Your message dated Tue, 11 Aug 2026 15:26:28 +0000
with message-id <[email protected]>
and subject line Bug#1140089: fixed in cctbx 2026.7+ds2+~3.30.0+ds1-3
has caused the Debian Bug report #1140089,
regarding cctbx: FTBFS against HDF5 2.1.0 - cannot find -lhdf5: No such file or
directory
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
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--
1140089: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1140089
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: cctbx
Version: 2026.4+ds2+~3.28.0+ds1-2
Severity: important
Tags: ftbfs patch
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Hi,
During a test rebuild of HDF5's reverse dependcies against HDF5 2.1.0
currently in experimental, cctbx FTBFS with:
g++ -o lib/dxtbx_format_image_ext.so.0.0.1 -shared -rdynamic -std=c++14
-Wl,-soname=dxtbx_format_image_ext.so.0
dxtbx/src/dxtbx/format/boost_python/image_ext.o
dxtbx/src/dxtbx/format/boost_python/cbf_read_buffer.o -L/usr/lib -L/usr/lib64
-L/usr/lib/x86_64-linux-gnu -Llib
-L/build/cctbx-TF7EYi/cctbx-2026.4+ds2+~3.28.0+ds1/lib -Llib
-L/build/cctbx-TF7EYi/cctbx-2026.4+ds2+~3.28.0+ds1/lib
-L/build/cctbx-TF7EYi/cctbx-2026.4+ds2+~3.28.0+ds1/.pybuild/cpython3_3.13_cctbx/base/lib
-Llib -L/build/cctbx-TF7EYi/cctbx-2026.4+ds2+~3.28.0+ds1/lib -L/usr/lib -lm
-ltiff -lboost_python313 -lcbf -lhdf5
/usr/bin/x86_64-linux-gnu-ld.bfd: cannot find -lhdf5: No such file or directory
collect2: error: ld returned 1 exit status
scons: *** [lib/dxtbx_format_image_ext.so.0.0.1] Error 1
Tha attached patch has a workaround for this issue and works with both
HDF5 1.14.6 in unstable and HDF5 2.1.0 in experimental.
But ideally the same technique should be use in dxtbx/SConscript than
in cbflib_adaptbx/SConscript, using pkg-config on the hdf5 module to
retrieve the correct build flags for building against HDF5.
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 cctbx-2026.4+ds2+~3.28.0+ds1/debian/changelog
cctbx-2026.4+ds2+~3.28.0+ds1/debian/changelog
--- cctbx-2026.4+ds2+~3.28.0+ds1/debian/changelog 2026-05-09
16:23:00.000000000 +0200
+++ cctbx-2026.4+ds2+~3.28.0+ds1/debian/changelog 2026-06-15
11:12:51.000000000 +0200
@@ -1,3 +1,10 @@
+cctbx (2026.4+ds2+~3.28.0+ds1-2.1) UNRELEASED; urgency=medium
+
+ * Non-maintainer upload.
+ * Fix FTBFS against HDF5 2.1.0
+
+ -- Gilles Filippini <[email protected]> Mon, 15 Jun 2026 11:12:51 +0200
+
cctbx (2026.4+ds2+~3.28.0+ds1-2) unstable; urgency=medium
* Various packaging improvements thanks to "debcraft improve".
diff -Nru cctbx-2026.4+ds2+~3.28.0+ds1/debian/patches/hdf5-2.1.0.patch
cctbx-2026.4+ds2+~3.28.0+ds1/debian/patches/hdf5-2.1.0.patch
--- cctbx-2026.4+ds2+~3.28.0+ds1/debian/patches/hdf5-2.1.0.patch
1970-01-01 01:00:00.000000000 +0100
+++ cctbx-2026.4+ds2+~3.28.0+ds1/debian/patches/hdf5-2.1.0.patch
2026-06-15 11:12:51.000000000 +0200
@@ -0,0 +1,13 @@
+Index: cctbx-2026.4+ds2+~3.28.0+ds1/dxtbx/SConscript
+===================================================================
+--- cctbx-2026.4+ds2+~3.28.0+ds1.orig/dxtbx/SConscript
++++ cctbx-2026.4+ds2+~3.28.0+ds1/dxtbx/SConscript
+@@ -49,7 +49,7 @@ env_etc.dxtbx_lib_paths = [
+ os.path.join(sys.prefix, "lib"),
+ ]
+
+-env_etc.dxtbx_hdf5_libs = ["hdf5"]
++env_etc.dxtbx_hdf5_libs = ["hdf5_serial"]
+ env_etc.dxtbx_hdf5_lib_paths = []
+
+ if sys.platform == "win32" and env_etc.compiler == "win32_cl":
diff -Nru cctbx-2026.4+ds2+~3.28.0+ds1/debian/patches/series
cctbx-2026.4+ds2+~3.28.0+ds1/debian/patches/series
--- cctbx-2026.4+ds2+~3.28.0+ds1/debian/patches/series 2026-05-05
17:57:25.000000000 +0200
+++ cctbx-2026.4+ds2+~3.28.0+ds1/debian/patches/series 2026-06-15
11:12:51.000000000 +0200
@@ -28,3 +28,4 @@
0028-dxtbx-force-pathlib-in-data-fetcher.patch
0030_broken_six.patch
0030-Stop-linking-against-boost_system.patch
+hdf5-2.1.0.patch
--- End Message ---
--- Begin Message ---
Source: cctbx
Source-Version: 2026.7+ds2+~3.30.0+ds1-3
Done: Roland Mas <[email protected]>
We believe that the bug you reported is fixed in the latest version of
cctbx, 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.
Roland Mas <[email protected]> (supplier of updated cctbx 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: Sun, 09 Aug 2026 15:54:08 +0200
Source: cctbx
Architecture: source
Version: 2026.7+ds2+~3.30.0+ds1-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Maintainers
<[email protected]>
Changed-By: Roland Mas <[email protected]>
Closes: 1140089
Changes:
cctbx (2026.7+ds2+~3.30.0+ds1-3) unstable; urgency=medium
.
* Bug fix: "FTBFS against HDF5 2.1.0 - cannot find -lhdf5: No such file
or directory", thanks to Gilles Filippini (Closes: #1140089).
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