[Debian-med-packaging] Bug#925737: libbpp-seq-omics: ftbfs with GCC-9

[Matthias Klose]

Package: src:libbpp-seq-omics
Version: 2.4.1-3
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-seq-omics_2.4.1-3_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.

[...]
@@ -476,7 +480,7 @@
  _ZNK3bpp8SeqRange5cloneEv at Base 2.4.1
  _ZNK3bpp8SeqRange9getStrandEv at Base 2.4.1
  _ZNK3bpp9BppDouble5cloneEv at Base 2.4.1
- _ZNKSt15_Deque_iteratorISt6vectorIbSaIbEERS2_PS2_EplEl at Base 2.4.1
+#MISSING: 2.4.1-3# _ZNKSt15_Deque_iteratorISt6vectorIbSaIbEERS2_PS2_EplEl at Base 2.4.1
  _ZNKSt5ctypeIcE8do_widenEc at Base 2.4.1
  _ZNSt11_Deque_baseIPN3bpp8MafBlockESaIS2_EED1Ev at Base 2.4.1
  _ZNSt11_Deque_baseIPN3bpp8MafBlockESaIS2_EED2Ev at Base 2.4.1
@@ -486,9 +490,9 @@
  _ZNSt13_Bvector_baseISaIbEE13_M_deallocateEv at Base 2.4.1
  _ZNSt15_Sp_counted_ptrIDnLN9__gnu_cxx12_Lock_policyE2EE10_M_disposeEv at Base 2.4.1
  _ZNSt16_Sp_counted_baseILN9__gnu_cxx12_Lock_policyE2EE10_M_destroyEv at Base 2.4.1
- _ZNSt20__uninitialized_copyILb0EE13__uninit_copyIN9__gnu_cxx17__normal_iteratorIPKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt6vectorIS9_SaIS9_EEEEPS9_EET0_T_SI_SH_ at Base 2.4.1
+#MISSING: 2.4.1-3# _ZNSt20__uninitialized_copyILb0EE13__uninit_copyIN9__gnu_cxx17__normal_iteratorIPKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt6vectorIS9_SaIS9_EEEEPS9_EET0_T_SI_SH_ at Base 2.4.1
  _ZNSt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEPN3bpp10BppNumberIESt4lessIS5_ESaISt4pairIKS5_S8_EEEixERSC_ at Base 2.4.1
- _ZNSt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES5_St4lessIS5_ESaISt4pairIKS5_S5_EEEixEOS5_ at Base 2.4.1
+#MISSING: 2.4.1-3# _ZNSt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES5_St4lessIS5_ESaISt4pairIKS5_S5_EEEixEOS5_ 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
  _ZNSt5dequeIPN3bpp8MafBlockESaIS2_EE16_M_push_back_auxIJRKS2_EEEvDpOT_ at Base 2.4.1
@@ -497,6 +501,7 @@
  _ZNSt5dequeISt6vectorIiSaIiEESaIS2_EE16_M_push_back_auxIJRKS2_EEEvDpOT_ at Base 2.4.1
  _ZNSt5dequeISt6vectorIiSaIiEESaIS2_EE19_M_destroy_data_auxESt15_Deque_iteratorIS2_RS2_PS2_ES8_ at Base 2.4.1
  _ZNSt5dequeIjSaIjEE16_M_push_back_auxIJjEEEvDpOT_ at Base 2.4.1
+ _ZNSt5dequeImSaImEE17_M_push_front_auxIJmEEEvDpOT_ at Base 2.4.1-3
  _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE12emplace_backIJS5_EEEvDpOT_ 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
@@ -507,7 +512,7 @@
  _ZNSt6vectorIPKN3bpp11MafSequenceESaIS3_EE17_M_realloc_insertIJRKS3_EEEvN9__gnu_cxx17__normal_iteratorIPS3_S5_EEDpOT_ at Base 2.4.1
  _ZNSt6vectorIPN3bpp13AlphabetStateESaIS2_EE17_M_realloc_insertIJS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ at Base 2.4.1
