Your message dated Sat, 29 Aug 2020 17:19:03 +0000
with message-id <e1kc4vl-000gqi...@fasolo.debian.org>
and subject line Bug#966863: fixed in gmap 2020-06-30+ds-2
has caused the Debian Bug report #966863,
regarding gmap: FTBFS: ld: gmap_nosimd-dynprog_end.o:./src/dynprog_end.c:112:
multiple definition of `homopolymerp';
gmap_nosimd-dynprog_single.o:./src/dynprog_single.c:94: first defined here
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
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immediately.)
--
966863: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=966863
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: gmap
Version: 2020-06-30+ds-1
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):
> gcc -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\"
> -DLARGE_GENOMES=1 -mpopcnt -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=.
> -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro
> -Wl,-z,now -o gmapl.nosimd gmapl_nosimd-except.o gmapl_nosimd-assert.o
> gmapl_nosimd-mem.o gmapl_nosimd-intlist.o gmapl_nosimd-uintlist.o
> gmapl_nosimd-uint8list.o gmapl_nosimd-list.o gmapl_nosimd-littleendian.o
> gmapl_nosimd-bigendian.o gmapl_nosimd-univinterval.o gmapl_nosimd-interval.o
> gmapl_nosimd-stopwatch.o gmapl_nosimd-semaphore.o gmapl_nosimd-access.o
> gmapl_nosimd-filestring.o gmapl_nosimd-iit-read-univ.o
> gmapl_nosimd-iit-read.o gmapl_nosimd-md5.o gmapl_nosimd-bzip2.o
> gmapl_nosimd-fopen.o gmapl_nosimd-sequence.o gmapl_nosimd-reader.o
> gmapl_nosimd-genomicpos.o gmapl_nosimd-compress.o
> gmapl_nosimd-compress-write.o gmapl_nosimd-gbuffer.o gmapl_nosimd-genome.o
> gmapl_nosimd-popcount.o gmapl_nosimd-genome_sites.o
> gmapl_nosimd-genome-write.o gmapl_nosimd-bitpack64-read.o
> gmapl_nosimd-bitpack64-readtwo.o gmapl_nosimd-indexdb.o gmapl_nosimd-oligo.o
> gmapl_nosimd-block.o gmapl_nosimd-chrom.o gmapl_nosimd-segmentpos.o
> gmapl_nosimd-chrnum.o gmapl_nosimd-uinttable_rh.o gmapl_nosimd-gregion.o
> gmapl_nosimd-match.o gmapl_nosimd-matchpool.o gmapl_nosimd-diagnostic.o
> gmapl_nosimd-stage1.o gmapl_nosimd-diag.o gmapl_nosimd-diagpool.o
> gmapl_nosimd-cmet.o gmapl_nosimd-atoi.o gmapl_nosimd-orderstat.o
> gmapl_nosimd-oligoindex_hr.o gmapl_nosimd-transcript.o gmapl_nosimd-intron.o
> gmapl_nosimd-maxent.o gmapl_nosimd-maxent_hr.o gmapl_nosimd-pair.o
> gmapl_nosimd-pairpool.o gmapl_nosimd-cellpool.o gmapl_nosimd-stage2.o
> gmapl_nosimd-doublelist.o gmapl_nosimd-smooth.o
> gmapl_nosimd-splicestringpool.o gmapl_nosimd-splicetrie_build.o
> gmapl_nosimd-splicetrie.o gmapl_nosimd-boyer-moore.o gmapl_nosimd-dynprog.o
> gmapl_nosimd-dynprog_simd.o gmapl_nosimd-dynprog_single.o
> gmapl_nosimd-dynprog_genome.o gmapl_nosimd-dynprog_cdna.o
> gmapl_nosimd-dynprog_end.o gmapl_nosimd-translation.o gmapl_nosimd-pbinom.o
> gmapl_nosimd-changepoint.o gmapl_nosimd-stage3.o gmapl_nosimd-request.o
> gmapl_nosimd-result.o gmapl_nosimd-output.o gmapl_nosimd-inbuffer.o
> gmapl_nosimd-samheader.o gmapl_nosimd-outbuffer.o gmapl_nosimd-chimera.o
> gmapl_nosimd-datadir.o gmapl_nosimd-parserange.o gmapl_nosimd-getline.o
> gmapl_nosimd-gmap.o -lz -lbz2 -lm
> /usr/bin/ld: gmap_nosimd-dynprog_end.o:./src/dynprog_end.c:112: multiple
> definition of `homopolymerp';
> gmap_nosimd-dynprog_single.o:./src/dynprog_single.c:94: first defined here
> /usr/bin/ld: gmapl_nosimd-dynprog_end.o:./src/dynprog_end.c:112: multiple
> definition of `homopolymerp';
> gmapl_nosimd-dynprog_single.o:./src/dynprog_single.c:94: first defined here
