[Debian-med-packaging] Bug#1012969: libbpp-popgen: ftbfs with GCC-12

Thu Jun 16 13:10:37 BST 2022

Package: src:libbpp-popgen
Version: 2.4.1-6
Severity: normal
Tags: sid bookworm
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-12

[This bug is targeted to the upcoming bookworm 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-12/g++-12, but succeeds to build with gcc-11/g++-11. The
severity of this report will be raised before the bookworm release.

The full build log can be found at:
http://qa-logs.debian.net/2022/06/09/gcc12/libbpp-popgen_2.4.1-6_unstable_gcc12.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.

[...]
  _ZNSt6vectorIdSaIdEE17_M_default_appendEm at Base 2.4.1
  _ZNSt6vectorIdSaIdEE17_M_realloc_insertIJRKdEEEvN9__gnu_cxx17__normal_iteratorIPdS1_EEDpOT_ at Base 2.4.1
  _ZNSt6vectorIdSaIdEE17_M_realloc_insertIJdEEEvN9__gnu_cxx17__normal_iteratorIPdS1_EEDpOT_ at Base 2.4.1
@@ -983,7 +988,7 @@
  _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
- _ZNSt6vectorImSaImEE8_M_eraseEN9__gnu_cxx17__normal_iteratorIPmS1_EE at Base 2.4.1
+#MISSING: 2.4.1-6# _ZNSt6vectorImSaImEE8_M_eraseEN9__gnu_cxx17__normal_iteratorIPmS1_EE at Base 2.4.1
  _ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC1IS3_EEPKcRKS3_ at Base 2.4.1
  _ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC2IS3_EEPKcRKS3_ at Base 2.4.1
  _ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED0Ev at Base 2.4.1
@@ -994,17 +999,20 @@
  _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_PN3bpp23VectorSequenceContainerEESt10_Select1stISB_ESt4lessIS5_ESaISB_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorISB_ERS7_ at Base 2.4.1
  _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_St3setIS5_St4lessIS5_ESaIS5_EEESt10_Select1stISD_ESA_SaISD_EE24_M_get_insert_unique_posERS7_ at Base 2.4.1
  _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_St3setIS5_St4lessIS5_ESaIS5_EEESt10_Select1stISD_ESA_SaISD_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorISD_ERS7_ at Base 2.4.1
- _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_St3setIS5_St4lessIS5_ESaIS5_EEESt10_Select1stISD_ESA_SaISD_EE8_M_eraseEPSt13_Rb_tree_nodeISD_E at Base 2.4.1
+#MISSING: 2.4.1-6# _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_St3setIS5_St4lessIS5_ESaIS5_EEESt10_Select1stISD_ESA_SaISD_EE8_M_eraseEPSt13_Rb_tree_nodeISD_E at Base 2.4.1
  _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_dESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE24_M_get_insert_unique_posERS7_ at Base 2.4.1
  _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_dESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS8_ERS7_ at Base 2.4.1
  _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_iESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE24_M_get_insert_unique_posERS7_ at Base 2.4.1
  _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_iESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS8_ERS7_ at Base 2.4.1
- _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_iESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE8_M_eraseEPSt13_Rb_tree_nodeIS8_E at Base 2.4.1
+#MISSING: 2.4.1-6# _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_iESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE8_M_eraseEPSt13_Rb_tree_nodeIS8_E at Base 2.4.1
  _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_mESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE24_M_get_insert_unique_posERS7_ at Base 2.4.1
  _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_mESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS8_ERS7_ at Base 2.4.1
- _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_mESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE8_M_eraseEPSt13_Rb_tree_nodeIS8_E at Base 2.4.1