  _ZNSt6vectorIPN3bpp13SiteContainerESaIS2_EE17_M_realloc_insertIJS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ at Base 2.4.1
- _ZNSt6vectorIPN3bpp15SequenceFeatureESaIS2_EE12emplace_backIJS2_EEEvDpOT_ at Base 2.4.1
+#MISSING: 2.4.1-3# _ZNSt6vectorIPN3bpp15SequenceFeatureESaIS2_EE12emplace_backIJS2_EEEvDpOT_ at Base 2.4.1
  _ZNSt6vectorIPN3bpp15SequenceFeatureESaIS2_EE17_M_realloc_insertIJS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ at Base 2.4.1
  _ZNSt6vectorIPN3bpp17IterationListenerESaIS2_EE17_M_realloc_insertIJRKS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ at Base 2.4.1
  _ZNSt6vectorIPN3bpp18SymbolListListenerESaIS2_EE17_M_realloc_insertIJRKS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ at Base 2.4.1
@@ -523,21 +528,21 @@
  _ZNSt6vectorIS_IiSaIiEESaIS1_EED2Ev at Base 2.4.1
  _ZNSt6vectorIS_ImSaImEESaIS1_EED1Ev at Base 2.4.1
  _ZNSt6vectorIS_ImSaImEESaIS1_EED2Ev at Base 2.4.1
- _ZNSt6vectorIbSaIbEEC1ERKS1_ at Base 2.4.1
- _ZNSt6vectorIbSaIbEEC2ERKS1_ at Base 2.4.1
+#MISSING: 2.4.1-3# _ZNSt6vectorIbSaIbEEC1ERKS1_ at Base 2.4.1
+#MISSING: 2.4.1-3# _ZNSt6vectorIbSaIbEEC2ERKS1_ at Base 2.4.1
  _ZNSt6vectorIiSaIiEE17_M_default_appendEm at Base 2.4.1
  _ZNSt6vectorIiSaIiEE17_M_realloc_insertIJRKiEEEvN9__gnu_cxx17__normal_iteratorIPiS1_EEDpOT_ at Base 2.4.1
- _ZNSt6vectorIiSaIiEEC1ERKS1_ at Base 2.4.1
- _ZNSt6vectorIiSaIiEEC2ERKS1_ at Base 2.4.1
+#MISSING: 2.4.1-3# _ZNSt6vectorIiSaIiEEC1ERKS1_ at Base 2.4.1
+#MISSING: 2.4.1-3# _ZNSt6vectorIiSaIiEEC2ERKS1_ at Base 2.4.1
  _ZNSt6vectorIiSaIiEEaSERKS1_ at Base 2.4.1
  _ZNSt6vectorIjSaIjEE14_M_fill_assignEmRKj at Base 2.4.1
  _ZNSt6vectorIjSaIjEE17_M_realloc_insertIJjEEEvN9__gnu_cxx17__normal_iteratorIPjS1_EEDpOT_ at Base 2.4.1
  _ZNSt6vectorImSaImEE12emplace_backIJmEEEvDpOT_ 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
- _ZNSt6vectorImSaImEEC1ISt15_Deque_iteratorImRmPmEvEET_S7_RKS0_ at Base 2.4.1
- _ZNSt6vectorImSaImEEC2ISt15_Deque_iteratorImRmPmEvEET_S7_RKS0_ at Base 2.4.1
+#MISSING: 2.4.1-3# _ZNSt6vectorImSaImEE9push_backERKm at Base 2.4.1
+#MISSING: 2.4.1-3# _ZNSt6vectorImSaImEEC1ISt15_Deque_iteratorImRmPmEvEET_S7_RKS0_ at Base 2.4.1
+#MISSING: 2.4.1-3# _ZNSt6vectorImSaImEEC2ISt15_Deque_iteratorImRmPmEvEET_S7_RKS0_ at Base 2.4.1
  _ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE12_M_constructIN9__gnu_cxx17__normal_iteratorIPcS4_EEEEvT_SA_St20forward_iterator_tag at Base 2.4.1
  _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
dh_makeshlibs: failing due to earlier errors
make: *** [debian/rules:10: binary-arch] Error 2
dpkg-buildpackage: error: fakeroot debian/rules binary-arch subprocess returned exit status 2