[Debian-med-packaging] Bug#925736: libbpp-seq: ftbfs with GCC-9

[Matthias Klose]

Package: src:libbpp-seq
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_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.

[...]
  _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
@@ -1760,13 +1764,13 @@
  _ZNSt6vectorIPN3bpp8SequenceESaIS2_EE17_M_realloc_insertIJRKS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ at Base 2.4.1
  _ZNSt6vectorIPN3bpp8SequenceESaIS2_EE17_M_realloc_insertIJS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ at Base 2.4.1
  _ZNSt6vectorIPN3bpp8SequenceESaIS2_EE8_M_eraseEN9__gnu_cxx17__normal_iteratorIPS2_S4_EE at Base 2.4.1
- _ZNSt6vectorIPN3bpp8SequenceESaIS2_EEC1EmRKS3_ at Base 2.4.1
- _ZNSt6vectorIPN3bpp8SequenceESaIS2_EEC2EmRKS3_ at Base 2.4.1
+#MISSING: 2.4.1-3# _ZNSt6vectorIPN3bpp8SequenceESaIS2_EEC1EmRKS3_ at Base 2.4.1
+#MISSING: 2.4.1-3# _ZNSt6vectorIPN3bpp8SequenceESaIS2_EEC2EmRKS3_ at Base 2.4.1
  _ZNSt6vectorIPS_INSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EESaIS8_EE17_M_default_appendEm at Base 2.4.1
  _ZNSt6vectorIPS_INSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EESaIS8_EE17_M_realloc_insertIJS8_EEEvN9__gnu_cxx17__normal_iteratorIPS8_SA_EEDpOT_ at Base 2.4.1
  _ZNSt6vectorIPS_INSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EESaIS8_EE8_M_eraseEN9__gnu_cxx17__normal_iteratorIPS8_SA_EE at Base 2.4.1
- _ZNSt6vectorIPS_INSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EESaIS8_EEC1EmRKS9_ at Base 2.4.1
- _ZNSt6vectorIPS_INSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EESaIS8_EEC2EmRKS9_ at Base 2.4.1
+#MISSING: 2.4.1-3# _ZNSt6vectorIPS_INSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EESaIS8_EEC1EmRKS9_ at Base 2.4.1
+#MISSING: 2.4.1-3# _ZNSt6vectorIPS_INSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EESaIS8_EEC2EmRKS9_ at Base 2.4.1
  _ZNSt6vectorIS_IcSaIcEESaIS1_EE17_M_default_appendEm at Base 2.4.1
  _ZNSt6vectorIS_IcSaIcEESaIS1_EED1Ev at Base 2.4.1
  _ZNSt6vectorIS_IcSaIcEESaIS1_EED2Ev at Base 2.4.1
@@ -1791,8 +1795,8 @@
  _ZNSt6vectorIiSaIiEE6insertEN9__gnu_cxx17__normal_iteratorIPKiS1_EERS4_ at Base 2.4.1
  _ZNSt6vectorIiSaIiEE8_M_eraseEN9__gnu_cxx17__normal_iteratorIPiS1_EE at Base 2.4.1
  _ZNSt6vectorIiSaIiEE8_M_eraseEN9__gnu_cxx17__normal_iteratorIPiS1_EES5_ at Base 2.4.1
- _ZNSt6vectorIiSaIiEEC1ISt15_Deque_iteratorIiRiPiEvEET_S7_RKS0_ at Base 2.4.1
- _ZNSt6vectorIiSaIiEEC2ISt15_Deque_iteratorIiRiPiEvEET_S7_RKS0_ at Base 2.4.1
+#MISSING: 2.4.1-3# _ZNSt6vectorIiSaIiEEC1ISt15_Deque_iteratorIiRiPiEvEET_S7_RKS0_ at Base 2.4.1
+#MISSING: 2.4.1-3# _ZNSt6vectorIiSaIiEEC2ISt15_Deque_iteratorIiRiPiEvEET_S7_RKS0_ at Base 2.4.1
  _ZNSt6vectorIiSaIiEEaSERKS1_ at Base 2.4.1
  _ZNSt6vectorImSaImEE12emplace_backIJmEEEvDpOT_ at Base 2.4.1
  _ZNSt6vectorImSaImEE17_M_default_appendEm at Base 2.4.1
@@ -1866,6 +1870,7 @@
  _ZNSt8_Rb_treeIiSt4pairIKidESt10_Select1stIS2_ESt4lessIiESaIS2_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS2_ERS1_ at Base 2.4.1
  _ZNSt8_Rb_treeIiSt4pairIKidESt10_Select1stIS2_ESt4lessIiESaIS2_EE8_M_eraseEPSt13_Rb_tree_nodeIS2_E at Base 2.4.1
  _ZNSt8_Rb_treeIiSt4pairIKiiESt10_Select1stIS2_ESt4lessIiESaIS2_EE14_M_insert_nodeEPSt18_Rb_tree_node_baseSA_PSt13_Rb_tree_nodeIS2_E at Base 2.4.1
