[Debian-med-packaging] Bug#966865: kalign: FTBFS: ld: esl_stopwatch.o:./src/tldevel.h:567: multiple definition of `logsum_lookup'; tldevel.o:./src/tldevel.h:567: first defined here

[Lucas Nussbaum]

Source: kalign
Version: 1:3.2.3-3
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):
> /bin/bash ../libtool  --tag=CC   --mode=link gcc -fopenmp -O3 -std=gnu11 -DHAVE_AVX2=1 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2  -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections  -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z,relro -Wl,-z,now -o timescorealn tldevel.o esl_stopwatch.o time_and_score_aln.o parameters.o alphabet.o rwalign.o misc.o  -lpthread -lm 
> libtool: link: gcc -fopenmp -O3 -std=gnu11 -DHAVE_AVX2=1 -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -Wl,--gc-sections -Wl,--as-needed -Wno-undef -Wl,-z -Wl,relro -Wl,-z -Wl,now -o timescorealn tldevel.o esl_stopwatch.o time_and_score_aln.o parameters.o alphabet.o rwalign.o misc.o  -lpthread -lm -fopenmp
> /usr/bin/ld: esl_stopwatch.o:./src/tldevel.h:567: multiple definition of `logsum_lookup'; tldevel.o:./src/tldevel.h:567: first defined here
> /usr/bin/ld: time_and_score_aln.o:./src/tldevel.h:567: multiple definition of `logsum_lookup'; tldevel.o:./src/tldevel.h:567: first defined here
> /usr/bin/ld: parameters.o:./src/tldevel.h:567: multiple definition of `logsum_lookup'; tldevel.o:./src/tldevel.h:567: first defined here
> /usr/bin/ld: alphabet.o:./src/tldevel.h:567: multiple definition of `logsum_lookup'; tldevel.o:./src/tldevel.h:567: first defined here
> /usr/bin/ld: rwalign.o:./src/tldevel.h:567: multiple definition of `logsum_lookup'; tldevel.o:./src/tldevel.h:567: first defined here
> /usr/bin/ld: misc.o:./src/tldevel.h:567: multiple definition of `logsum_lookup'; tldevel.o:./src/tldevel.h:567: first defined here
> collect2: error: ld returned 1 exit status

The full build log is available from:
   http://qa-logs.debian.net/2020/08/02/kalign_3.2.3-3_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.