[Debian-med-packaging] Bug#1042114: libssw: FTBFS: dpkg-gensymbols: error: some symbols or patterns disappeared in the symbols file: see diff output below

[Lucas Nussbaum]

Source: libssw
Version: 1.1-13
Severity: serious
Justification: FTBFS
Tags: trixie sid ftbfs
User: lucas at debian.org
Usertags: ftbfs-20230726 ftbfs-trixie

Hi,

During a rebuild of all packages in sid, your package failed to build
on amd64.


Relevant part (hopefully):
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> LD_LIBRARY_PATH=`pwd`/src help2man --version-string=' ' --help-option=' ' \
>           -I debian/extra-man-info.txt \
>           -N -n 'fast Smith-Waterman aligner' \
>           --no-discard-stderr src/ssw-align \
>             | fgrep -v ERROR > debian/ssw-align.1
> dh_installman
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
>    dh_perl
>    dh_link
>    jh_installlibs
>    jh_classpath
>    jh_manifest
>    jh_exec
>    jh_depends
>    mh_installpoms
>    mh_linkjars --skip-clean-poms
>    dh_strip_nondeterminism
>    dh_compress
>    dh_fixperms
>    dh_missing
>    dh_dwz -a
>    dh_strip -a
>    dh_makeshlibs -a
> dpkg-gensymbols: error: some symbols or patterns disappeared in the symbols file: see diff output below
> dpkg-gensymbols: warning: debian/libssw0/DEBIAN/symbols doesn't match completely debian/libssw0.symbols
> --- debian/libssw0.symbols (libssw0_1.1-13_amd64)
> +++ dpkg-gensymbolsLQ_iNr	2023-07-26 19:14:10.300342095 +0000
> @@ -22,9 +22,9 @@
>   _ZNK20StripedSmithWaterman7Aligner5AlignEPKcRKNS_6FilterEPNS_9AlignmentE at Base 1.1
>   _ZNK20StripedSmithWaterman7Aligner5AlignEPKcS2_RKiRKNS_6FilterEPNS_9AlignmentE at Base 1.1
>   (optional)_ZNSt6vectorIjSaIjEE17_M_realloc_insertIJRKjEEEvN9__gnu_cxx17__normal_iteratorIPjS1_EEDpOT_ at Base 1.1
> - _ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED0Ev at Base 1.1
> - _ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED1Ev at Base 1.1
> - _ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED2Ev at Base 1.1
> +#MISSING: 1.1-13# _ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED0Ev at Base 1.1
> +#MISSING: 1.1-13# _ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED1Ev at Base 1.1
> +#MISSING: 1.1-13# _ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED2Ev at Base 1.1
>   align_destroy at Base 1.1
>   init_destroy at Base 1.1
>   mark_mismatch at Base 1.1
> dh_makeshlibs: error: failing due to earlier errors
> make: *** [debian/rules:20: binary] Error 25


The full build log is available from:
http://qa-logs.debian.net/2023/07/26/libssw_1.1-13_unstable.log

All bugs filed during this archive rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20230726;users=lucas@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20230726&fusertaguser=lucas@debian.org&allbugs=1&cseverity=1&ctags=1&caffected=1#results

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!

If you reassign this bug to another package, please mark it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects

If you fail to reproduce this, please provide a build log and diff it with mine
so that we can identify if something relevant changed in the meantime.