Your message dated Tue, 11 Aug 2026 10:33:45 +0000
with message-id <[email protected]>
and subject line Bug#1139605: fixed in libtrexio 2.2.3-4
has caused the Debian Bug report #1139605,
regarding libtrexio: FTBFS against HDF5 2.1.0
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact [email protected]
immediately.)
--
1139605: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1139605
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: libtrexio
Version: 2.2.3-3
Severity: important
Tags: ftbfs patch
-----BEGIN PGP SIGNED MESSAGE-----
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 <[email protected]> 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
--- End Message ---
--- Begin Message ---
Source: libtrexio
Source-Version: 2.2.3-4
Done: Santiago Vila <[email protected]>
We believe that the bug you reported is fixed in the latest version of
libtrexio, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Santiago Vila <[email protected]> (supplier of updated libtrexio package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Tue, 11 Aug 2026 11:55:00 +0200
Source: libtrexio
Architecture: source
Version: 2.2.3-4
Distribution: unstable
Urgency: medium
Maintainer: Debichem Team <[email protected]>
Changed-By: Santiago Vila <[email protected]>
Closes: 1139605
Changes:
libtrexio (2.2.3-4) unstable; urgency=medium
.
* Team upload.
.
[ Gilles Filippini ]
* Fix FTBFS against HDF5 2.1.0. Closes: #1139605.
.
[ Santiago Vila ]
* Drop "Priority: optional" (default).
* Update standards-version.
* Add debian/salsa-ci.yml.
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