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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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 1140089@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Roland Mas <lolando@debian.org> (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 ftpmaster@ftp-master.debian.org)
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 <debian-science-maintainers@lists.alioth.debian.org>
Changed-By: Roland Mas <lolando@debian.org>
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).
Checksums-Sha1:
 66286f473a88e543b7b655cf305151a6c43ec48f 4191 cctbx_2026.7+ds2+~3.30.0+ds1-3.dsc
 f78d098c376a225cb2eb495c7979620e5f21c3b7 419828 cctbx_2026.7+ds2+~3.30.0+ds1-3.debian.tar.xz
 bdee504ee929e7d4c59f16794cb661623488ab92 24045 cctbx_2026.7+ds2+~3.30.0+ds1-3_amd64.buildinfo
Checksums-Sha256:
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 a982ca09b773e97fa3f94df396bffd196dd99a504c1bed0152ed1b7e31f9ef90 419828 cctbx_2026.7+ds2+~3.30.0+ds1-3.debian.tar.xz
 9b79b15ea90e40b10f91a25cf742166b97723449d87252f44bd502415a087826 24045 cctbx_2026.7+ds2+~3.30.0+ds1-3_amd64.buildinfo
Files:
 b4f6a204e9d6862e4b4ac602edb33a36 4191 science optional cctbx_2026.7+ds2+~3.30.0+ds1-3.dsc
 49d9e7a8661597fb23535b8d6247d743 419828 science optional cctbx_2026.7+ds2+~3.30.0+ds1-3.debian.tar.xz
 3a0933a6042c5e855945e92bba96c68b 24045 science optional cctbx_2026.7+ds2+~3.30.0+ds1-3_amd64.buildinfo
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