[Debian-med-packaging] Bug#1075152: libbpp-raa: ftbfs with GCC-14

[Matthias Klose]

Package: src:libbpp-raa
Version: 2.4.1-8
Severity: important
Tags: sid trixie
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-14

[This bug is targeted to the upcoming trixie release]

Please keep this issue open in the bug tracker for the package it
was filed for.  If a fix in another package is required, please
file a bug for the other package (or clone), and add a block in this
package. Please keep the issue open until the package can be built in
a follow-up test rebuild.

The package fails to build in a test rebuild on at least amd64 with
gcc-14/g++-14, but succeeds to build with gcc-13/g++-13. The
severity of this report will be raised before the trixie release.

The full build log can be found at:
http://qa-logs.debian.net/2024/07/01/libbpp-raa_2.4.1-8_unstable_gccexp.log
The last lines of the build log are at the end of this report.

To build with GCC 14, either set CC=gcc-14 CXX=g++-14 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.

  apt-get -t=experimental install g++ 

Common build failures are new warnings resulting in build failures with
-Werror turned on, or new/dropped symbols in Debian symbols files.
For other C/C++ related build failures see the porting guide at
http://gcc.gnu.org/gcc-14/porting_to.html

[...]
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Raa/RaaSpeciesTree.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Raa/RaaSeqAttributes.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/include/Bpp/Raa/RaaList.h
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/bpp-raa/bpp-raa-targets.cmake
-- Installing: /<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/bpp-raa/bpp-raa-targets-none.cmake
make[1]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
   debian/rules override_dh_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_install
d-shlibmove --commit \
	    --t64 \
	    --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.
 --> zlib1g-dev package exists.
set -e
install -d -m 755 debian/libbpp-raa-dev/usr/lib/x86_64-linux-gnu
install -d -m 755 debian/libbpp-raa4t64/usr/lib/x86_64-linux-gnu
mv debian/tmp/usr/lib/x86_64-linux-gnu/libbpp-raa.a debian/libbpp-raa-dev/usr/lib/x86_64-linux-gnu
mv debian/tmp/usr/lib/x86_64-linux-gnu/libbpp-raa.so debian/libbpp-raa-dev/usr/lib/x86_64-linux-gnu
mv /<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu/libbpp-raa.so.4 debian/libbpp-raa4t64/usr/lib/x86_64-linux-gnu
mv /<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu/libbpp-raa.so.4.0.0 debian/libbpp-raa4t64/usr/lib/x86_64-linux-gnu
PKGDEV=libbpp-raa-dev
PKGSHL=libbpp-raa4t64
install -d -m 755 debian/libbpp-raa-dev/usr/include
mv debian/tmp/usr/include/Bpp debian/libbpp-raa-dev/usr/include
install -d -m 755 debian/libbpp-raa-dev/usr/lib/x86_64-linux-gnu
mv debian/tmp/usr/lib/x86_64-linux-gnu/cmake debian/libbpp-raa-dev/usr/lib/x86_64-linux-gnu
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_installdocs
   dh_installchangelogs
   dh_lintian
   dh_perl
   dh_link
   dh_strip_nondeterminism
   dh_compress
   dh_fixperms
   dh_missing
   dh_dwz -a
   dh_strip -a
   dh_makeshlibs -a
dpkg-gensymbols: warning: some new symbols appeared in the symbols file: see diff output below
dpkg-gensymbols: error: some symbols or patterns disappeared in the symbols file: see diff output below
dpkg-gensymbols: warning: debian/libbpp-raa4t64/DEBIAN/symbols doesn't match completely debian/libbpp-raa4t64.symbols.amd64
--- debian/libbpp-raa4t64.symbols.amd64 (libbpp-raa4t64_2.4.1-8_amd64)
+++ dpkg-gensymbols5f90_r	2024-07-02 01:24:58.992144809 +0000
@@ -72,10 +72,11 @@
  _ZN3bpp7RaaListC1Ev at Base 2.4.1
  _ZN3bpp7RaaListC2Ev at Base 2.4.1
  _ZNK3bpp17AlphabetException11getAlphabetEv at Base 2.4.1
- _ZNSt12_Vector_baseINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED1Ev at Base 2.4.1
- _ZNSt12_Vector_baseINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED2Ev at Base 2.4.1
+#MISSING: 2.4.1-8# _ZNSt12_Vector_baseINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED1Ev at Base 2.4.1
+#MISSING: 2.4.1-8# _ZNSt12_Vector_baseINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED2Ev 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_insertIJS5_EEEvN9__gnu_cxx17__normal_iteratorIPS5_S7_EEDpOT_ at Base 2.4.1
+ _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE17_M_realloc_appendIJS5_EEEvDpOT_ at Base 2.4.1-8
+#MISSING: 2.4.1-8# _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE17_M_realloc_insertIJS5_EEEvN9__gnu_cxx17__normal_iteratorIPS5_S7_EEDpOT_ at Base 2.4.1
  _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED1Ev at Base 2.4.1
  _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED2Ev at Base 2.4.1
  _ZSt18__do_uninit_fill_nIPNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEmS5_ET_S7_T0_RKT1_ at Base 2.4.1
dh_makeshlibs: error: failing due to earlier errors
make: *** [debian/rules:8: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2