[med-svn] [Git][med-team/flexbar][master] 8 commits: Packaging update (routine-update)
Andreas Tille (@tille)
gitlab at salsa.debian.org
Thu Apr 30 20:17:16 BST 2026
Andreas Tille pushed to branch master at Debian Med / flexbar
Commits:
4757de5e by Andreas Tille at 2026-04-30T20:34:56+02:00
Packaging update (routine-update)
- - - - -
ab1fdebe by Andreas Tille at 2026-04-30T20:34:56+02:00
Standards-Version: 4.7.4 (routine-update)
- - - - -
b143d478 by Andreas Tille at 2026-04-30T20:35:00+02:00
Changes made by cme
- - - - -
7dbfe9dd by Andreas Tille at 2026-04-30T20:35:02+02:00
Drop default 'Rules-Requires-Root: no' from d/control (routine- update)
- - - - -
93e38d74 by Andreas Tille at 2026-04-30T20:59:15+02:00
Build with libseqan2 2.5 Closes: #1125731
- - - - -
b82bc58b by Andreas Tille at 2026-04-30T21:13:00+02:00
Fix lintian-overrides
- - - - -
63abcfca by Andreas Tille at 2026-04-30T21:14:47+02:00
Upload to unstable
- - - - -
bb684db5 by Andreas Tille at 2026-04-30T21:17:09+02:00
Fix Last-Updated format to match DEP3
- - - - -
10 changed files:
- debian/changelog
- debian/control
- debian/lintian-overrides
- debian/patches/195a1ab2c2715b07df5acff58dc2a0396d9cd52d.patch
- debian/patches/19722f2743c96235ff57948eda82f963cf734131.patch
- debian/patches/1c872fa10d474f090633fc95d409aa60607a3f96.patch
- debian/patches/a9b0eb87a391aeaf760f8116dca777749c8b4f96.patch
- + debian/patches/libseqan2.5.patch
- debian/patches/no_march_native.patch
- debian/patches/series
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,22 @@
+flexbar (1:3.5.0-9) UNRELEASED; urgency=medium
+
+ * Fix Last-Updated format to match DEP3
+
+ -- Andreas Tille <tille at debian.org> Thu, 30 Apr 2026 21:16:30 +0200
+
+flexbar (1:3.5.0-8) unstable; urgency=medium
+
+ * Packaging update (routine-update)
+ * Standards-Version: 4.7.4 (routine-update)
+ * Remove Priority field (cme)
+ * Drop default 'Rules-Requires-Root: no' from d/control (routine-
+ update)
+ * Build with libseqan2 2.5
+ Closes: #1125731
+ * Fix lintian-overrides
+
+ -- Andreas Tille <tille at debian.org> Thu, 30 Apr 2026 21:13:07 +0200
+
flexbar (1:3.5.0-7) unstable; urgency=medium
* Fix build with CMake 4
=====================================
debian/control
=====================================
@@ -1,11 +1,10 @@
Source: flexbar
-Standards-Version: 4.7.2
+Standards-Version: 4.7.4
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders:
Andreas Tille <tille at debian.org>,
Tony Travis <ajt at minke.ukfsn.org>,
Section: science
-Priority: optional
Build-Depends:
debhelper-compat (= 13),
libtbb-dev,
@@ -16,7 +15,6 @@ Build-Depends:
Vcs-Browser: https://salsa.debian.org/med-team/flexbar
Vcs-Git: https://salsa.debian.org/med-team/flexbar.git
Homepage: https://github.com/seqan/flexbar
-Rules-Requires-Root: no
Package: flexbar
Architecture: any
=====================================
debian/lintian-overrides
=====================================
@@ -1,2 +1,2 @@
# Upstream intends to provide both kind of compressions to test
-flexbar: compressed-duplicate usr/share/doc/flexbar/examples/*
+flexbar: compressed-duplicate *
=====================================
debian/patches/195a1ab2c2715b07df5acff58dc2a0396d9cd52d.patch
=====================================
@@ -1,6 +1,6 @@
From 195a1ab2c2715b07df5acff58dc2a0396d9cd52d Mon Sep 17 00:00:00 2001
From: Liam Keegan <liam at keegan.ch>
-Date: Thu, 9 Feb 2023 16:27:37 +0100
+Last-Update: 2023-02-09
Subject: [PATCH] Migrate from tbb to onetbb
- add `FlexbarAtomic`
=====================================
debian/patches/19722f2743c96235ff57948eda82f963cf734131.patch
=====================================
@@ -1,6 +1,6 @@
From 19722f2743c96235ff57948eda82f963cf734131 Mon Sep 17 00:00:00 2001
From: Liam Keegan <liam at keegan.ch>
-Date: Fri, 10 Feb 2023 10:21:22 +0100
+Last-Update: 2023-02-10
Subject: [PATCH] revert accidental removal of pthread linking in
src/CMakeLists.txt
=====================================
