Your message dated Thu, 02 Jul 2026 17:34:35 +0000
with message-id <[email protected]>
and subject line Bug#1139602: fixed in gwyddion 3.11-1
has caused the Debian Bug report #1139602,
regarding gwyddion: 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.)
--
1139602: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1139602
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: gwyddion
Version: 3.10-6
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, gwyddion 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
-----BEGIN PGP SIGNATURE-----
iQEzBAEBCgAdFiEEoJObzArDE05WtIyR7+hsbH/+z4MFAmopGEgACgkQ7+hsbH/+
z4NZtQf/SYfQluMI3gWzGvvsYutx/Zp2uU+PdQq7WLhFGaSTotORaxNB191qkQuF
zsnJoPzQenus641IHBKhAwU/gHMU8+9hy79/ZzkGJ9vsNr1tyCQf5TIrmioyh7gL
OtxPJrzpqqo8fEr6PDQzFhvR4q4oj5qg6SHxRi1dEt1nGOLSxOlr5JukkD+QD9RA
vxKX8IDgC80CVnGetAX2wG+AEZ0lrwBBYywxqTdVN2yTfbPHo1bC9Xsc34xjzeQF
rtouV7FheMjlHXpuVTeDE55AduJWuFQrEwxnkGgperZyq2Vuy9li1KuovrIXBBtr
aYhbpqxCegWvlVJ7NY630RtSfcvfWQ==
=M5M4
-----END PGP SIGNATURE-----
diff -Nru gwyddion-3.10/debian/changelog gwyddion-3.10/debian/changelog
--- gwyddion-3.10/debian/changelog 2026-05-11 07:24:59.000000000 +0200
+++ gwyddion-3.10/debian/changelog 2026-05-28 15:03:17.000000000 +0200
@@ -1,3 +1,10 @@
+gwyddion (3.10-6.1) UNRELEASED; urgency=medium
+
+ * Non-maintainer upload.
+ * Fix FTBFS against HDF5 2.1.0
+
+ -- Gilles Filippini <[email protected]> Thu, 28 May 2026 15:03:17 +0200
+
gwyddion (3.10-6) unstable; urgency=medium
* Rename -dev and -doc package to not use the version number
diff -Nru gwyddion-3.10/debian/patches/hdf5-2.1.0.patch
gwyddion-3.10/debian/patches/hdf5-2.1.0.patch
--- gwyddion-3.10/debian/patches/hdf5-2.1.0.patch 1970-01-01
01:00:00.000000000 +0100
+++ gwyddion-3.10/debian/patches/hdf5-2.1.0.patch 2026-05-28
15:03:17.000000000 +0200
@@ -0,0 +1,87 @@
+Index: gwyddion-3.10/configure
+===================================================================
+--- gwyddion-3.10.orig/configure
++++ gwyddion-3.10/configure
+@@ -25841,7 +25841,7 @@ esac
+ esac
+ done
+
+- HDF5_LIBS="$HDF5_LIBS -lhdf5"
++ HDF5_LIBS="$HDF5_LIBS -lhdf5_serial"
+ { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: yes
(version $HDF5_VERSION)" >&5
+ printf "%s\n" "yes (version $HDF5_VERSION)" >&6; }
+
+@@ -25862,14 +25862,14 @@ else case e in #(
+ esac
+ fi
+
+- { printf "%s\n" "$as_me:${as_lineno-$LINENO}:
checking for H5free_memory in -lhdf5" >&5
+-printf %s "checking for H5free_memory in -lhdf5... " >&6; }
++ { printf "%s\n" "$as_me:${as_lineno-$LINENO}:
checking for H5free_memory in -lhdf5_serial" >&5
++printf %s "checking for H5free_memory in -lhdf5_serial... " >&6; }
+ if test ${ac_cv_lib_hdf5_H5free_memory+y}
+ then :
+ printf %s "(cached) " >&6
+ else case e in #(
+ e) ac_check_lib_save_LIBS=$LIBS
+-LIBS="-lhdf5 $LIBS"
++LIBS="-lhdf5_serial $LIBS"
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+ /* end confdefs.h. */
+
+@@ -25917,14 +25917,14 @@ fi
+ { printf "%s\n" "$as_me:${as_lineno-$LINENO}: WARNING: Unable to
compile HDF5 test program" >&5
+ printf "%s\n" "$as_me: WARNING: Unable to compile HDF5 test program" >&2;}
+ fi
+- { printf "%s\n" "$as_me:${as_lineno-$LINENO}:
checking for main in -lhdf5_hl" >&5
+-printf %s "checking for main in -lhdf5_hl... " >&6; }
++ { printf "%s\n" "$as_me:${as_lineno-$LINENO}:
checking for main in -lhdf5_serial_hl" >&5
++printf %s "checking for main in -lhdf5_serial_hl... " >&6; }
+ if test ${ac_cv_lib_hdf5_hl_main+y}
+ then :
+ printf %s "(cached) " >&6
+ else case e in #(
+ e) ac_check_lib_save_LIBS=$LIBS
+-LIBS="-lhdf5_hl $LIBS"
++LIBS="-lhdf5_serial_hl $LIBS"
