Your message dated Sat, 04 Jul 2020 17:33:53 +0000 with message-id <e1jrm2z-000gho...@fasolo.debian.org> and subject line Bug#948919: fixed in sambamba 0.7.1-3 has caused the Debian Bug report #948919, regarding sambamba FTBFS: undefined reference to 'cram_to_bam' 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.) -- 948919: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=948919 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Source: libbiod Version: 0.7.1-1 Severity: serious Tags: ftbfs Hello, This new FTBFS is also being discussed on #907489 but I think they are separate issues. I have quoted the error message from the log below. https://buildd.debian.org/status/fetch.php?pkg=sambamba&arch=amd64&ver=0.7.1-1&stamp=1576381970&raw=0 ---- FAILED: sambamba ldc2 -of=sambamba 'sambamba@exe/sambamba_main.d.o' 'sambamba@exe/sambamba_depth.d.o' 'sambamba@exe/sambamba_fixbins.d.o' 'sambamba@exe/sambamba_flagstat.d.o' 'sambamba@exe/sambamba_index.d.o' 'sambamba@exe/sambamba_markdup2.d.o' 'sambamba@exe/sambamba_markdup.d.o' 'sambamba@exe/sambamba_merge.d.o' 'sambamba@exe/sambamba_pileup.d.o' 'sambamba@exe/sambamba_slice.d.o' 'sambamba@exe/sambamba_sort.d.o' 'sambamba@exe/sambamba_subsample.d.o' 'sambamba@exe/sambamba_utils_common_bed.d.o' 'sambamba@exe/sambamba_utils_common_file.d.o' 'sambamba@exe/sambamba_utils_common_filtering.d.o' 'sambamba@exe/sambamba_utils_common_intervaltree.d.o' 'sambamba@exe/sambamba_utils_common_ldc_gc_workaround.d.o' 'sambamba@exe/sambamba_utils_common_overwrite.d.o' 'sambamba@exe/sambamba_utils_common_pratt_parser.d.o' 'sambamba@exe/sambamba_utils_common_progressbar.d.o' 'sambamba@exe/sambamba_utils_common_queryparser.d.o' 'sambamba@exe/sambamba_utils_common_readstorage.d.o' 'sambamba@exe/sambamba_utils_common_tmpdir.d.o' 'sambamba@exe/sambamba_utils_view_alignmentrangeprocessor.d.o' 'sambamba@exe/sambamba_utils_view_headerserializer.d.o' 'sambamba@exe/sambamba_validate.d.o' 'sambamba@exe/sambamba_view.d.o' 'sambamba@exe/utils_lz4.d.o' 'sambamba@exe/utils_strip_bcf_header.d.o' 'sambamba@exe/utils_version_.d.o' 'sambamba@exe/cram_exception.d.o' 'sambamba@exe/cram_htslib.d.o' 'sambamba@exe/cram_reader.d.o' 'sambamba@exe/cram_reference.d.o' 'sambamba@exe/cram_slicereader.d.o' 'sambamba@exe/cram_wrappers.d.o' 'sambamba@exe/cram_writer.d.o' 'sambamba@exe/thirdparty_mergesort.d.o' 'sambamba@exe/thirdparty_unstablesort.d.o' 'sambamba@exe/ldc_version_info_.d.o' -L=-L--allow-shlib-undefined -O -g -release -wi -L=-z -L=relro -L=--start-group -L=/usr/lib/x86_64-linux-gnu/libbiod.a -L=/usr/lib/x86_64-linux-gnu/libz.a /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/liblz4.so /usr/lib/x86_64-linux-gnu/libhts.so -L=--end-group -L=-rpath -L=/usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu slicereader.d:71: error: undefined reference to 'cram_to_bam' collect2: error: ld returned 1 exit status ----- Regards, Juhani
