[Debian-med-packaging] Bug#957427: libbpp-popgen: ftbfs with GCC-10

Fri Apr 17 12:04:03 BST 2020

Package: src:libbpp-popgen
Version: 2.4.1-3
Severity: normal
Tags: sid bullseye
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-10

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-10/g++-10, but succeeds to build with gcc-9/g++-9. 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/gcc10-20200225/libbpp-popgen_2.4.1-3_unstable_gcc10.log
The last lines of the build log are at the end of this report.

To build with GCC 10, either set CC=gcc-10 CXX=g++-10 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-10/porting_to.html

[...]
  _ZNSt8_Rb_treeIiSt4pairIKimESt10_Select1stIS2_ESt4lessIiESaIS2_EE24_M_get_insert_unique_posERS1_ at Base 2.4.1
  _ZNSt8_Rb_treeIiSt4pairIKimESt10_Select1stIS2_ESt4lessIiESaIS2_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS2_ERS1_ at Base 2.4.1
- _ZNSt8_Rb_treeIiSt4pairIKimESt10_Select1stIS2_ESt4lessIiESaIS2_EE8_M_eraseEPSt13_Rb_tree_nodeIS2_E at Base 2.4.1
- _ZNSt8_Rb_treeImSt4pairIKmN3bpp28MultilocusGenotypeStatistics6FstatsEESt10_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
+#MISSING: 2.4.1-3# _ZNSt8_Rb_treeIiSt4pairIKimESt10_Select1stIS2_ESt4lessIiESaIS2_EE8_M_eraseEPSt13_Rb_tree_nodeIS2_E at Base 2.4.1
+#MISSING: 2.4.1-3# _ZNSt8_Rb_treeImSt4pairIKmN3bpp28MultilocusGenotypeStatistics6FstatsEESt10_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
  _ZNSt8_Rb_treeImSt4pairIKmN3bpp28MultilocusGenotypeStatistics6FstatsEESt10_Select1stIS5_ESt4lessImESaIS5_EE24_M_get_insert_unique_posERS1_ at Base 2.4.1
  _ZNSt8_Rb_treeImSt4pairIKmN3bpp28MultilocusGenotypeStatistics6FstatsEESt10_Select1stIS5_ESt4lessImESaIS5_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS5_ERS1_ at Base 2.4.1
- _ZNSt8_Rb_treeImSt4pairIKmN3bpp28MultilocusGenotypeStatistics6FstatsEESt10_Select1stIS5_ESt4lessImESaIS5_EE8_M_eraseEPSt13_Rb_tree_nodeIS5_E at Base 2.4.1
+#MISSING: 2.4.1-3# _ZNSt8_Rb_treeImSt4pairIKmN3bpp28MultilocusGenotypeStatistics6FstatsEESt10_Select1stIS5_ESt4lessImESaIS5_EE8_M_eraseEPSt13_Rb_tree_nodeIS5_E at Base 2.4.1
  _ZNSt8_Rb_treeImSt4pairIKmN3bpp28MultilocusGenotypeStatistics7VarCompEESt10_Select1stIS5_ESt4lessImESaIS5_EE24_M_get_insert_unique_posERS1_ at Base 2.4.1
  _ZNSt8_Rb_treeImSt4pairIKmN3bpp28MultilocusGenotypeStatistics7VarCompEESt10_Select1stIS5_ESt4lessImESaIS5_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS5_ERS1_ at Base 2.4.1
- _ZNSt8_Rb_treeImSt4pairIKmN3bpp28MultilocusGenotypeStatistics7VarCompEESt10_Select1stIS5_ESt4lessImESaIS5_EE8_M_eraseEPSt13_Rb_tree_nodeIS5_E at Base 2.4.1
- _ZNSt8_Rb_treeImSt4pairIKmNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEESt10_Select1stIS8_ESt4lessImESaIS8_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJRS1_EESJ_IJEEEEESt17_Rb_tree_iteratorIS8_ESt23_Rb_tree_const_iteratorIS8_EDpOT_ at Base 2.4.1
+#MISSING: 2.4.1-3# _ZNSt8_Rb_treeImSt4pairIKmN3bpp28MultilocusGenotypeStatistics7VarCompEESt10_Select1stIS5_ESt4lessImESaIS5_EE8_M_eraseEPSt13_Rb_tree_nodeIS5_E at Base 2.4.1
+#MISSING: 2.4.1-3# _ZNSt8_Rb_treeImSt4pairIKmNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEESt10_Select1stIS8_ESt4lessImESaIS8_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJRS1_EESJ_IJEEEEESt17_Rb_tree_iteratorIS8_ESt23_Rb_tree_const_iteratorIS8_EDpOT_ at Base 2.4.1
