[Debian-med-packaging] Bug#1139607: mapsembler2: FTBFS against HDF5 2.1.0

[Gilles Filippini]

Source: mapsembler2
Version: 2.2.4+dfsg1-6
Severity: important
Tags: ftbfs patch

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Hi,

During a test rebuild of HDF5's reverse dependencies against HDF5 2.1.0
currently in experimental, mapsembler2 FTBFS because its build toolchain
doesn't support this new major release.

The attached patch is a workaround for this issue and supports both
HDF5 1.14.6 in unstable and HDF5 2.1.0 in experimental.

Best,
_g.


- -- System Information:
Debian Release: 12.0
Architecture: amd64 (x86_64)

Kernel: Linux 6.1.0-44-amd64 (SMP w/12 CPU threads; PREEMPT)
Kernel taint flags: TAINT_OOT_MODULE, TAINT_UNSIGNED_MODULE
Locale: LANG=fr_FR.UTF-8, LC_CTYPE=fr_FR.UTF-8 (charmap=UTF-8), LANGUAGE not set
Shell: /bin/sh linked to /usr/bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled

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diff -Nru mapsembler2-2.2.4+dfsg1/debian/changelog mapsembler2-2.2.4+dfsg1/debian/changelog
--- mapsembler2-2.2.4+dfsg1/debian/changelog	2026-04-28 14:51:08.000000000 +0200
+++ mapsembler2-2.2.4+dfsg1/debian/changelog	2026-06-01 17:29:09.000000000 +0200
@@ -1,3 +1,10 @@
+mapsembler2 (2.2.4+dfsg1-6.1) UNRELEASED; urgency=medium
+
+  * Non-maintainer upload.
+  * Fix FTBFS against HDF5 2.1.0
+
+ -- Gilles Filippini <pini at debian.org>  Mon, 01 Jun 2026 17:29:09 +0200
+
 mapsembler2 (2.2.4+dfsg1-6) unstable; urgency=medium
 
   * Fix build with CMake 4
diff -Nru mapsembler2-2.2.4+dfsg1/debian/patches/hdf5-2.1.0.patch mapsembler2-2.2.4+dfsg1/debian/patches/hdf5-2.1.0.patch
--- mapsembler2-2.2.4+dfsg1/debian/patches/hdf5-2.1.0.patch	1970-01-01 01:00:00.000000000 +0100
+++ mapsembler2-2.2.4+dfsg1/debian/patches/hdf5-2.1.0.patch	2026-06-01 17:29:09.000000000 +0200
@@ -0,0 +1,12 @@
+Index: mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/CMakeLists.txt
+===================================================================
+--- mapsembler2-2.2.4+dfsg1.orig/mapsembler2_extremities/thirdparty/gatb-core/CMakeLists.txt
++++ mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/CMakeLists.txt
+@@ -221,7 +221,6 @@ ADD_SUBDIRECTORY(thirdparty)
+ find_package (HDF5 REQUIRED)
+ if (HDF5_FOUND)
+     include_directories (${HDF5_INCLUDE_DIRS})
+-    set (gatb-core-libraries ${gatb-core-libraries} ${HDF5_LIBRARIES})
+     set (gatb-core-libraries ${gatb-core-libraries} PARENT_SCOPE)
+ endif()
+ 
diff -Nru mapsembler2-2.2.4+dfsg1/debian/patches/series mapsembler2-2.2.4+dfsg1/debian/patches/series
--- mapsembler2-2.2.4+dfsg1/debian/patches/series	2026-04-28 14:51:08.000000000 +0200
+++ mapsembler2-2.2.4+dfsg1/debian/patches/series	2026-06-01 17:29:09.000000000 +0200
@@ -11,3 +11,4 @@
 cross.patch
 gcc11.patch
 cmake4.patch
+hdf5-2.1.0.patch