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 <[email protected]> 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 <[email protected]> ---- lambda-align.orig/src/CMakeLists.txt -+++ lambda-align/src/CMakeLists.txt -@@ -208,8 +208,8 @@ +From: Sascha Steinbiss <[email protected]> +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 $SEQAN_LIBRARIES (until this is fixed in libseqan2-dev). +--- + src/CMakeLists.txt | 4 ++-- + 1 file changed, 2 insertions(+), 2 deletions(-) + +diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt +index da7ff38..9fc2e08 100644 +--- a/src/CMakeLists.txt ++++ b/src/CMakeLists.txt +@@ -208,8 +208,8 @@ add_executable (lambda_indexer lambda_indexer.cpp radix_inplace.h) # Add dependencies found by find_package (SeqAn). ===================================== debian/patches/series ===================================== @@ -1,3 +1,4 @@ set-seqan-cmake-dir.patch force-link-rt-pthread.patch +0003-Upgrade-to-SeqAn-2.5.0.patch 0004-make-test-not-depend-on-CXX.patch ===================================== debian/patches/set-seqan-cmake-dir.patch ===================================== @@ -1,8 +1,16 @@ -Description: set SeqAn_DIR to find CMake modules -Author: Sascha Steinbiss <[email protected]> +From: Sascha Steinbiss <[email protected]> +Date: Sat, 21 Jan 2017 14:01:48 +0000 +Subject: set SeqAn_DIR to find CMake modules + +--- + src/CMakeLists.txt | 2 ++ + 1 file changed, 2 insertions(+) + +diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt +index f89706a..da7ff38 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt -@@ -22,6 +22,8 @@ +@@ -22,6 +22,8 @@ set (SEQAN_APP_VERSION "${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 You're receiving this email because of your account on salsa.debian.org.
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