  _ZNSt8_Rb_treeImSt4pairIKmNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEESt10_Select1stIS8_ESt4lessImESaIS8_EE24_M_get_insert_unique_posERS1_ at Base 2.4.1
  _ZNSt8_Rb_treeImSt4pairIKmNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEESt10_Select1stIS8_ESt4lessImESaIS8_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS8_ERS1_ at Base 2.4.1
- _ZNSt8_Rb_treeImSt4pairIKmNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEESt10_Select1stIS8_ESt4lessImESaIS8_EE8_M_eraseEPSt13_Rb_tree_nodeIS8_E at Base 2.4.1
- _ZNSt8_Rb_treeImSt4pairIKmdESt10_Select1stIS2_ESt4lessImESaIS2_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJRS1_EESD_IJEEEEESt17_Rb_tree_iteratorIS2_ESt23_Rb_tree_const_iteratorIS2_EDpOT_ at Base 2.4.1
+#MISSING: 2.4.1-3# _ZNSt8_Rb_treeImSt4pairIKmNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEESt10_Select1stIS8_ESt4lessImESaIS8_EE8_M_eraseEPSt13_Rb_tree_nodeIS8_E at Base 2.4.1
+#MISSING: 2.4.1-3# _ZNSt8_Rb_treeImSt4pairIKmdESt10_Select1stIS2_ESt4lessImESaIS2_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_treeImSt4pairIKmdESt10_Select1stIS2_ESt4lessImESaIS2_EE24_M_get_insert_unique_posERS1_ at Base 2.4.1
  _ZNSt8_Rb_treeImSt4pairIKmdESt10_Select1stIS2_ESt4lessImESaIS2_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS2_ERS1_ at Base 2.4.1
- _ZNSt8_Rb_treeImSt4pairIKmdESt10_Select1stIS2_ESt4lessImESaIS2_EE8_M_eraseEPSt13_Rb_tree_nodeIS2_E at Base 2.4.1
- _ZNSt8_Rb_treeImSt4pairIKmmESt10_Select1stIS2_ESt4lessImESaIS2_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJRS1_EESD_IJEEEEESt17_Rb_tree_iteratorIS2_ESt23_Rb_tree_const_iteratorIS2_EDpOT_ at Base 2.4.1
+#MISSING: 2.4.1-3# _ZNSt8_Rb_treeImSt4pairIKmdESt10_Select1stIS2_ESt4lessImESaIS2_EE8_M_eraseEPSt13_Rb_tree_nodeIS2_E at Base 2.4.1
+#MISSING: 2.4.1-3# _ZNSt8_Rb_treeImSt4pairIKmmESt10_Select1stIS2_ESt4lessImESaIS2_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_treeImSt4pairIKmmESt10_Select1stIS2_ESt4lessImESaIS2_EE24_M_get_insert_unique_posERS1_ at Base 2.4.1
  _ZNSt8_Rb_treeImSt4pairIKmmESt10_Select1stIS2_ESt4lessImESaIS2_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS2_ERS1_ at Base 2.4.1
- _ZNSt8_Rb_treeImSt4pairIKmmESt10_Select1stIS2_ESt4lessImESaIS2_EE8_M_eraseEPSt13_Rb_tree_nodeIS2_E at Base 2.4.1
- _ZNSt8_Rb_treeImmSt9_IdentityImESt4lessImESaImEE16_M_insert_uniqueIRKmEESt4pairISt17_Rb_tree_iteratorImEbEOT_ at Base 2.4.1
- _ZNSt8_Rb_treeImmSt9_IdentityImESt4lessImESaImEE8_M_eraseEPSt13_Rb_tree_nodeImE at Base 2.4.1
+#MISSING: 2.4.1-3# _ZNSt8_Rb_treeImSt4pairIKmmESt10_Select1stIS2_ESt4lessImESaIS2_EE8_M_eraseEPSt13_Rb_tree_nodeIS2_E at Base 2.4.1
+#MISSING: 2.4.1-3# _ZNSt8_Rb_treeImmSt9_IdentityImESt4lessImESaImEE16_M_insert_uniqueIRKmEESt4pairISt17_Rb_tree_iteratorImEbEOT_ at Base 2.4.1
+#MISSING: 2.4.1-3# _ZNSt8_Rb_treeImmSt9_IdentityImESt4lessImESaImEE8_M_eraseEPSt13_Rb_tree_nodeImE at Base 2.4.1
  _ZSt10scientificRSt8ios_base at Base 2.4.1
  _ZSt11__make_heapIN9__gnu_cxx17__normal_iteratorIPNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt6vectorIS7_SaIS7_EEEENS0_5__ops15_Iter_less_iterEEvT_SF_RT0_ at Base 2.4.1
- _ZSt13__adjust_heapIN9__gnu_cxx17__normal_iteratorIPNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt6vectorIS7_SaIS7_EEEElS7_NS0_5__ops15_Iter_less_iterEEvT_T0_SG_T1_T2_ at Base 2.4.1
