[Debian-med-packaging] Bug#984094: libbpp-seq: ftbfs with GCC-11

[Matthias Klose]

Package: src:libbpp-seq
Version: 2.4.1-5
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-seq_2.4.1-5_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.

[...]
   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-seq12/DEBIAN/symbols doesn't match completely debian/libbpp-seq12.symbols.amd64
--- debian/libbpp-seq12.symbols.amd64 (libbpp-seq12_2.4.1-5_amd64)
+++ dpkg-gensymbolshOzBBI	2021-03-01 20:58:11.875930185 +0000
@@ -98,6 +98,7 @@
  _ZN3bpp13AAVolumeIndexD0Ev at Base 2.4.1
  _ZN3bpp13AAVolumeIndexD1Ev at Base 2.4.1
  _ZN3bpp13AlphabetStateC1EiRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_ at Base 2.4.1
+ _ZN3bpp13AlphabetStateC2EiRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_ at Base 2.4.1-5
  _ZN3bpp13AlphabetStateD0Ev at Base 2.4.1
  _ZN3bpp13AlphabetStateD1Ev at Base 2.4.1
  _ZN3bpp13AlphabetStateD2Ev at Base 2.4.1
@@ -272,6 +273,7 @@
  _ZN3bpp15NexusIOSequenceD1Ev at Base 2.4.1
  _ZN3bpp15NucleicAlphabet10getStateAtEm at Base 2.4.1
  _ZN3bpp15NucleicAlphabet13registerStateEPNS_13AlphabetStateE at Base 2.4.1
+ _ZN3bpp15NucleicAlphabet14updateBinMaps_EmRKNS_20NucleicAlphabetStateE at Base 2.4.1-5
  _ZN3bpp15NucleicAlphabet8setStateEmPNS_13AlphabetStateE at Base 2.4.1
  _ZN3bpp15NucleicAlphabetD2Ev at Base 2.4.1
  _ZN3bpp15NumericAlphabet10getStateAtEm at Base 2.4.1
@@ -1723,7 +1725,9 @@
  _ZNKSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_mESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE4findERS7_ at Base 2.4.1
  _ZNSt10unique_ptrIN3bpp8SequenceESt14default_deleteIS1_EED1Ev at Base 2.4.1
  _ZNSt10unique_ptrIN3bpp8SequenceESt14default_deleteIS1_EED2Ev at Base 2.4.1
- _ZNSt11_Deque_baseIiSaIiEE17_M_initialize_mapEm at Base 2.4.1
+#MISSING: 2.4.1-5# _ZNSt11_Deque_baseIiSaIiEE17_M_initialize_mapEm at Base 2.4.1
+ _ZNSt11_Deque_baseIiSaIiEEC1Ev at Base 2.4.1-5
+ _ZNSt11_Deque_baseIiSaIiEEC2Ev at Base 2.4.1-5
  _ZNSt11_Deque_baseIiSaIiEED1Ev at Base 2.4.1
  _ZNSt11_Deque_baseIiSaIiEED2Ev at Base 2.4.1
  _ZNSt12_Vector_baseINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED1Ev at Base 2.4.1
@@ -1753,13 +1757,14 @@
  _ZNSt3mapIiiSt4lessIiESaISt4pairIKiiEEEixEOi at Base 2.4.1
  _ZNSt5dequeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED1Ev at Base 2.4.1
  _ZNSt5dequeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED2Ev at Base 2.4.1
- _ZNSt5dequeIiSaIiEE13emplace_frontIJiEEEvDpOT_ at Base 2.4.1
+#MISSING: 2.4.1-5# _ZNSt5dequeIiSaIiEE13emplace_frontIJiEEEvDpOT_ at Base 2.4.1
  _ZNSt5dequeIiSaIiEE17_M_push_front_auxIJRKiEEEvDpOT_ at Base 2.4.1
  _ZNSt5dequeIiSaIiEE17_M_reallocate_mapEmb at Base 2.4.1
  _ZNSt6vectorIN3bpp13BasicSequenceESaIS1_EE17_M_realloc_insertIJS1_EEEvN9__gnu_cxx17__normal_iteratorIPS1_S3_EEDpOT_ at Base 2.4.1
  _ZNSt6vectorIN3bpp13BasicSequenceESaIS1_EED1Ev at Base 2.4.1
  _ZNSt6vectorIN3bpp13BasicSequenceESaIS1_EED2Ev at Base 2.4.1
- _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE12emplace_backIJS5_EEEvDpOT_ at Base 2.4.1
+ _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE12emplace_backIJS5_EEERS5_DpOT_ at Base 2.4.1-5
+#MISSING: 2.4.1-5# _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
  _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE17_M_realloc_insertIJS5_EEEvN9__gnu_cxx17__normal_iteratorIPS5_S7_EEDpOT_ at Base 2.4.1
@@ -1811,10 +1816,15 @@
  _ZNSt6vectorIiSaIiEE17_M_realloc_insertIJiEEEvN9__gnu_cxx17__normal_iteratorIPiS1_EEDpOT_ at Base 2.4.1
  _ZNSt6vectorIiSaIiEE6insertEN9__gnu_cxx17__normal_iteratorIPKiS1_EERS4_ at Base 2.4.1
  _ZNSt6vectorIiSaIiEE8_M_eraseEN9__gnu_cxx17__normal_iteratorIPiS1_EE at Base 2.4.1
+ _ZNSt6vectorIiSaIiEEC1ISt15_Deque_iteratorIiRiPiEvEET_S7_RKS0_ at Base 2.4.1-5
+ _ZNSt6vectorIiSaIiEEC2ISt15_Deque_iteratorIiRiPiEvEET_S7_RKS0_ at Base 2.4.1-5
  _ZNSt6vectorIiSaIiEEaSERKS1_ at Base 2.4.1
  _ZNSt6vectorImSaImEE17_M_default_appendEm at Base 2.4.1
  _ZNSt6vectorImSaImEE17_M_realloc_insertIJRKmEEEvN9__gnu_cxx17__normal_iteratorIPmS1_EEDpOT_ at Base 2.4.1
  _ZNSt6vectorImSaImEE17_M_realloc_insertIJmEEEvN9__gnu_cxx17__normal_iteratorIPmS1_EEDpOT_ at Base 2.4.1
+ _ZNSt6vectorImSaImEE9push_backERKm at Base 2.4.1-5
+ _ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC1IS3_EEPKcRKS3_ at Base 2.4.1-5
+ _ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC2IS3_EEPKcRKS3_ at Base 2.4.1-5
  _ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED0Ev at Base 2.4.1
  _ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED1Ev at Base 2.4.1
  _ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED2Ev at Base 2.4.1
dh_makeshlibs: error: failing due to earlier errors
make: *** [debian/rules:10: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2