[med-svn] [Git][med-team/lambda-align][master] 2 commits: Add SeqAn 2.5.x namespace patch

[Enrico Seiler (@eseiler)]

Enrico Seiler pushed to branch master at Debian Med / lambda-align


Commits:
4de7f568 by Enrico Seiler at 2026-02-22T20:01:00+01:00
Add SeqAn 2.5.x namespace patch

- - - - -
fd694933 by Enrico Seiler at 2026-02-22T20:01:46+01:00
Fix autopkgtest using CMake 4

- - - - -


6 changed files:

- debian/changelog
- + debian/patches/0003-Upgrade-to-SeqAn-2.5.0.patch
- debian/patches/force-link-rt-pthread.patch
- debian/patches/series
- debian/patches/set-seqan-cmake-dir.patch
- debian/tests/run-tests


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+lambda-align (1.0.3-9) UNRELEASED; urgency=medium
+
+  * Team upload.
+  * Add SeqAn 2.5.x namespace patch
+  * Fix autopkgtest using CMake 4
+
+ -- Enrico Seiler <enrico.seiler.debian at outlook.com>  Sun, 22 Feb 2026 19:59:51 +0100
+
 lambda-align (1.0.3-8) unstable; urgency=medium
 
   * Team upload.


=====================================
debian/patches/0003-Upgrade-to-SeqAn-2.5.0.patch
=====================================
Binary files /dev/null and b/debian/patches/0003-Upgrade-to-SeqAn-2.5.0.patch differ


=====================================
debian/patches/force-link-rt-pthread.patch
=====================================
@@ -1,10 +1,18 @@
-Description: enforce linking of -lrt -lpthread
- This patch makes sure that these get linked even though they might
- be missing in $SEQAN_LIBRARIES (until this is fixed in libseqan2-dev).
-Author: Sascha Steinbiss <satta at debian.org>
---- lambda-align.orig/src/CMakeLists.txt
-+++ lambda-align/src/CMakeLists.txt
-@@ -208,8 +208,8 @@
+From: Sascha Steinbiss <satta at debian.org>
+Date: Sun, 9 Oct 2016 15:06:20 +0000
+Subject: enforce linking of -lrt -lpthread
+
+This patch makes sure that these get linked even though they might
+be missing in $SEQAN_LIBRARIES (until this is fixed in libseqan2-dev).
+---
+ src/CMakeLists.txt | 4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
+index da7ff38..9fc2e08 100644
+--- a/src/CMakeLists.txt
++++ b/src/CMakeLists.txt
+@@ -208,8 +208,8 @@ add_executable (lambda_indexer lambda_indexer.cpp
                  radix_inplace.h)
  
  # Add dependencies found by find_package (SeqAn).


=====================================
debian/patches/series
=====================================
@@ -1,3 +1,4 @@
 set-seqan-cmake-dir.patch
 force-link-rt-pthread.patch
+0003-Upgrade-to-SeqAn-2.5.0.patch
 0004-make-test-not-depend-on-CXX.patch


=====================================
debian/patches/set-seqan-cmake-dir.patch
=====================================
@@ -1,8 +1,16 @@
-Description: set SeqAn_DIR to find CMake modules
-Author: Sascha Steinbiss <satta at debian.org>
+From: Sascha Steinbiss <satta at debian.org>
+Date: Sat, 21 Jan 2017 14:01:48 +0000
+Subject: set SeqAn_DIR to find CMake modules
+
+---
+ src/CMakeLists.txt | 2 ++
+ 1 file changed, 2 insertions(+)
+
+diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
+index f89706a..da7ff38 100644
 --- a/src/CMakeLists.txt
 +++ b/src/CMakeLists.txt
-@@ -22,6 +22,8 @@
+@@ -22,6 +22,8 @@ set (SEQAN_APP_VERSION "${SEQAN_APP_VERSION_MAJOR}.${SEQAN_APP_VERSION_MINOR}.${
  # Dependencies (continued)
  # ----------------------------------------------------------------------------
  


=====================================
debian/tests/run-tests
=====================================
@@ -3,7 +3,7 @@
 mkdir build
 cd build
 cmake -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON \
-	-DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON ../tests
+	-DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_POLICY_VERSION_MINIMUM=3.5 ../tests
 ln -s ../tests ../tests/tests
 mkdir bin
 for binary in $(dpkg -L lambda-align | grep bin/); do ln -s ${binary} bin/; done



View it on GitLab: https://salsa.debian.org/med-team/lambda-align/-/compare/18fa37a2c87af63de184b10993101aa1b12345fc...fd694933479eb6ff60f876850c420b223217f6ba

-- 
View it on GitLab: https://salsa.debian.org/med-team/lambda-align/-/compare/18fa37a2c87af63de184b10993101aa1b12345fc...fd694933479eb6ff60f876850c420b223217f6ba
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