- _ZSt13__adjust_heapIN9__gnu_cxx17__normal_iteratorIPmSt6vectorImSaImEEEElmNS0_5__ops15_Iter_less_iterEEvT_T0_SA_T1_T2_ at Base 2.4.1
- _ZSt16__insertion_sortIN9__gnu_cxx17__normal_iteratorIPNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt6vectorIS7_SaIS7_EEEENS0_5__ops15_Iter_less_iterEEvT_SF_T0_ at Base 2.4.1
- _ZSt16__insertion_sortIN9__gnu_cxx17__normal_iteratorIPmSt6vectorImSaImEEEENS0_5__ops15_Iter_less_iterEEvT_S9_T0_ at Base 2.4.1
+#MISSING: 2.4.1-3# _ZSt13__adjust_heapIN9__gnu_cxx17__normal_iteratorIPNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt6vectorIS7_SaIS7_EEEElS7_NS0_5__ops15_Iter_less_iterEEvT_T0_SG_T1_T2_ at Base 2.4.1
+#MISSING: 2.4.1-3# _ZSt13__adjust_heapIN9__gnu_cxx17__normal_iteratorIPmSt6vectorImSaImEEEElmNS0_5__ops15_Iter_less_iterEEvT_T0_SA_T1_T2_ at Base 2.4.1
+#MISSING: 2.4.1-3# _ZSt16__insertion_sortIN9__gnu_cxx17__normal_iteratorIPNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt6vectorIS7_SaIS7_EEEENS0_5__ops15_Iter_less_iterEEvT_SF_T0_ at Base 2.4.1
+#MISSING: 2.4.1-3# _ZSt16__insertion_sortIN9__gnu_cxx17__normal_iteratorIPmSt6vectorImSaImEEEENS0_5__ops15_Iter_less_iterEEvT_S9_T0_ at Base 2.4.1
+ _ZSt16__introsort_loopIN9__gnu_cxx17__normal_iteratorIPNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt6vectorIS7_SaIS7_EEEElNS0_5__ops15_Iter_less_iterEEvT_SF_T0_T1_ at Base 2.4.1-3
  _ZSt16__introsort_loopIN9__gnu_cxx17__normal_iteratorIPmSt6vectorImSaImEEEElNS0_5__ops15_Iter_less_iterEEvT_S9_T0_T1_ at Base 2.4.1
- _ZSt25__unguarded_linear_insertIN9__gnu_cxx17__normal_iteratorIPNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt6vectorIS7_SaIS7_EEEENS0_5__ops14_Val_less_iterEEvT_T0_ at Base 2.4.1
+#MISSING: 2.4.1-3# _ZSt25__unguarded_linear_insertIN9__gnu_cxx17__normal_iteratorIPNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt6vectorIS7_SaIS7_EEEENS0_5__ops14_Val_less_iterEEvT_T0_ at Base 2.4.1
  _ZSt5fixedRSt8ios_base at Base 2.4.1
  _ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EEOS8_PKS5_ at Base 2.4.1
  _ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EEPKS5_RKS8_ at Base 2.4.1
@@ -1303,7 +1348,7 @@
  _ZTv0_n24_N3bpp27SimpleSiteContainerIteratorD0Ev at Base 2.4.1
  _ZTv0_n24_N3bpp29PolymorphismSequenceContainerD0Ev at Base 2.4.1
  _ZTv0_n24_N3bpp29PolymorphismSequenceContainerD1Ev at Base 2.4.1
- _ZTv0_n24_N3bpp3DNAD0Ev at Base 2.4.1
+#MISSING: 2.4.1-3# _ZTv0_n24_N3bpp3DNAD0Ev at Base 2.4.1
  _ZTv0_n24_N3bpp4MaseD1Ev at Base 2.4.1
  _ZTv0_n24_N3bpp4SiteD0Ev at Base 2.4.1
  _ZTv0_n24_N3bpp4SiteD1Ev at Base 2.4.1
@@ -1355,3 +1400,4 @@
  _ZTv0_n80_NK3bpp15DarwinVarSingle5writeERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKNS_7DataSetEb at Base 2.4.1
  _ZTv0_n80_NK3bpp9DarwinDon5writeERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKNS_7DataSetEb at Base 2.4.1
  _ZTv0_n96_N3bpp29PolymorphismSequenceContainer14removeSequenceERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 2.4.1
+ _ZZNSt8__detail18__to_chars_10_implImEEvPcjT_E8__digits at Base 2.4.1-3
dh_makeshlibs: error: failing due to earlier errors
make: *** [debian/rules:8: binary] Error 25
dpkg-buildpackage: error: fakeroot debian/rules binary subprocess returned exit status 2

