[Debian-med-packaging] Bug#925735: libbpp-raa: ftbfs with GCC-9

[Matthias Klose]

Package: src:libbpp-raa
Version: 2.4.1-1
Severity: normal
Tags: sid bullseye
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-9

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-9/g++-9, but succeeds to build with gcc-8/g++-8. The
severity of this report will be raised before the bullseye release,
so nothing has to be done for the buster release.

The full build log can be found at:
http://people.debian.org/~doko/logs/gcc9-20190321/libbpp-raa_2.4.1-1_unstable_gcc9.log
The last lines of the build log are at the end of this report.

To build with GCC 9, either set CC=gcc-9 CXX=g++-9 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-9/porting_to.html

GCC 9 also passes the linker option --as-needed by default; typical
build issues are passing libraries before object files to the linker,
or underlinking of convenience libraries built from the same source.

[...]
	    --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-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 -a
   dh_installchangelogs -a
   dh_perl -a
   dh_link -a
   dh_strip_nondeterminism -a
   dh_compress -a
   dh_fixperms -a
   dh_missing -a
   dh_strip -a
   debian/rules override_dh_makeshlibs
make[1]: Entering directory '/<<PKGBUILDDIR>>'
echo "Architecture amd64 is the only one where a symbols file is provided"
Architecture amd64 is the only one where a symbols file is provided
dh_makeshlibs
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
--- debian/libbpp-raa4.symbols (libbpp-raa4_2.4.1-1_amd64)
+++ dpkg-gensymbolsMqy5ii	2019-03-26 16:58:28.951719660 +0000
@@ -17,6 +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 2.4.1-1
  _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
@@ -76,10 +77,12 @@
  _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
- _ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE12_M_constructIPKcEEvT_S8_St20forward_iterator_tag at Base 2.4.1
+ _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EEaSERKS7_ at Base 2.4.1-1
+#MISSING: 2.4.1-1# _ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE12_M_constructIPKcEEvT_S8_St20forward_iterator_tag at Base 2.4.1
  _ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE12_M_constructIPcEEvT_S7_St20forward_iterator_tag at Base 2.4.1
  _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 2.4.1-1
  ajout_reponse at Base 2.4.1
  aminoacids at Base 2.4.1
  atoi_u at Base 2.4.1
dh_makeshlibs: failing due to earlier errors
make[1]: *** [debian/rules:12: override_dh_makeshlibs] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:8: binary-arch] Error 2
dpkg-buildpackage: error: fakeroot debian/rules binary-arch subprocess returned exit status 2