Bug#1139600: gmtsar: FTBFS against HDF5 2.1.0

[Gilles Filippini]

Source: gmtsar
Version: 6.6+ds-1
Severity: important
Tags: ftbfs patch

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Hash: SHA512

Hi,

During a test rebuild of HDF5's reverse dependencies against HDF5 2.1.0
currently in experimental, gmtsar FTBFS because the related m4 macro
doesn't support this new major release.

The attached patch fixes this issue and support 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 gmtsar-6.6+ds/debian/changelog gmtsar-6.6+ds/debian/changelog
--- gmtsar-6.6+ds/debian/changelog	2025-10-21 08:33:29.000000000 +0200
+++ gmtsar-6.6+ds/debian/changelog	2026-05-28 14:36:01.000000000 +0200
@@ -1,3 +1,10 @@
+gmtsar (6.6+ds-1.1) UNRELEASED; urgency=medium
+
+  * Non-maintainer upload.
+  * Fix FTBFS against HDF5 2.1.0
+
+ -- Gilles Filippini <pini at debian.org>  Thu, 28 May 2026 14:36:01 +0200
+
 gmtsar (6.6+ds-1) unstable; urgency=medium
 
   [ Bas Couwenberg ]
diff -Nru gmtsar-6.6+ds/debian/patches/hdf5-2.1.0.patch gmtsar-6.6+ds/debian/patches/hdf5-2.1.0.patch
--- gmtsar-6.6+ds/debian/patches/hdf5-2.1.0.patch	1970-01-01 01:00:00.000000000 +0100
+++ gmtsar-6.6+ds/debian/patches/hdf5-2.1.0.patch	2026-05-28 14:36:01.000000000 +0200
@@ -0,0 +1,54 @@
+Index: gmtsar-6.6+ds/ax_lib_hdf5.m4
+===================================================================
+--- gmtsar-6.6+ds.orig/ax_lib_hdf5.m4
++++ gmtsar-6.6+ds/ax_lib_hdf5.m4
+@@ -226,7 +226,14 @@ HDF5 support is being disabled (equivale
+           esac
+         done
+ 
+-        HDF5_LIBS="$HDF5_LIBS -lhdf5"
++        HDF5_INFIX=
++        case "$HDF5_LIBS" in
++            -lhdf5_*)
++                HDF5_INFIX="${HDF5_LIBS#-lhdf5_}"
++                HDF5_INFIX="_${HDF5_INFIX%%_*}"
++                ;;
++        esac
++        HDF5_LIBS="$HDF5_LIBS -lhdf5$HDF5_INFIX"
+         AC_MSG_RESULT([yes (version $[HDF5_VERSION])])
+ 
+         dnl See if we can compile
+@@ -245,7 +252,7 @@ HDF5 support is being disabled (equivale
+           AC_MSG_WARN([Unable to compile HDF5 test program])
+         fi
+         dnl Look for HDF5's high level library
+-        AC_CHECK_LIB([hdf5_hl], [H5TBread_table], [HDF5_LIBS="$HDF5_LIBS -lhdf5_hl"], [], [])
++        AC_CHECK_LIB([hdf5${HDF5_INFIX}_hl], [H5TBread_table], [HDF5_LIBS="$HDF5_LIBS -lhdf5${HDF5_INFIX}_hl"], [], [])
+ 
+         CC=$ax_lib_hdf5_save_CC
+         CPPFLAGS=$ax_lib_hdf5_save_CPPFLAGS
+@@ -281,9 +288,9 @@ HDF5 support is being disabled (equivale
+             for arg in $HDF5_LIBS
+             do
+               case "$arg" in #(
+-                -lhdf5_hl) HDF5_FLIBS="$HDF5_FLIBS -lhdf5hl_fortran $arg"
++                -lhdf5${HDF5_INFIX}_hl) HDF5_FLIBS="$HDF5_FLIBS -lhdf5${HDF5_INFIX}_hl_fortran $arg"
+                   ;; #(
+-                -lhdf5)    HDF5_FLIBS="$HDF5_FLIBS -lhdf5_fortran $arg"
++                -lhdf5${HDF5_INFIX})    HDF5_FLIBS="$HDF5_FLIBS -lhdf5${HDF5_INFIX}_fortran $arg"
+                   ;; #(
+                 *) HDF5_FLIBS="$HDF5_FLIBS $arg"
+                   ;;
+Index: gmtsar-6.6+ds/configure.ac
+===================================================================
+--- gmtsar-6.6+ds.orig/configure.ac
++++ gmtsar-6.6+ds/configure.ac
+@@ -153,7 +153,7 @@ dnl ------------------------------------
+ dnl Set the HDF5 include and lib stuff
+ dnl ------------------------------------------------------------------
+ AX_LIB_HDF5()
+-HDF5_LIBS="$HDF5_LIBS -lhdf5_cpp"	# Add the C++ library
++HDF5_LIBS="$HDF5_LIBS -lhdf5${HDF5_INFIX}_cpp"	# Add the C++ library
+ AC_MSG_CHECKING(for HDF5 include)
+ AC_MSG_RESULT($HDF5_CPPFLAGS)
+ AC_MSG_CHECKING(for HDF5 libs)
diff -Nru gmtsar-6.6+ds/debian/patches/series gmtsar-6.6+ds/debian/patches/series
--- gmtsar-6.6+ds/debian/patches/series	2025-10-21 08:33:29.000000000 +0200
+++ gmtsar-6.6+ds/debian/patches/series	2026-05-28 14:36:01.000000000 +0200
@@ -1,3 +1,4 @@
+hdf5-2.1.0.patch
 0001-No-snaphu-and-epr-api.patch
 0002-Fix-interpreter.patch
 0003-Clean.patch