Your message dated Mon, 13 Apr 2020 07:04:17 +0000 with message-id <e1jnt8j-0004iu...@fasolo.debian.org> and subject line Bug#956136: fixed in minimap2 2.17+dfsg-8 has caused the Debian Bug report #956136, regarding "-flto flag breaks nanopolish" 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.) -- 956136: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=956136 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Source: nanopolish Version: 0.12.1-1 Severity: serious Tags: ftbfs Justification: makes the package in question unusable or mostly so Control: block 954654 by -1 Dear Maintainer, Your packages fails to build in unstable: /usr/bin/ld: /tmp/nanopolish.HEB8tw.ltrans12.ltrans.o: in function `populate_maps_from_fastq(OutputHandles&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::unordered_map<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::hash<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::equal_to<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >&, std::unordered_map<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::vector<bam1_t*, std::allocator<bam1_t*> >, std::hash<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::equal_to<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, std::vector<bam1_t*, std::allocator<bam1_t*> > > > >&, sam_hdr_t*, mm_mapopt_t, mm_idx_t*) [clone ._omp_fn.0]': ./src/nanopolish_call_methylation.cpp:536: undefined reference to `mm_map' /usr/bin/ld: ./src/nanopolish_call_methylation.cpp:551: undefined reference to `mm_write_sam' /usr/bin/ld: /tmp/nanopolish.HEB8tw.ltrans12.ltrans.o: in function `run_watch_mode(__faidx_t const*)': ./src/nanopolish_call_methylation.cpp:668: undefined reference to `mm_verbose' /usr/bin/ld: ./src/nanopolish_call_methylation.cpp:669: undefined reference to `mm_set_opt' /usr/bin/ld: ./src/nanopolish_call_methylation.cpp:674: undefined reference to `mm_idx_reader_open' /usr/bin/ld: ./src/nanopolish_call_methylation.cpp:677: undefined reference to `mm_idx_reader_read' /usr/bin/ld: ./src/nanopolish_call_methylation.cpp:678: undefined reference to `mm_mapopt_update' /usr/bin/ld: ./src/nanopolish_call_methylation.cpp:681: undefined reference to `mm_idx_reader_read' /usr/bin/ld: ./src/nanopolish_call_methylation.cpp:758: undefined reference to `mm_idx_destroy' /usr/bin/ld: ./src/nanopolish_call_methylation.cpp:759: undefined reference to `mm_idx_reader_close' /usr/bin/ld: ./src/nanopolish_call_methylation.cpp:520: undefined reference to `mm_tbuf_init' /usr/bin/ld: /tmp/nanopolish.HEB8tw.ltrans12.ltrans.o:./src/nanopolish_call_methylation.cpp:577: undefined reference to `mm_tbuf_destroy' collect2: error: ld returned 1 exit status make[1]: *** [Makefile:165: nanopolish] Error 1 https://buildd.debian.org/status/fetch.php?pkg=nanopolish&arch=amd64&ver=0.12.1-1&stamp=1586252670&raw=0 Kind Regards, Bas
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--- Begin Message ---Source: minimap2 Source-Version: 2.17+dfsg-8 Done: Hamid Nassiby <h.nass...@gmail.com> We believe that the bug you reported is fixed in the latest version of minimap2, 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 956...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Hamid Nassiby <h.nass...@gmail.com> (supplier of updated minimap2 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: Mon, 13 Apr 2020 08:18:05 +0200 Source: minimap2 Architecture: source Version: 2.17+dfsg-8 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Hamid Nassiby <h.nass...@gmail.com> Closes: 956136 Changes: minimap2 (2.17+dfsg-8) unstable; urgency=medium . * Team upload. * Delete addLTO.patch Closes: #956136 Checksums-Sha1: e59ea0c274e8df41c6094eb20cfb798e3a9a476b 2150 minimap2_2.17+dfsg-8.dsc ef99ce1afdc7a0c51b650b3e89c506be10718f1d 53412 minimap2_2.17+dfsg-8.debian.tar.xz 131297262aa5520828d1e50b5f298062e0e67653 17657 minimap2_2.17+dfsg-8_source.buildinfo Checksums-Sha256: d5b9e7ef1f65c495d988a1d4f50816f26102d1e501c2818894c186686cce3ee7 2150 minimap2_2.17+dfsg-8.dsc 11366c6f60253e692d373bbe41d8506b490c4e29672c09369d611644f600a5c3 53412 minimap2_2.17+dfsg-8.debian.tar.xz 1f45ddcbd1e1450463e4eaea16630801ee50f3fbff4cf88202777b2e6b3ccfc1 17657 minimap2_2.17+dfsg-8_source.buildinfo Files: f9a804b6dc513b1fb953b7649d673d33 2150 science optional minimap2_2.17+dfsg-8.dsc d917f698c33d70151569bac14c00d06f 53412 science optional minimap2_2.17+dfsg-8.debian.tar.xz 0a56eae88f06a6ffa2b5637b3d584053 17657 science optional minimap2_2.17+dfsg-8_source.buildinfo -----BEGIN PGP SIGNATURE----- iQJCBAEBCAAsFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAl6UCaYOHHRpbGxlYUBy a2kuZGUACgkQV4oElNHGRtHGBxAAhGcfygx8OmPp8OJl3qSecpzVYHi6+izkEAt6 1eNC/SPHGeV5zsHQNKJSP1nc/yNdRW0MSahPcxZOtJTO09VlqERsf4QdXG034TCR YoptKK98YKv2OFStzz+jnz8weddKPpzFxQl0ZpzbRjtbyKu40yElB9XVAsPRt/1B GLvQOPH1pBll5SH+1S74ccaJ2/3oxZ0+tBuOOrlrauQNaUPDTAuLYMXNO0sfqrM/ V4drLMUdeq9Uk39/wLdJQjA6vVBUbtl6RyJvYzj8E2pvgWcTQE3solorOLpKE7Pg 22kJfWLBQy7DoFHc8906snD9OIx+3TXiUS6j+CfJFfLKqa1l/Nu//3XRh7fdmW5L W49nuz7TANoaCV48WFahcpAo3h3IjE3Il3BFTnxMfDWbWQLcq5rH19ofNKiIy6Xi INDYH6sMYDUzDcnGR4c9TG3ZcRWLTed8ssQlBhjYCKqQVSCI1fEN0jhxpBCzP9Xn uBndaLg1v2yhmmHuP00myWJNzfDtmwfVeWIaztvG0MV02wtT+iRF1owBj5VTPsyH GcKCv0mSBcDikvdC2x9EiFcrRjN1IRIha9r6agqou5TgDCNFa2uy/YkUuaVvEQGA rM0hthTcie3//RPrTHxxv7Yu34YypIgbDzywH1fc7EI/kHKWQhR6Ufy2wzffLjh8 TZPsZzA= =OWWF -----END PGP SIGNATURE-----
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