Your message dated Thu, 04 Feb 2016 09:49:22 +0000 with message-id <e1argxs-0001la...@franck.debian.org> and subject line Bug#813465: fixed in bcftools 1.3-1 has caused the Debian Bug report #813465, regarding bcftools: FTBFS: vcfmerge.c:424:6: error: conflicting types for 'bcf_hdr_merge' 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.) -- 813465: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=813465 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Source: bcftools Version: 1.2-2 Severity: serious Justification: fails to build from source User: reproducible-bui...@lists.alioth.debian.org Usertags: ftbfs X-Debbugs-Cc: reproducible-bui...@lists.alioth.debian.org Dear Maintainer, bcftools fails to build from source in unstable/amd64: [..] cc -c -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -g -Wall -Wc++-compat -O2 -DPLUGINPATH=\"/usr/lib/x86_64-linux-gnu/bcftools\" -DUSE_GPL -I. -I/usr/include vcfsom.c -o vcfsom.o vcfmerge.c:424:6: error: conflicting types for 'bcf_hdr_merge' void bcf_hdr_merge(bcf_hdr_t *hw, const bcf_hdr_t *hr, const char *clash_prefix, int force_samples) ^ In file included from vcfmerge.c:30:0: /usr/include/htslib/vcf.h:407:16: note: previous declaration of 'bcf_hdr_merge' was here bcf_hdr_t *bcf_hdr_merge(bcf_hdr_t *dst, const bcf_hdr_t *src); ^ vcfmerge.c: In function 'bcf_hdr_merge': vcfmerge.c:427:5: warning: 'bcf_hdr_combine' is deprecated: Please use bcf_hdr_merge instead [-Wdeprecated-declarations] int ret = bcf_hdr_combine(hw, hr); ^ In file included from vcfmerge.c:30:0: /usr/include/htslib/vcf.h:391:9: note: declared here int bcf_hdr_combine(bcf_hdr_t *dst, const bcf_hdr_t *src) HTS_DEPRECATED("Please use bcf_hdr_merge instead"); ^ Makefile:90: recipe for target 'vcfmerge.o' failed make[1]: *** [vcfmerge.o] Error 1 make[1]: *** Waiting for unfinished jobs.... make[1]: Leaving directory '/home/lamby/temp/cdt.20160202103852.cx8O6CogYx/bcftools-1.2' dh_auto_build: make -j9 returned exit code 2 debian/rules:15: recipe for target 'build' failed make: *** [build] Error 2 [..] The full build log is attached. Regards, -- ,''`. : :' : Chris Lamb `. `'` la...@debian.org / chris-lamb.co.uk `-
bcftools.1.2-2.unstable.amd64.log.txt.gz
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--- Begin Message ---Source: bcftools Source-Version: 1.3-1 We believe that the bug you reported is fixed in the latest version of bcftools, 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 813...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Afif Elghraoui <a...@ghraoui.name> (supplier of updated bcftools 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: Wed, 03 Feb 2016 23:44:03 -0800 Source: bcftools Binary: bcftools Architecture: source Version: 1.3-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Afif Elghraoui <a...@ghraoui.name> Description: bcftools - genomic variant calling and manipulation of VCF/BCF files Closes: 813465 Changes: bcftools (1.3-1) unstable; urgency=medium . * New upstream release (Closes: #813465) * Disable building with libgsl until build issue with GSL2 is addressed * Update d/TODO to indicate GSL issue forwarded * Simplify d/rules as a result of improvements to build system * Update htslib minimum dependency * Add libhts-dev dependency for CI tests Checksums-Sha1: bef49ad67c2133b157364f983f10ae3d0cf1a6b2 1973 bcftools_1.3-1.dsc 49fee48c62a3d248ea51f7995f86397bce6f2618 943041 bcftools_1.3.orig.tar.gz 551385ffae67a53403c0322ab979211d8d718c19 5816 bcftools_1.3-1.debian.tar.xz Checksums-Sha256: d11e2afe7c10921ed05b278ef54915322eeb3789b721478a24f6502274686c2e 1973 bcftools_1.3-1.dsc 3f4d4bf68637070cb7dbb5d5619ece7e3315727e651eab751d849085439b11d8 943041 bcftools_1.3.orig.tar.gz 336ce19c6d740b1f556a07e38feb52489b1d89d5a3dd5914243f24b3731ae778 5816 bcftools_1.3-1.debian.tar.xz Files: 7494c500f3a9fa3e8b6a13267ec889b7 1973 science optional bcftools_1.3-1.dsc b851b3da39201b1c1a80780213d1196c 943041 science optional bcftools_1.3.orig.tar.gz 7fa3d7c71efb708da0e145f85fea980e 5816 science optional bcftools_1.3-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJWswH3AAoJEM6uatOv6Cb72wkQAK81MsqUd4yEdI/Zyb18rpce RAraWd/UvMUWR+qeVdaTwziu3pFOKu8dKLJBip1M0QV5ZAbGvTV8vjIFPm+CyIan Ngqca8WfBJpYHHz3GwuRDn5HLNFSFm/AR6s95vLdkBtw29gO6pun7Gf9lyqP/GrY 55S5uT2Bz8Wvz+HHCzrawR7daQiGRfZsGjIKhWM6CjhG+6oHdaBNbOgsO/rsVIO6 ESzbpuvgpX3Aio8snZIBIRqPDQDGRI5HYNt9Mz1JmJw6ciD/IZqWi54k8S4StP5l Zm/MIbqYUG1Ge2cIFamhyNhnaOtZpB31GapeSYhA4KDRPJz0kJFC/1VNi7QF3CRE /WAOEzAyzv1Ph2l1UPg2dqnW6ouI6F4FYCvqKA7O4OxdhedErlJqI87gYxF3vcpC 4zne6S56MMLaQuWv+Q7Ruml71GCc0+rR17ef/L4czqBQkTXL4G/dO5HcIuniQSWV NaOqSuXkfwLxu1WemcCNitYnNBN6qbi/Zkudy+5jL+JRd/V8fpVLvB2SGjDPTjN1 dZPDCiq73hNnUAf7dj2j+uVoDxFxxbiwIe9pEMsGz9ysQ/ZWOZBwvuAOp3/FS1xQ 8OzyFFOyycPFDdj1Vbrc0JE5ctOjobDvZEOikvE3gqkE7z+jakg2qeDAt3giZUE+ SSvIb/NvilfOLT0Vg6N+ =G+it -----END PGP SIGNATURE-----
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