[From nobody Thu Sep 24 09:51:07 2026 Received: (at submit) by bugs.debian.org; 9 Aug 2026 15:29:43 +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=-108.0 required=4.0 tests=ALL_TRUSTED,BAYES_00, DKIMWL_WL_HIGH,DKIM_SIGNED,DKIM_VALID,DKIM_VALID_AU,DKIM_VALID_EF, FROMDEVELOPER,SPF_HELO_NONE,SPF_PASS,USER_IN_DKIM_WELCOMELIST autolearn=ham autolearn_force=no version=4.0.1-bugs.debian.org_2005_01_02 X-Spam-Bayes: score:0.0000 Tokens: new, 55; hammy, 150; neutral, 76; spammy, 0. spammytokens: hammytokens:0.000-+--Hx-spam-relays-external:sk:stravin, 0.000-+--H*RT:sk:stravin, 0.000-+--Hx-spam-relays-external:311, 0.000-+--H*RT:311, 0.000-+--H*RT:108 Return-path: <sramacher@debian.org> Received: from stravinsky.debian.org ([2001:41b8:202:deb::311:108]:58926) by buxtehude.debian.org with esmtps (TLS1.3:ECDHE_SECP256R1__RSA_PSS_RSAE_SHA256__AES_256_GCM:256) (Exim 4.96) (envelope-from <sramacher@debian.org>) id 1wt5T5-005DFd-1p for submit@bugs.debian.org; 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Sun, 09 Aug 2026 17:29:41 +0200 (CEST) Date: Sun, 9 Aug 2026 17:29:41 +0200 From: Sebastian Ramacher <sramacher@debian.org> To: Debian Bug Tracking System <submit@bugs.debian.org> Subject: uncalled: FTBFS: /usr/bin/x86_64-linux-gnu-ld.bfd: cannot find -lhdf5: No such file or directory Message-ID: <anic5ZKYIEZcFK7H@ramacher.at> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline Content-Transfer-Encoding: quoted-printable X-Reportbug-Version: 13.2.0 X-Debian-User: sramacher Delivered-To: submit@bugs.debian.org Source: uncalled Version: 2.3+ds-3 Severity: serious Tags: ftbfs Justification: fails to build from source (but built successfully in the pa= st) X-Debbugs-Cc: sramacher@debian.org Dear maintainer, uncalled FTBFS: x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=3D/build/reproducible-path/un= called-2.3+ds=3D. -fstack-protector-strong -fstack-clash-protection -Wforma= t -Werror=3Dformat-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE= =3D2 -DH5_USE_110_API -fPIC -DPYBIND -I./submods -I/usr/include/hdf5/serial= -I/usr/include/fast5/ -I/usr/include/ -I/usr/lib/python3/dist-packages/pyb= ind11/include -I/usr/include/python3.14 -c src/self_align_ref.cpp -o build/= temp.linux-x86_64-cpython-314/src/self_align_ref.o -std=3Dc++11 -O3 x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=3D/build/reproducible-path/un= called-2.3+ds=3D. -fstack-protector-strong -fstack-clash-protection -Wforma= t -Werror=3Dformat-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE= =3D2 -DH5_USE_110_API -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro= -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -g -O2 -ffile-prefix-map=3D/build/r= eproducible-path/uncalled-2.3+ds=3D. -fstack-protector-strong -fstack-clash= -protection -Wformat -Werror=3Dformat-security -fcf-protection -Wdate-time = -D_FORTIFY_SOURCE=3D2 -DH5_USE_110_API build/temp.linux-x86_64-cpython-314/= src/chunk.o build/temp.linux-x86_64-cpython-314/src/client_sim.o build/temp= =2Elinux-x86_64-cpython-314/src/event_detector.o build/temp.linux-x86_64-cp= ython-314/src/event_profiler.o build/temp.linux-x86_64-cpython-314/src/fast= 5_reader.o build/temp.linux-x86_64-cpython-314/src/map_pool.o build/temp.li= nux-x86_64-cpython-314/src/mapper.o build/temp.linux-x86_64-cpython-314/src= /normalizer.o build/temp.linux-x86_64-cpython-314/src/pybinder.o build/temp= =2Elinux-x86_64-cpython-314/src/range.o build/temp.linux-x86_64-cpython-314= /src/read_buffer.o build/temp.linux-x86_64-cpython-314/src/realtime_pool.o = build/temp.linux-x86_64-cpython-314/src/seed_tracker.o build/temp.linux-x86= _64-cpython-314/src/self_align_ref.o -L -L/usr/lib/x86_64-linux-gnu -lbwa -= lhdf5 -lz -ldl -lm -o /build/reproducible-path/uncalled-2.3+ds/.pybuild/cpy= thon3_3.14_uncalled/build/_uncalled.cpython-314-x86_64-linux-gnu.so /usr/bin/x86_64-linux-gnu-ld.bfd: cannot find -lhdf5: No such file or direc= tory collect2: error: ld returned 1 exit status error: command '/usr/bin/x86_64-linux-gnu-g++' failed with exit code 1 E: pybuild pybuild:485: build: plugin distutils failed with: exit code=3D1:= /usr/bin/python3 setup.py build See https://buildd.debian.org/status/fetch.php?pkg=3Duncalled&arch=3Damd64&ver= =3D2.3%2Bds-3%2Bb5&stamp=3D1786284410&raw=3D0 for details. Cheers --=20 Sebastian Ramacher ]