[From nobody Tue Aug 11 16:27:11 2026 Received: (at submit) by bugs.debian.org; 15 Jun 2026 16:02:16 +0000 X-Spam-Checker-Version: SpamAssassin 4.0.1-bugs.debian.org_2005_01_02 (2024-03-25) on buxtehude.debian.org X-Spam-Level: X-Spam-Status: No, score=-10.6 required=4.0 tests=BAYES_00,FOURLA, FROMDEVELOPER,FVGT_m_MULTI_ODD,HEADER_FROM_DIFFERENT_DOMAINS, PGPSIGNATURE,SPF_HELO_NONE,SPF_PASS autolearn=ham autolearn_force=no version=4.0.1-bugs.debian.org_2005_01_02 X-Spam-Bayes: score:0.0000 Tokens: new, 90; hammy, 150; neutral, 201; spammy, 0. spammytokens: hammytokens:0.000-+--H*Ad:N*Bug, 0.000-+--HTo:N*Debian, 0.000-+--H*Ad:N*Tracking, 0.000-+--sk:taint_o, 0.000-+--sk:TAINT_O Return-path: <SRS0=Em90=EL=debian.org=pini@bou-fi.net> Received: from mail.bou-fi.net ([51.255.91.82]:47266) by buxtehude.debian.org with esmtps (TLS1.3:ECDHE_X25519__RSA_PSS_RSAE_SHA256__AES_256_GCM:256) (Exim 4.96) (envelope-from <SRS0=Em90=EL=debian.org=pini@bou-fi.net>) id 1wZ9lP-00Ck7e-33 for submit@bugs.debian.org; Mon, 15 Jun 2026 16:02:16 +0000 Content-Type: multipart/mixed; boundary="===============2421913672701027746==" Authentication-Results: mail.bou-fi.net; auth=pass smtp.mailfrom=pini@debian.org MIME-Version: 1.0 From: Gilles Filippini <pini@debian.org> To: Debian Bug Tracking System <submit@bugs.debian.org> Subject: cctbx: FTBFS against HDF5 2.1.0 - cannot find -lhdf5: No such file or directory Message-ID: <178153881764.27857.6880801171943645778.reportbug@pinibrem14> Date: Mon, 15 Jun 2026 17:53:37 +0200 X-Spamd-Bar: -- X-Greylist: delayed 513 seconds by postgrey-1.37 at buxtehude; Mon, 15 Jun 2026 16:02:15 UTC Delivered-To: submit@bugs.debian.org This is a multi-part MIME message sent by reportbug. --===============2421913672701027746== Content-Type: text/plain; charset="us-ascii" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Content-Disposition: inline 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 -----BEGIN PGP SIGNATURE----- iQEzBAEBCgAdFiEEoJObzArDE05WtIyR7+hsbH/+z4MFAmowH/gACgkQ7+hsbH/+ z4OaZAf+Ko23TNIX1c4Ux7d1GVm79niSFA6x24mw3dV5no+xbnYppenVC7GzHGzR G9Zy5aCJZm6b3LPXNo7NeAUhoa2CIcgVhb457lkPRSTAjfFbDAmlPTwRvafAxL3p LAK3hu6AUmyqBC/WHTVsRktehXOVL0gKF2LzaRyxCXyz8KFbGdS5EN7BbC48wKMM O+ltl/WfAt8uTW5R+3WYmJhYs8KC70QjOK4yYQ+96TsBPXAbGatD/0YbjGodsxnW v4nDiEFUdm9Bu9PwVz1mEslt0hZYBQjwjRAbx1BBi8Tvg35S4zh+Z5ojGUM9iJ9B U/dkXXQhD6m48h1pH6Xw+hEbMvInqQ== =NfcT -----END PGP SIGNATURE----- --===============2421913672701027746== Content-Type: text/plain; charset="us-ascii" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="cctbx.debdiff" 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 <pini@debian.org> 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 --===============2421913672701027746==-- ]