+#MISSING: 2.4.1-6# _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_mESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE8_M_eraseEPSt13_Rb_tree_nodeIS8_E at Base 2.4.1
+ _ZNSt8_Rb_treeIiSt4pairIKidESt10_Select1stIS2_ESt4lessIiESaIS2_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJOiEESD_IJEEEEESt17_Rb_tree_iteratorIS2_ESt23_Rb_tree_const_iteratorIS2_EDpOT_ at Base 2.4.1-6
+ _ZNSt8_Rb_treeIiSt4pairIKidESt10_Select1stIS2_ESt4lessIiESaIS2_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJRS1_EESD_IJEEEEESt17_Rb_tree_iteratorIS2_ESt23_Rb_tree_const_iteratorIS2_EDpOT_ at Base 2.4.1-6
  _ZNSt8_Rb_treeIiSt4pairIKidESt10_Select1stIS2_ESt4lessIiESaIS2_EE24_M_get_insert_unique_posERS1_ at Base 2.4.1
  _ZNSt8_Rb_treeIiSt4pairIKidESt10_Select1stIS2_ESt4lessIiESaIS2_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS2_ERS1_ at Base 2.4.1
+ _ZNSt8_Rb_treeIiSt4pairIKimESt10_Select1stIS2_ESt4lessIiESaIS2_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJRS1_EESD_IJEEEEESt17_Rb_tree_iteratorIS2_ESt23_Rb_tree_const_iteratorIS2_EDpOT_ at Base 2.4.1-6
  _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_treeImSt4pairIKmN3bpp28MultilocusGenotypeStatistics6FstatsEESt10_Select1stIS5_ESt4lessImESaIS5_EE24_M_get_insert_unique_posERS1_ at Base 2.4.1
@@ -1013,13 +1021,21 @@
  _ZNSt8_Rb_treeImSt4pairIKmN3bpp28MultilocusGenotypeStatistics7VarCompEESt10_Select1stIS5_ESt4lessImESaIS5_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS5_ERS1_ 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_treeImSt4pairIKmdESt10_Select1stIS2_ESt4lessImESaIS2_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJRS1_EESD_IJEEEEESt17_Rb_tree_iteratorIS2_ESt23_Rb_tree_const_iteratorIS2_EDpOT_ at Base 2.4.1-6
  _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_treeImSt4pairIKmmESt10_Select1stIS2_ESt4lessImESaIS2_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJRS1_EESD_IJEEEEESt17_Rb_tree_iteratorIS2_ESt23_Rb_tree_const_iteratorIS2_EDpOT_ at Base 2.4.1-6
  _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
  _ZSt10scientificRSt8ios_base at Base 2.4.1
+ _ZSt13__heap_selectIN9__gnu_cxx17__normal_iteratorIPNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt6vectorIS7_SaIS7_EEEENS0_5__ops15_Iter_less_iterEEvT_SF_SF_T0_ at Base 2.4.1-6
+ _ZSt16__do_uninit_copyIN9__gnu_cxx17__normal_iteratorIPKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt6vectorIS7_SaIS7_EEEEPS7_ET0_T_SG_SF_ at Base 2.4.1-6
+ _ZSt16__do_uninit_copyIN9__gnu_cxx17__normal_iteratorIPKSt6vectorIdSaIdEES2_IS4_SaIS4_EEEEPS4_ET0_T_SC_SB_ at Base 2.4.1-6
+ _ZSt16__do_uninit_copyIPKN3bpp9LocusInfoEPS1_ET0_T_S6_S5_ at Base 2.4.1-6
+ _ZSt19piecewise_construct at Base 2.4.1-6
  _ZSt5fixedRSt8ios_base at Base 2.4.1
- _ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EEOS8_PKS5_ at Base 2.4.1
+#MISSING: 2.4.1-6# _ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EEOS8_PKS5_ at Base 2.4.1
+ _ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EEOS8_S9_ at Base 2.4.1-6
  _ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EEPKS5_RKS8_ at Base 2.4.1
  _ZTIN3bpp10AlleleInfoE at Base 2.4.1
  _ZTIN3bpp10IndividualE at Base 2.4.1
@@ -1285,6 +1301,7 @@
  _ZTv0_n24_N3bpp11PopgenlibIOD0Ev at Base 2.4.1
  _ZTv0_n24_N3bpp11PopgenlibIOD1Ev at Base 2.4.1
  _ZTv0_n24_N3bpp13BasicSequenceD0Ev at Base 2.4.1
+ _ZTv0_n24_N3bpp13BasicSequenceD1Ev at Base 2.4.1-6
  _ZTv0_n24_N3bpp14DistanceMatrixD0Ev at Base 2.4.1
  _ZTv0_n24_N3bpp14DistanceMatrixD1Ev at Base 2.4.1
  _ZTv0_n24_N3bpp15BasicAlleleInfoD0Ev at Base 2.4.1
dh_makeshlibs: error: failing due to earlier errors
make: *** [debian/rules:8: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2

