[Debichem-devel] Bug#1139605: libtrexio: FTBFS against HDF5 2.1.0

[Gilles Filippini]

Source: libtrexio
Version: 2.2.3-3
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, libtrexio FTBFS because the related m4 macro
doesn't support this new major release.

The attached patch fixes 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 libtrexio-2.2.3/debian/changelog libtrexio-2.2.3/debian/changelog
--- libtrexio-2.2.3/debian/changelog	2022-10-07 14:07:45.000000000 +0200
+++ libtrexio-2.2.3/debian/changelog	2026-05-29 10:11:35.000000000 +0200
@@ -1,3 +1,10 @@
+libtrexio (2.2.3-3.1) UNRELEASED; urgency=medium
+
+  * Non-maintainer upload.
+  * Fix FTBFS against HDF5 2.1.0
+
+ -- Gilles Filippini <pini at debian.org>  Fri, 29 May 2026 10:11:35 +0200
+
 libtrexio (2.2.3-3) unstable; urgency=medium
 
   * Team upload.
diff -Nru libtrexio-2.2.3/debian/patches/hdf5-2.1.0.patch libtrexio-2.2.3/debian/patches/hdf5-2.1.0.patch
--- libtrexio-2.2.3/debian/patches/hdf5-2.1.0.patch	1970-01-01 01:00:00.000000000 +0100
+++ libtrexio-2.2.3/debian/patches/hdf5-2.1.0.patch	2026-05-29 10:11:35.000000000 +0200
@@ -0,0 +1,49 @@
+Index: libtrexio-2.2.3/m4/ax_lib_hdf5.m4
+===================================================================
+--- libtrexio-2.2.3.orig/m4/ax_lib_hdf5.m4
++++ libtrexio-2.2.3/m4/ax_lib_hdf5.m4
+@@ -237,7 +237,15 @@ HDF5 support is being disabled (equivale
+           esac
+         done
+ 
+-        HDF5_LIBS="-lhdf5 $HDF5_LIBS"
++        HDF5_INFIX=
++        HDF5_LIBS="${HDF5_LIBS#"${HDF5_LIBS%%[![:space:]]*}"}"
++        case "$HDF5_LIBS" in
++            -lhdf5_*)
++                HDF5_INFIX="${HDF5_LIBS#-lhdf5_}"
++                HDF5_INFIX="_${HDF5_INFIX%%_*}"
++                ;;
++        esac
++        HDF5_LIBS="-lhdf5$HDF5_INFIX $HDF5_LIBS"
+         AC_MSG_RESULT([yes (version $[HDF5_VERSION])])
+ 
+         dnl See if we can compile
+@@ -251,13 +259,13 @@ HDF5 support is being disabled (equivale
+         LIBS=$HDF5_LIBS
+         LDFLAGS=$HDF5_LDFLAGS
+         AC_CHECK_HEADER([hdf5.h], [ac_cv_hadf5_h=yes], [ac_cv_hadf5_h=no])
+-        AC_CHECK_LIB([hdf5], [H5Fcreate], [ac_cv_libhdf5=yes],
++        AC_CHECK_LIB([hdf5${HDF5_INFIX}], [H5Fcreate], [ac_cv_libhdf5=yes],
+                      [ac_cv_libhdf5=no])
+         if test "$ac_cv_hadf5_h" = "no" && test "$ac_cv_libhdf5" = "no" ; then
+           AC_MSG_WARN([Unable to compile HDF5 test program])
+         fi
+         dnl Look for HDF5's high level library
+-        AC_CHECK_LIB([hdf5_hl], [main],[HDF5_LIBS="-lhdf5_hl $HDF5_LIBS"], [], [])
++        AC_CHECK_LIB([hdf5${HDF5_INFIX}_hl], [main],[HDF5_LIBS="-lhdf5${HDF5_INFIX}_hl $HDF5_LIBS"], [], [])
+ 
+         CC=$ax_lib_hdf5_save_CC
+         CPPFLAGS=$ax_lib_hdf5_save_CPPFLAGS
+@@ -294,9 +302,9 @@ HDF5 support is being disabled (equivale
+             for arg in $HDF5_LIBS
+             do
+               case "$arg" in #(
+-                -lhdf5_hl) HDF5_FLIBS="$HDF5_FLIBS -lhdf5hl_fortran $arg"
++                -lhdf5_hl) HDF5_FLIBS="$HDF5_FLIBS -lhdf5${HDF5_INFIX}_hl_fortran $arg"
+                   ;; #(
+-                -lhdf5)    HDF5_FLIBS="$HDF5_FLIBS -lhdf5_fortran $arg"
++                -lhdf5)    HDF5_FLIBS="$HDF5_FLIBS -lhdf5${HDF5_INFIX}_fortran $arg"
+                   ;; #(
+                 *) HDF5_FLIBS="$HDF5_FLIBS $arg"
+                   ;;
diff -Nru libtrexio-2.2.3/debian/patches/series libtrexio-2.2.3/debian/patches/series
--- libtrexio-2.2.3/debian/patches/series	2022-10-07 14:07:38.000000000 +0200
+++ libtrexio-2.2.3/debian/patches/series	2026-05-29 10:11:35.000000000 +0200
@@ -1,2 +1,3 @@
 fixParallelTests.diff
 fix32bitBuilds.diff
+hdf5-2.1.0.patch