debian/patches/1c872fa10d474f090633fc95d409aa60607a3f96.patch
=====================================
@@ -1,6 +1,6 @@
From 1c872fa10d474f090633fc95d409aa60607a3f96 Mon Sep 17 00:00:00 2001
From: Liam Keegan <liam at keegan.ch>
-Date: Fri, 10 Feb 2023 09:55:58 +0100
+Last-Update: 2023-02-10
Subject: [PATCH] Fix parallel_pipeline issues
- pass a lambda with a reference to the filter instead of directly passing the filter to parallel_pipeline
=====================================
debian/patches/a9b0eb87a391aeaf760f8116dca777749c8b4f96.patch
=====================================
@@ -1,6 +1,6 @@
From a9b0eb87a391aeaf760f8116dca777749c8b4f96 Mon Sep 17 00:00:00 2001
From: Liam Keegan <liam at keegan.ch>
-Date: Fri, 10 Feb 2023 10:52:35 +0100
+Last-Update: 2023-02-10
Subject: [PATCH] use `std::atomic` instead of `FlexbarAtomic` in filters as
they are no longer require copy constructors
=====================================
debian/patches/libseqan2.5.patch
=====================================
@@ -0,0 +1,62 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: 2026-04-30
+Bug-Debian: https://bugs.debian.org/1125731
+Description: Build with libseqan2 2.5
+
+--- a/src/FlexbarTypes.h
++++ b/src/FlexbarTypes.h
+@@ -5,6 +5,13 @@
+
+ #include <atomic>
+
++// SeqAn 2.5 renamed the namespace from 'seqan' to 'seqan2'.
++// Provide a backward-compatibility alias for older code.
++#include <seqan/version.h>
++#if defined(SEQAN_VERSION_MINOR) && SEQAN_VERSION_MINOR >= 5
++namespace seqan = seqan2;
++#endif
++
+ // A simple wrapper around std::atomic<T> with a copy-constructor
+ // This is a drop-in replacement for the previously used tbb::atomic (which is copyable),
+ // to avoid having to add copy-constructors to classes that used it
+--- a/src/FlexbarIO.h
++++ b/src/FlexbarIO.h
+@@ -47,7 +47,7 @@ void closeFile(std::fstream &strm){
+ }
+
+
+-namespace seqan{
++namespace seqan2{
+
+ // Extension for input fasta file with dat ending
+
+--- a/src/SeqInput.h
++++ b/src/SeqInput.h
+@@ -6,6 +6,12 @@
+ #include <seqan/seq_io.h>
+ #include "QualTrimming.h"
+
++// SeqAn 2.5 renamed the namespace from 'seqan' to 'seqan2'.
++// Provide a backward-compatibility alias for older code.
++#include <seqan/version.h>
++#if defined(SEQAN_VERSION_MINOR) && SEQAN_VERSION_MINOR >= 5
++namespace seqan = seqan2;
++#endif
+
+ template <typename TSeqStr, typename TString>
+ class SeqInput {
+--- a/src/SeqAlignAlgo.h
++++ b/src/SeqAlignAlgo.h
+@@ -3,6 +3,12 @@
+ #ifndef FLEXBAR_SEQALIGNALGO_H
+ #define FLEXBAR_SEQALIGNALGO_H
+
++// SeqAn 2.5 renamed the namespace from 'seqan' to 'seqan2'.
++// Provide a backward-compatibility alias for older code.
++#include <seqan/version.h>
++#if defined(SEQAN_VERSION_MINOR) && SEQAN_VERSION_MINOR >= 5
++namespace seqan = seqan2;
++#endif
+
+ template <typename TSeqStr>
+ class SeqAlignAlgo {
=====================================
debian/patches/no_march_native.patch
=====================================
@@ -1,5 +1,5 @@
Author: Andreas Tille <tille at debian.org>
-Last-Update: Sun, 27 Aug 2017 22:04:31 +0200
+Last-Update: 2017-08-27
Bug-Debian: https://bugs.debian.org/873429
Forwarded: no
Description: Do not build with -march=native
=====================================
debian/patches/series
=====================================
@@ -3,3 +3,4 @@ no_march_native.patch
1c872fa10d474f090633fc95d409aa60607a3f96.patch
19722f2743c96235ff57948eda82f963cf734131.patch
a9b0eb87a391aeaf760f8116dca777749c8b4f96.patch
+libseqan2.5.patch
View it on GitLab: https://salsa.debian.org/med-team/flexbar/-/compare/02f76126ff643b75b1ef55346707d5db663001b3...bb684db563f1c8ce92ac35014b59187971d40d8a
--
View it on GitLab: https://salsa.debian.org/med-team/flexbar/-/compare/02f76126ff643b75b1ef55346707d5db663001b3...bb684db563f1c8ce92ac35014b59187971d40d8a
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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20260430/c1099ff4/attachment-0001.htm>
More information about the debian-med-commit
mailing list