+ _ZNSt8_Rb_treeIiSt4pairIKiiESt10_Select1stIS2_ESt4lessIiESaIS2_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJOiEESD_IJEEEEESt17_Rb_tree_iteratorIS2_ESt23_Rb_tree_const_iteratorIS2_EDpOT_ at Base 2.4.1-3
  _ZNSt8_Rb_treeIiSt4pairIKiiESt10_Select1stIS2_ESt4lessIiESaIS2_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJRS1_EESD_IJEEEEESt17_Rb_tree_iteratorIS2_ESt23_Rb_tree_const_iteratorIS2_EDpOT_ at Base 2.4.1
  _ZNSt8_Rb_treeIiSt4pairIKiiESt10_Select1stIS2_ESt4lessIiESaIS2_EE24_M_get_insert_unique_posERS1_ at Base 2.4.1
  _ZNSt8_Rb_treeIiSt4pairIKiiESt10_Select1stIS2_ESt4lessIiESaIS2_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS2_ERS1_ at Base 2.4.1
@@ -1880,6 +1885,7 @@
  _ZNSt8_Rb_treeIiSt4pairIKimESt10_Select1stIS2_ESt4lessIiESaIS2_EE7_M_copyINS8_20_Reuse_or_alloc_nodeEEEPSt13_Rb_tree_nodeIS2_EPKSC_PSt18_Rb_tree_node_baseRT_ at Base 2.4.1
  _ZNSt8_Rb_treeIiSt4pairIKimESt10_Select1stIS2_ESt4lessIiESaIS2_EE8_M_eraseEPSt13_Rb_tree_nodeIS2_E at Base 2.4.1
  _ZNSt8_Rb_treeIiSt4pairIKimESt10_Select1stIS2_ESt4lessIiESaIS2_EEaSERKS8_ at Base 2.4.1
+ _ZNSt8_Rb_treeImSt4pairIKmPN3bpp13SiteContainerEESt10_Select1stIS5_ESt4lessImESaIS5_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJRS1_EESG_IJEEEEESt17_Rb_tree_iteratorIS5_ESt23_Rb_tree_const_iteratorIS5_EDpOT_ at Base 2.4.1-3
  _ZNSt8_Rb_treeImSt4pairIKmPN3bpp13SiteContainerEESt10_Select1stIS5_ESt4lessImESaIS5_EE24_M_get_insert_unique_posERS1_ at Base 2.4.1
  _ZNSt8_Rb_treeImSt4pairIKmPN3bpp13SiteContainerEESt10_Select1stIS5_ESt4lessImESaIS5_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS5_ERS1_ at Base 2.4.1
  _ZNSt8_Rb_treeImSt4pairIKmPN3bpp13SiteContainerEESt10_Select1stIS5_ESt4lessImESaIS5_EE8_M_eraseEPSt13_Rb_tree_nodeIS5_E at Base 2.4.1
@@ -1892,7 +1898,7 @@
  _ZSt16__insertion_sortIN9__gnu_cxx17__normal_iteratorIPPN3bpp5RangeImEESt6vectorIS5_SaIS5_EEEENS0_5__ops15_Iter_comp_iterINS2_10rangeComp_ImEEEEEvT_SG_T0_ at Base 2.4.1
  _ZSt16__introsort_loopIN9__gnu_cxx17__normal_iteratorIPPN3bpp5RangeImEESt6vectorIS5_SaIS5_EEEElNS0_5__ops15_Iter_comp_iterINS2_10rangeComp_ImEEEEEvT_SG_T0_T1_ at Base 2.4.1
  _ZSt9__find_ifIN9__gnu_cxx17__normal_iteratorIPNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt6vectorIS7_SaIS7_EEEENS0_5__ops16_Iter_equals_valIKS7_EEET_SH_SH_T0_St26random_access_iterator_tag at Base 2.4.1
- _ZSteqIcEN9__gnu_cxx11__enable_ifIXsrSt9__is_charIT_E7__valueEbE6__typeERKNSt7__cxx1112basic_stringIS3_St11char_traitsIS3_ESaIS3_EEESE_ at Base 2.4.1
+#MISSING: 2.4.1-3# _ZSteqIcEN9__gnu_cxx11__enable_ifIXsrSt9__is_charIT_E7__valueEbE6__typeERKNSt7__cxx1112basic_stringIS3_St11char_traitsIS3_ESaIS3_EEESE_ at Base 2.4.1
  _ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EEOS8_PKS5_ at Base 2.4.1
  _ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EEOS8_S9_ at Base 2.4.1
  _ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EEPKS5_OS8_ at Base 2.4.1
@@ -2460,6 +2466,7 @@
  _ZTVN3bpp7ClustalE at Base 2.4.1
  _ZTVN3bpp7GenBankE at Base 2.4.1
  _ZTVN3bpp8BLOSUM50E at Base 2.4.1
+ _ZTVN3bpp8ClonableE at Base 2.4.1-3
  _ZTVN3bpp8DNAToRNAE at Base 2.4.1
  _ZTVN3bpp8PhredPhdE at Base 2.4.1
  _ZTVN3bpp9PhredPolyE at Base 2.4.1
dh_makeshlibs: failing due to earlier errors
make[1]: *** [debian/rules:15: override_dh_makeshlibs] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:10: binary-arch] Error 2
dpkg-buildpackage: error: fakeroot debian/rules binary-arch subprocess returned exit status 2