Your message dated Wed, 11 Nov 2020 09:34:43 +0000 with message-id <e1kcmwz-000dqo...@fasolo.debian.org> and subject line Bug#966914: fixed in sambamba 0.7.1-5 has caused the Debian Bug report #966914, regarding sambamba: FTBFS: collect2: error: ld returned 1 exit status 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 ow...@bugs.debian.org immediately.) -- 966914: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=966914 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Source: sambamba Version: 0.7.1-4 Severity: serious Justification: FTBFS on amd64 Tags: bullseye sid ftbfs Usertags: ftbfs-20200802 ftbfs-bullseye Hi, During a rebuild of all packages in sid, your package failed to build on amd64. Relevant part (hopefully): > ldc2 -of=sambamba sambamba.p/sambamba_main.d.o sambamba.p/sambamba_depth.d.o > sambamba.p/sambamba_fixbins.d.o sambamba.p/sambamba_flagstat.d.o > sambamba.p/sambamba_index.d.o sambamba.p/sambamba_markdup2.d.o > sambamba.p/sambamba_markdup.d.o sambamba.p/sambamba_merge.d.o > sambamba.p/sambamba_pileup.d.o sambamba.p/sambamba_slice.d.o > sambamba.p/sambamba_sort.d.o sambamba.p/sambamba_subsample.d.o > sambamba.p/sambamba_utils_common_bed.d.o > sambamba.p/sambamba_utils_common_file.d.o > sambamba.p/sambamba_utils_common_filtering.d.o > sambamba.p/sambamba_utils_common_intervaltree.d.o > sambamba.p/sambamba_utils_common_ldc_gc_workaround.d.o > sambamba.p/sambamba_utils_common_overwrite.d.o > sambamba.p/sambamba_utils_common_pratt_parser.d.o > sambamba.p/sambamba_utils_common_progressbar.d.o > sambamba.p/sambamba_utils_common_queryparser.d.o > sambamba.p/sambamba_utils_common_readstorage.d.o > sambamba.p/sambamba_utils_common_tmpdir.d.o > sambamba.p/sambamba_utils_view_alignmentrangeprocessor.d.o > sambamba.p/sambamba_utils_view_headerserializer.d.o > sambamba.p/sambamba_validate.d.o sambamba.p/sambamba_view.d.o > sambamba.p/utils_lz4.d.o sambamba.p/utils_strip_bcf_header.d.o > sambamba.p/utils_version_.d.o sambamba.p/cram_exception.d.o > sambamba.p/cram_htslib.d.o sambamba.p/cram_reader.d.o > sambamba.p/cram_reference.d.o sambamba.p/cram_slicereader.d.o > sambamba.p/cram_wrappers.d.o sambamba.p/cram_writer.d.o > sambamba.p/thirdparty_mergesort.d.o sambamba.p/thirdparty_unstablesort.d.o > sambamba.p/_build_sambamba-s4fhbx_sambamba-0.7.1_obj-x86_64-linux-gnu_utils_ldc_version_info_.d.o > -L=--allow-shlib-undefined -link-defaultlib-shared -O -g -release -wi -L=-z > -L=relro -L=/usr/lib/x86_64-linux-gnu/libbiod.a > -L=/usr/lib/x86_64-linux-gnu/libz.a -L=/usr/lib/x86_64-linux-gnu/libhts.a > -L=-z -L=relro -L=-z -L=now -L=-flto -fvisibility=hidden > -L=/usr/lib/x86_64-linux-gnu/libbz2.a > -L=/usr/lib/x86_64-linux-gnu/libdeflate.a -L=-lm -L=-lpthread > -L=/usr/lib/x86_64-linux-gnu/liblzma.a > /usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu/liblz4.so > /usr/lib/x86_64-linux-gnu/libcurl.so /usr/lib/x86_64-linux-gnu/libcrypto.so > /usr/lib/x86_64-linux-gnu/liblzma.so -L=-rpath > -L=/usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu > -L=-rpath-link -L=/usr/lib/gcc/x86_64-linux-gnu/10/../../../x86_64-linux-gnu > -L=-rpath-link -L=/usr/lib/x86_64-linux-gnu > lto1: fatal error: bytecode stream in file > ‘/usr/lib/x86_64-linux-gnu/libhts.a’ generated with GCC compiler older than > 10.0 > compilation terminated. > lto-wrapper: fatal error: /usr/bin/cc returned 1 exit status > compilation terminated. > /usr/bin/ld.gold: fatal error: lto-wrapper failed > collect2: error: ld returned 1 exit status The full build log is available from: http://qa-logs.debian.net/2020/08/02/sambamba_0.7.1-4_unstable.log A list of current common problems and possible solutions is available at http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute! About the archive rebuild: The rebuild was done on EC2 VM instances from Amazon Web Services, using a clean, minimal and up-to-date chroot. Every failed build was retried once to eliminate random failures.
