[Debian-med-packaging] Bug#952248: libbpp-popgen: FTBFS: dpkg-gensymbols: error: some symbols or patterns disappeared in the symbols file: see diff output below

[Lucas Nussbaum]

Source: libbpp-popgen
Version: 2.4.1-2
Severity: serious
Justification: FTBFS on amd64
Tags: bullseye sid ftbfs
Usertags: ftbfs-20200222 ftbfs-bullseye

Hi,

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

Relevant part (hopefully):
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> dh_install
> d-shlibmove --commit \
> 	    --multiarch \
> 	    --devunversioned \
> 	    --exclude-la \
>                     --movedev debian/tmp/usr/include/* usr/include \
>                     --movedev debian/tmp/usr/lib/*/cmake usr/lib/x86_64-linux-gnu \
>                     debian/tmp/usr/lib/*/*.so
> Library package automatic movement utility
>  --> libbpp-core-dev package exists.
>  --> libbpp-seq-dev package exists.
> set -e
> install -d -m 755 debian/libbpp-popgen-dev/usr/lib/x86_64-linux-gnu
> install -d -m 755 debian/libbpp-popgen8/usr/lib/x86_64-linux-gnu
> mv debian/tmp/usr/lib/x86_64-linux-gnu/libbpp-popgen.a debian/libbpp-popgen-dev/usr/lib/x86_64-linux-gnu
> mv debian/tmp/usr/lib/x86_64-linux-gnu/libbpp-popgen.so debian/libbpp-popgen-dev/usr/lib/x86_64-linux-gnu
> mv /<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu/libbpp-popgen.so.8 debian/libbpp-popgen8/usr/lib/x86_64-linux-gnu
> mv /<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu/libbpp-popgen.so.8.0.0 debian/libbpp-popgen8/usr/lib/x86_64-linux-gnu
> PKGDEV=libbpp-popgen-dev
> PKGSHL=libbpp-popgen8
> install -d -m 755 debian/libbpp-popgen-dev/usr/include
> mv debian/tmp/usr/include/Bpp debian/libbpp-popgen-dev/usr/include
> install -d -m 755 debian/libbpp-popgen-dev/usr/lib/x86_64-linux-gnu
> mv debian/tmp/usr/lib/x86_64-linux-gnu/cmake debian/libbpp-popgen-dev/usr/lib/x86_64-linux-gnu
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
>    dh_installdocs
>    dh_installchangelogs
>    dh_perl
>    dh_link
>    dh_strip_nondeterminism
>    dh_compress
>    dh_fixperms
>    dh_missing
>    dh_dwz
>    dh_strip
>    dh_makeshlibs
> dpkg-gensymbols: error: some symbols or patterns disappeared in the symbols file: see diff output below
> dpkg-gensymbols: warning: debian/libbpp-popgen8/DEBIAN/symbols doesn't match completely debian/libbpp-popgen8.symbols.amd64
> --- debian/libbpp-popgen8.symbols.amd64 (libbpp-popgen8_2.4.1-2_amd64)
> +++ dpkg-gensymbolstUa40O	2020-02-23 02:45:26.493958486 +0000
> @@ -910,8 +910,8 @@
>   _ZNSt5dequeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED2Ev at Base 2.4.1
>   _ZNSt6vectorIN3bpp19GeneMapperCsvExport6AlleleESaIS2_EE17_M_realloc_insertIJRKS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ at Base 2.4.1
>   _ZNSt6vectorIN3bpp9LocusInfoESaIS1_EE17_M_realloc_insertIJS1_EEEvN9__gnu_cxx17__normal_iteratorIPS1_S3_EEDpOT_ at Base 2.4.1
> - _ZNSt6vectorIN3bpp9LocusInfoESaIS1_EED1Ev at Base 2.4.1
> - _ZNSt6vectorIN3bpp9LocusInfoESaIS1_EED2Ev at Base 2.4.1
> +#MISSING: 2.4.1-2# _ZNSt6vectorIN3bpp9LocusInfoESaIS1_EED1Ev at Base 2.4.1
> +#MISSING: 2.4.1-2# _ZNSt6vectorIN3bpp9LocusInfoESaIS1_EED2Ev at Base 2.4.1
>   _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE12emplace_backIJS5_EEEvDpOT_ at Base 2.4.1
>   _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE17_M_default_appendEm at Base 2.4.1
>   _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE17_M_realloc_insertIJRKS5_EEEvN9__gnu_cxx17__normal_iteratorIPS5_S7_EEDpOT_ at Base 2.4.1
> dh_makeshlibs: error: failing due to earlier errors
> make: *** [debian/rules:8: binary] Error 25

The full build log is available from:
   http://qa-logs.debian.net/2020/02/22/libbpp-popgen_2.4.1-2_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.