: new. + This change adjusts arguments passed to kalign to use stdin as input + and stdout as output, per the new command version's usage + instructions. (Closes: #1129866) + * d/control: drop redundant Priority: optional. + * d/control: drop redundant Rules-Requires-Root: no. + * d/control: declare compliance to standards version 4.7.3. + * d/watch: rework to port to Github uscan template. + + -- Étienne Mollier <[email protected]> Mon, 09 Mar 2026 20:43:42 +0100 + bioperl-run (1.7.3-13) unstable; urgency=medium * Revert "skip_tests_for_ncbi-blast+.patch: remove." ===================================== debian/control ===================================== @@ -5,7 +5,6 @@ Uploaders: Charles Plessy <[email protected]>, Étienne Mollier <[email protected]> Section: science Testsuite: autopkgtest-pkg-perl -Priority: optional Build-Depends: debhelper-compat (= 13), libmodule-build-perl Build-Depends-Indep: perl, bioperl (>= 1.7.4), @@ -61,11 +60,10 @@ Build-Depends-Indep: perl, pftools [any-amd64], # Needed for the network tests: libwww-perl -Standards-Version: 4.7.0 +Standards-Version: 4.7.3 Vcs-Browser: https://salsa.debian.org/med-team/bioperl-run Vcs-Git: https://salsa.debian.org/med-team/bioperl-run.git Homepage: https://metacpan.org/release/BioPerl-Run -Rules-Requires-Root: no Package: bioperl-run Architecture: all ===================================== debian/patches/series ===================================== @@ -19,3 +19,4 @@ unscramble-erpin.patch fix-pod-conversion.patch adjust-muscle-test.patch update-blastdbcmd-error-output.patch +update-kalign-invocation.patch ===================================== debian/patches/update-kalign-invocation.patch ===================================== @@ -0,0 +1,18 @@ +Description: update kalign invocation arguments. +Author: Étienne Mollier <[email protected]> +Bug-Debian: https://bugs.debian.org/1129866 +Forwarded: no +Last-Update: 2026-03-09 +--- +This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ +--- bioperl-run.orig/lib/Bio/Tools/Run/Alignment/Kalign.pm ++++ bioperl-run/lib/Bio/Tools/Run/Alignment/Kalign.pm +@@ -464,7 +464,7 @@ + undef $tfh; + $self->outfile_name($outfile); + } +- $param_string .= " -out ".$self->outfile_name; ++ $param_string .= " -i - -o ".$self->outfile_name; + + if ($self->quiet() || $self->verbose < 0) { + my $null = ($^O =~ m/mswin/i) ? 'NUL' : '/dev/null'; ===================================== debian/watch ===================================== @@ -1,5 +1,7 @@ -version=4 -opts="uversionmangle=s/^release-\(.*\)$/\1/;s/[-_]/./g,filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE@-$1.tar.gz%" \ - https://github.com/bioperl/bioperl-run/tags (?:.*?/)?release-v?(\d[\d-]*)\.tar\.gz +Version: 5 -# http://search.cpan.org/dist/BioPerl-Run/ .*/BioPerl-Run-v?(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz|zip)$ +Template: Github +Project: bioperl-run +Owner: bioperl +# Workaround upstream's 07-branch; use dots for upstream dashes. +UVersion-Mangle: s/^0/0./; s/-/./g View it on GitLab: https://salsa.debian.org/med-team/bioperl-run/-/compare/7a192d251c38e1fceea12f95e38a51e60ee68e71...b5ffc81ad193a19dfb7ab7493d596ca54947661f -- View it on GitLab: https://salsa.debian.org/med-team/bioperl-run/-/compare/7a192d251c38e1fceea12f95e38a51e60ee68e71...b5ffc81ad193a19dfb7ab7493d596ca54947661f You're receiving this email because of your account on salsa.debian.org.
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