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--- Begin Message ---Source: sambamba Source-Version: 0.7.1-3 Done: Steffen Moeller <moel...@debian.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 948...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Steffen Moeller <moel...@debian.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: SHA256 Format: 1.8 Date: Sat, 04 Jul 2020 19:18:06 +0200 Source: sambamba Architecture: source Version: 0.7.1-3 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Steffen Moeller <moel...@debian.org> Closes: 948919 Changes: sambamba (0.7.1-3) unstable; urgency=medium . * Fixed build failure (Closes: # 948919) with - dependency on newer htslib package that is not stripped - and exports the cram_to_bam function - avoided use of inline htslib function by sambamba Upstream informed on https://github.com/samtools/htslib/issues/1098 Checksums-Sha1: ec0205b5ef54911cbb70bb8428d500541d79ed48 2060 sambamba_0.7.1-3.dsc ef82ae8c7f4e3404338a79d054c065dd2077e1a3 7888 sambamba_0.7.1-3.debian.tar.xz 12156738fc68d54cdaf6bd7556f617ccc67066d3 7812 sambamba_0.7.1-3_source.buildinfo Checksums-Sha256: 1d9ab95635e206a756347d7c43ac4a9939c83306d2e0efd4f76f07c03cacce1d 2060 sambamba_0.7.1-3.dsc 33f069e5331db9ecc1042ba0be662e172f2b164042138007fb267c084a7538b2 7888 sambamba_0.7.1-3.debian.tar.xz 75bc154ae4b4e1c714f3919ebecba84556901b0bf0db9e132f3bc65f9b5819b1 7812 sambamba_0.7.1-3_source.buildinfo Files: 4eecfd2cec458a5a059e892e06913c6b 2060 science optional sambamba_0.7.1-3.dsc 438efac506bf77fcd9d082a9dd2611c3 7888 science optional sambamba_0.7.1-3.debian.tar.xz 9063afac177572fae8fe8815604792a9 7812 science optional sambamba_0.7.1-3_source.buildinfo -----BEGIN PGP SIGNATURE----- iQJHBAEBCAAxFiEEhMGXeonn7+0+XKYuL9i+2sAg7tEFAl8Au3ATHG1vZWxsZXJA ZGViaWFuLm9yZwAKCRAv2L7awCDu0TdQD/4+jknudiq634gVrodoeLmANuhsUdGA D0MhPpOXZjOtUt9N4uWc9Jgq4S2/W1RHkpujZbzhhJJe0Ss0Tm/xN2U7vjxzWrzA EOGhMhc0AxMYh+yuGAnrNM8NL7s3sJWy08i0DaWD2/tWfPsD7GPBEBM3JPj7kOMF GvohtcZjQSmPsY0eF+YbYYduCdKpnwks8kbqx1Ok1VgapV2Z5u6/pLHNqlrT1g6Y XJnEYKqJFu3ceBr36KwSIZQtTnkUZnlGGri8IoTg768C0Rtixo+DPC63gulbsJn4 epDwisLMRUtAAKfBFyk3g7Fmvijr6PDtStNcZdT51MpKA9Al/dx7KeqK4WJ1ksLg IcsAZYgGFQEF7ph/1JvmCZorUHQKhnkLefBOz0d0ir5yerrPSECwGrhtE+cahNCg S5OMsZJ0PbhXWcySteljf9cCeSDWA/aolJm8V6IAAkr8GKX+1WN7/i7xAVnlUStW sqiwrQwp9/nx1IGPBlwUMjg+Lgxey5mWTzuUZ7Y/gy4D7Yzk0AdrJEPKDU4dg6mN LtQ+syljMso7SOSpa5LP4JNcHbmTCzYSMCqbFZ3gr4XVBsQubjd7I6984V6mvsOJ rC74z7SZA9z0Cu/XhX5IGVmxHfNg6U8JAu/HM29XZGu5R/1wKdNwdpj4z7PTKgxK 8NBtoysVkSVJtA== =jyTc -----END PGP SIGNATURE-----
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