[Debian-med-packaging] Bug#984090: libbpp-raa: ftbfs with GCC-11

[Matthias Klose]

Package: src:libbpp-raa
Version: 2.4.1-4
Severity: normal
Tags: sid bookworm
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-11

[This bug is not targeted to the upcoming bullseye 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-11/g++-11, but succeeds to build with gcc-10/g++-10. The
severity of this report will be raised before the bookworm release,
so nothing has to be done for the bullseye release.

The full build log can be found at:
http://people.debian.org/~doko/logs/20210228/filtered/gcc11/libbpp-raa_2.4.1-4_unstable_gcc11.log
The last lines of the build log are at the end of this report.

To build with GCC 11, either set CC=gcc-11 CXX=g++-11 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-11/porting_to.html

GCC 11 defaults to the GNU++17 standard.  If your package installs
header files in /usr/include, please don't work around C++17 issues
by choosing a lower C++ standard for the package build, but fix these
issues to build with the C++17 standard.

[...]
                    --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-raa4/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-raa4/usr/lib/x86_64-linux-gnu
mv /<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu/libbpp-raa.so.4.0.0 debian/libbpp-raa4/usr/lib/x86_64-linux-gnu
PKGDEV=libbpp-raa-dev
PKGSHL=libbpp-raa4
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_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-raa4/DEBIAN/symbols doesn't match completely debian/libbpp-raa4.symbols.amd64
--- debian/libbpp-raa4.symbols.amd64 (libbpp-raa4_2.4.1-4_amd64)
+++ dpkg-gensymbolsYzL713	2021-03-01 21:10:54.111892382 +0000
@@ -17,7 +17,7 @@
  _ZN3bpp17AlphabetExceptionD0Ev at Base 2.4.1
  _ZN3bpp17AlphabetExceptionD1Ev at Base 2.4.1
  _ZN3bpp17AlphabetExceptionD2Ev at Base 2.4.1
- _ZN3bpp20AbstractCoreSequence11setCommentsERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS7_EE at Base 2.4.1
+#MISSING: 2.4.1-4# _ZN3bpp20AbstractCoreSequence11setCommentsERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS7_EE at Base 2.4.1
  _ZN3bpp3RAA10deleteListEPNS_7RaaListE at Base 2.4.1
  _ZN3bpp3RAA10getSeqFragERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiiRS6_ at Base 2.4.1
  _ZN3bpp3RAA10getSeqFragEiiiRNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 2.4.1
@@ -74,15 +74,17 @@
  _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
- _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE12emplace_backIJS5_EEEvDpOT_ at Base 2.4.1
+#MISSING: 2.4.1-4# _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_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
- _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EEaSERKS7_ at Base 2.4.1
+#MISSING: 2.4.1-4# _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EEaSERKS7_ at Base 2.4.1
+ _ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC1IS3_EEPKcRKS3_ at Base 2.4.1-4
+ _ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC2IS3_EEPKcRKS3_ at Base 2.4.1-4
  _ZTINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 2.4.1
  _ZTSNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 2.4.1
- _ZTv0_n72_N3bpp20AbstractCoreSequence11setCommentsERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS7_EE at Base 2.4.1
+#MISSING: 2.4.1-4# _ZTv0_n72_N3bpp20AbstractCoreSequence11setCommentsERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS7_EE at Base 2.4.1
  ajout_reponse at Base 2.4.1
  aminoacids at Base 2.4.1
  atoi_u 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