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+ /* end confdefs.h. */
+
+@@ -25953,7 +25953,7 @@ fi
+ printf "%s\n" "$ac_cv_lib_hdf5_hl_main" >&6; }
+ if test "x$ac_cv_lib_hdf5_hl_main" = xyes
+ then :
+- HDF5_LIBS="$HDF5_LIBS -lhdf5_hl"
++ HDF5_LIBS="$HDF5_LIBS -lhdf5_serial_hl"
+ fi
+
+ ac_cv_lib_hdf5_hl=ac_cv_lib_hdf5_hl_main
+Index: gwyddion-3.10/m4/gwy-hdf5.m4
+===================================================================
+--- gwyddion-3.10.orig/m4/gwy-hdf5.m4
++++ gwyddion-3.10/m4/gwy-hdf5.m4
+@@ -157,7 +157,14 @@ 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 $[HDF5_VERSION])])
+
+ dnl See if we can compile
+@@ -176,7 +183,7 @@ HDF5 support is being disabled (equivale
+ AC_MSG_WARN([Unable to compile HDF5 test program])
+ fi
+ dnl Look for HDF5's high level library
+- AC_CHECK_LIB([hdf5_hl],[main],[HDF5_LIBS="$HDF5_LIBS
-lhdf5_hl"],[],[])
++ AC_CHECK_LIB([hdf5_hl],[main],[HDF5_LIBS="$HDF5_LIBS
-lhdf5${HDF5_INFIX}_hl"],[],[])
+ ac_cv_lib_hdf5_hl=ac_cv_lib_hdf5_hl_main
+
+ CC=$gwy_hdf5_save_CC
diff -Nru gwyddion-3.10/debian/patches/series
gwyddion-3.10/debian/patches/series
--- gwyddion-3.10/debian/patches/series 2026-05-11 07:24:59.000000000 +0200
+++ gwyddion-3.10/debian/patches/series 2026-05-28 15:03:17.000000000 +0200
@@ -1,3 +1,4 @@
+hdf5-2.1.0.patch
launcher.patch
skip_test.patch
flaky.patch
--- End Message ---
--- Begin Message ---
Source: gwyddion
Source-Version: 3.11-1
Done: Andreas Tille <[email protected]>
We believe that the bug you reported is fixed in the latest version of
gwyddion, 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.
Andreas Tille <[email protected]> (supplier of updated gwyddion 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: Thu, 02 Jul 2026 18:57:00 +0200
Source: gwyddion
Architecture: source
Version: 3.11-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Closes: 1139602
Changes:
gwyddion (3.11-1) unstable; urgency=medium
.
[ Andreas Tille ]
* New upstream version
* d/copyright: review
* Add d/lrc.config
.
[ Gilles Filippini ]
* Fix FTBFS against HDF5 2.1.0
Closes: #1139602
Checksums-Sha1:
58126f15870abb5272dd1feea68aa329874a6c42 2790 gwyddion_3.11-1.dsc
95de730a0fedbd43ddfe3c9b15e84b4be4f8b8c9 5662540 gwyddion_3.11.orig.tar.xz
bdd15bbb6e7f1db165e1d7ef5d06a37f6c9a80e2 228 gwyddion_3.11.orig.tar.xz.asc
a54e71e6fb7a9f91b957cf3f3b6e218242389529 17972 gwyddion_3.11-1.debian.tar.xz
819f91e6cf84c31cd140c9c4a5f9bf78e1b71897 19380 gwyddion_3.11-1_amd64.buildinfo
Checksums-Sha256:
6f57ce749722ef0e743b1293c9bcb2317d346cb8c7af26851a98b965396fa1fe 2790
gwyddion_3.11-1.dsc
b0c4ad829b9d101500f75b47e4fab5c8055338a602c3ba1f3d98f72e6ce1b60a 5662540
gwyddion_3.11.orig.tar.xz
fb5def1fc2fbb4c8e56696ebfd587707bf264f13caedc2159baf8b50c932c618 228
gwyddion_3.11.orig.tar.xz.asc
d2e10d7a1e023af2d57e1fa1921a82c689a52abba4505b12b1f5701e96776dde 17972
gwyddion_3.11-1.debian.tar.xz
ab274d77160e31ad7e398fd5c3251bfdee147839eecbccfb2682fea1a0f1d419 19380
gwyddion_3.11-1_amd64.buildinfo
Files:
f3a07d9c41cf4177d6588b022e09f338 2790 science optional gwyddion_3.11-1.dsc
5ccf1900ad6d7a129ddfcc97ad8f3998 5662540 science optional
gwyddion_3.11.orig.tar.xz
f35878e4bba999cc491ea6611fe51357 228 science optional
gwyddion_3.11.orig.tar.xz.asc
b2b3b0cba69108c4653a15ccbc915e04 17972 science optional
gwyddion_3.11-1.debian.tar.xz
2a09491436aea11e6eb5d7ed33fbb853 19380 science optional
gwyddion_3.11-1_amd64.buildinfo
-----BEGIN PGP SIGNATURE-----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=es7H
-----END PGP SIGNATURE-----
pgp4iNIHuOSGp.pgp
Description: PGP signature
--- End Message ---