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--- Begin Message ---Source: sambamba Source-Version: 0.7.1-5 Done: =?utf-8?q?=C3=89tienne_Mollier?= <etienne.moll...@mailoo.org> We believe that the bug you reported is fixed in the latest version of sambamba, 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 966...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Étienne Mollier <etienne.moll...@mailoo.org> (supplier of updated sambamba 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 ftpmas...@ftp-master.debian.org) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Wed, 11 Nov 2020 09:27:56 +0100 Source: sambamba Architecture: source Version: 0.7.1-5 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Étienne Mollier <etienne.moll...@mailoo.org> Closes: 966914 Changes: sambamba (0.7.1-5) unstable; urgency=medium . * Team upload. . [ Andreas Tille ] * Respect DEB_BUILD_OPTIONS in override_dh_auto_test target (routine- update) * Remove trailing whitespace in debian/changelog (routine-update) * Add salsa-ci file (routine-update) * Set upstream metadata fields: Bug-Database, Bug-Submit. * DEP3 * Lintian-override for static linking . [ Étienne Mollier ] * Define zlib dependency in meson.build. (Closes: #966914) * Default to libcurl4-gnutls-dev as libcurl-dev dependency. (Fixes lintian virtual-package-depends-without-real-package-depends) Checksums-Sha1: a5e09e8c926fbf3215f5dca84855737aafd6fc37 2159 sambamba_0.7.1-5.dsc 0bcecc0c6fd15c75166ea87e7fcb390262252ce7 8524 sambamba_0.7.1-5.debian.tar.xz d9bcfd3b9d367788c7174aa6567b6f01c4364429 7612 sambamba_0.7.1-5_amd64.buildinfo Checksums-Sha256: 9d8f668ab75b016316cec545eb3ce662d658a18c773a0f6cca0595c65434521a 2159 sambamba_0.7.1-5.dsc 197228e1652cd58a256d9ac31264bd2767ee714d25841aa2e3c5595a966b7ad1 8524 sambamba_0.7.1-5.debian.tar.xz 7bfb1c8cffbd78755f114ba32536e14b79ad9be7a692594b41738b8ed6671d9d 7612 sambamba_0.7.1-5_amd64.buildinfo Files: 65f25ea9cf251d922edb428f725fef80 2159 science optional sambamba_0.7.1-5.dsc 8b73acc19aa05eb0cf0415fafc72638a 8524 science optional sambamba_0.7.1-5.debian.tar.xz e5aa97684b1f98afaf08c671ed0b49bc 7612 science optional sambamba_0.7.1-5_amd64.buildinfo -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAl+rqn0RHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtHXcw//eLoxE4e15amLIR0a1yozEcqkYCQGC5tG OKsDVds7ht84A+gayZM+fL0ldByEXZxFJEDji5dPYIigK0zOpT4yevvuNyQxhBkk UenvS30jpqK6LyI9+o/UNSnwNBJ1aNF0yU4hVYz4MeASxx4hgOhfDr2u/rxiqUd2 YkYGpgQO5eOfJFLiCi3j5KWwAWpRF5gfcbXTLGDZE7fGEVKKRB4ZZF6vrU/9Yt7P JTKDLQf1rFxvgZH1XdsGLFUVAfqF88Oynyh+X9aS8weclOyfpfh36pzYbsmWAVyj uNz3gRuTnddN4V7o+a+kfVYoJb6+rZlIPK1NeN/Rs+sNyFDO1Nz7qmx9clDlA0P3 J1UdNZwpmCtuIBn8ioH2CPHckVb4/VxuShm0PV2QM5NcXu5rsbr1GI3T3M0uzALM 6QyWAMH3kIAkRHg1St5xBTOcKvbVtTDXQpYvgWcsxAmUbmicwrf6tdb9ckhPhi1D 9DGr/zLGmmnNqqP4aBs9iJDVcDS6P4gI+YfZr9uCBMj3bzkUwbzO1bU+vrONElYx vzKzUXLx2hhr//pJtnebdMDNZ7T9ZV+n+tmDf6gt/wQSM5/yV3xKAa44UruQ1mPz VHsAqLdoXCoPwkuA0rXb/dqjZ4dhiZjszpzpagVsgxkzm+6wridm/WmTBi7Lp0O/ fBwTyuaW6m4= =pcbz -----END PGP SIGNATURE-----
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