> gcc -pthread -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\"
> -DMAX_STACK_READLENGTH=300 -DGSNAP=1 -mpopcnt -g -O2
> -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
> -Werror=format-security -Wl,-z,relro -Wl,-z,now -o gsnap.nosimd
> gsnap_nosimd-except.o gsnap_nosimd-assert.o gsnap_nosimd-mem.o
> gsnap_nosimd-intlist.o gsnap_nosimd-uintlist.o gsnap_nosimd-list.o
> gsnap_nosimd-littleendian.o gsnap_nosimd-bigendian.o
> gsnap_nosimd-univinterval.o gsnap_nosimd-interval.o gsnap_nosimd-stopwatch.o
> gsnap_nosimd-semaphore.o gsnap_nosimd-access.o gsnap_nosimd-filestring.o
> gsnap_nosimd-iit-read-univ.o gsnap_nosimd-iit-read.o gsnap_nosimd-bzip2.o
> gsnap_nosimd-reader.o gsnap_nosimd-genomicpos.o gsnap_nosimd-compress.o
> gsnap_nosimd-genome.o gsnap_nosimd-transcriptome.o gsnap_nosimd-popcount.o
> gsnap_nosimd-genome128_hr.o gsnap_nosimd-genome128_consec.o
> gsnap_nosimd-genome_sites.o gsnap_nosimd-bitpack64-read.o
> gsnap_nosimd-bitpack64-readtwo.o gsnap_nosimd-merge-uint4.o
> gsnap_nosimd-merge-diagonals-simd-uint4.o gsnap_nosimd-indexdb.o
> gsnap_nosimd-regiondb.o gsnap_nosimd-oligo.o gsnap_nosimd-chrnum.o
> gsnap_nosimd-maxent_hr.o gsnap_nosimd-mdprint.o gsnap_nosimd-cigar.o
> gsnap_nosimd-samprint.o gsnap_nosimd-mapq.o gsnap_nosimd-fopen.o
> gsnap_nosimd-shortread.o gsnap_nosimd-substring.o gsnap_nosimd-junction.o
> gsnap_nosimd-transcript.o gsnap_nosimd-method.o gsnap_nosimd-stage3hr.o
> gsnap_nosimd-ladder.o gsnap_nosimd-concordance.o gsnap_nosimd-simplepair.o
> gsnap_nosimd-maxent.o gsnap_nosimd-orderstat.o gsnap_nosimd-intlistpool.o
> gsnap_nosimd-uintlistpool.o gsnap_nosimd-listpool.o
> gsnap_nosimd-hitlistpool.o gsnap_nosimd-intron.o gsnap_nosimd-gbuffer.o
> gsnap_nosimd-knownsplicing.o gsnap_nosimd-splice.o gsnap_nosimd-indel.o
> gsnap_nosimd-bitpack64-access.o gsnap_nosimd-univdiag.o
> gsnap_nosimd-univdiagpool.o gsnap_nosimd-sedgesort.o gsnap_nosimd-intersect.o
> gsnap_nosimd-kmer-search.o gsnap_nosimd-path-solve.o
> gsnap_nosimd-extension-search.o gsnap_nosimd-segment-search.o
> gsnap_nosimd-terminal.o gsnap_nosimd-distant-rna.o gsnap_nosimd-distant-dna.o
> gsnap_nosimd-uint8table_rh.o gsnap_nosimd-uinttable_rh.o
> gsnap_nosimd-stage1hr.o gsnap_nosimd-request.o gsnap_nosimd-resulthr.o
> gsnap_nosimd-output.o gsnap_nosimd-inbuffer.o gsnap_nosimd-samheader.o
> gsnap_nosimd-outbuffer.o gsnap_nosimd-datadir.o gsnap_nosimd-parserange.o
> gsnap_nosimd-getline.o gsnap_nosimd-gsnap.o -lz -lbz2 -lm
> collect2: error: ld returned 1 exit status
The full build log is available from:
http://qa-logs.debian.net/2020/08/02/gmap_2020-06-30+ds-1_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.
--- End Message ---
--- Begin Message ---
Source: gmap
Source-Version: 2020-06-30+ds-2
Done: Nilesh Patra <npatra...@gmail.com>
We believe that the bug you reported is fixed in the latest version of
gmap, 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.
Nilesh Patra <npatra...@gmail.com> (supplier of updated gmap 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: Sat, 29 Aug 2020 21:03:54 +0530
Source: gmap
Architecture: source
Version: 2020-06-30+ds-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Nilesh Patra <npatra...@gmail.com>
Closes: 966863
Changes:
gmap (2020-06-30+ds-2) unstable; urgency=medium
.
* Team Upload.
* Refresh patch
* Fix gcc-10 FTBFS (Closes: #966863)
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--- End Message ---
