[Debian-med-packaging] Bug#1037719: libbpp-popgen: ftbfs with GCC-13

Wed Jun 14 10:26:32 BST 2023

Package: src:libbpp-popgen
Version: 2.4.1-8
Severity: normal
Tags: sid trixie
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-13

[This bug is targeted to the upcoming trixie 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-13/g++-13, but succeeds to build with gcc-12/g++-12. The
severity of this report will be raised before the trixie release.

The full build log can be found at:
http://qa-logs.debian.net/2023/05/22/logs/libbpp-popgen_2.4.1-8_unstable_gccexp.log
The last lines of the build log are at the end of this report.

To build with GCC 13, either set CC=gcc-13 CXX=g++-13 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-13/porting_to.html

[...]
  _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
- (optional)_ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_iESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE8_M_eraseEPSt13_Rb_tree_nodeIS8_E at Base 2.4.1
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  _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
- (optional)_ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_mESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE8_M_eraseEPSt13_Rb_tree_nodeIS8_E at Base 2.4.1
- (optional)_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
- (optional)_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
- _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
- (optional)_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
- _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
- _ZNSt8_Rb_treeImSt4pairIKmN3bpp28MultilocusGenotypeStatistics6FstatsEESt10_Select1stIS5_ESt4lessImESaIS5_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS5_ERS1_ 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_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
- (optional)_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
- (optional)_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
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+#MISSING: 2.4.1-8# (optional)_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
+#MISSING: 2.4.1-8# (optional)_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
+#MISSING: 2.4.1-8# _ZNSt8_Rb_treeIiSt4pairIKidESt10_Select1stIS2_ESt4lessIiESaIS2_EE24_M_get_insert_unique_posERS1_ at Base 2.4.1
+#MISSING: 2.4.1-8# _ZNSt8_Rb_treeIiSt4pairIKidESt10_Select1stIS2_ESt4lessIiESaIS2_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS2_ERS1_ at Base 2.4.1
+#MISSING: 2.4.1-8# (optional)_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
+#MISSING: 2.4.1-8# _ZNSt8_Rb_treeIiSt4pairIKimESt10_Select1stIS2_ESt4lessIiESaIS2_EE24_M_get_insert_unique_posERS1_ at Base 2.4.1
+#MISSING: 2.4.1-8# _ZNSt8_Rb_treeIiSt4pairIKimESt10_Select1stIS2_ESt4lessIiESaIS2_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS2_ERS1_ at Base 2.4.1
+#MISSING: 2.4.1-8# _ZNSt8_Rb_treeImSt4pairIKmN3bpp28MultilocusGenotypeStatistics6FstatsEESt10_Select1stIS5_ESt4lessImESaIS5_EE24_M_get_insert_unique_posERS1_ at Base 2.4.1
+#MISSING: 2.4.1-8# _ZNSt8_Rb_treeImSt4pairIKmN3bpp28MultilocusGenotypeStatistics6FstatsEESt10_Select1stIS5_ESt4lessImESaIS5_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS5_ERS1_ at Base 2.4.1
+#MISSING: 2.4.1-8# _ZNSt8_Rb_treeImSt4pairIKmN3bpp28MultilocusGenotypeStatistics7VarCompEESt10_Select1stIS5_ESt4lessImESaIS5_EE24_M_get_insert_unique_posERS1_ at Base 2.4.1
+#MISSING: 2.4.1-8# _ZNSt8_Rb_treeImSt4pairIKmN3bpp28MultilocusGenotypeStatistics7VarCompEESt10_Select1stIS5_ESt4lessImESaIS5_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS5_ERS1_ at Base 2.4.1
+#MISSING: 2.4.1-8# _ZNSt8_Rb_treeImSt4pairIKmNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEESt10_Select1stIS8_ESt4lessImESaIS8_EE24_M_get_insert_unique_posERS1_ at Base 2.4.1
+#MISSING: 2.4.1-8# _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
+#MISSING: 2.4.1-8# (optional)_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: 2.4.1-8# _ZNSt8_Rb_treeImSt4pairIKmdESt10_Select1stIS2_ESt4lessImESaIS2_EE24_M_get_insert_unique_posERS1_ at Base 2.4.1
+#MISSING: 2.4.1-8# _ZNSt8_Rb_treeImSt4pairIKmdESt10_Select1stIS2_ESt4lessImESaIS2_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS2_ERS1_ at Base 2.4.1
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+#MISSING: 2.4.1-8# _ZNSt8_Rb_treeImSt4pairIKmmESt10_Select1stIS2_ESt4lessImESaIS2_EE24_M_get_insert_unique_posERS1_ at Base 2.4.1
+#MISSING: 2.4.1-8# _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
  (optional)_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
  (optional)_ZSt16__do_uninit_copyIN9__gnu_cxx17__normal_iteratorIPKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt6vectorIS7_SaIS7_EEEEPS7_ET0_T_SG_SF_ at Base 2.4.1
  (optional)_ZSt16__do_uninit_copyIN9__gnu_cxx17__normal_iteratorIPKSt6vectorIdSaIdEES2_IS4_SaIS4_EEEEPS4_ET0_T_SC_SB_ at Base 2.4.1
  (optional)_ZSt16__do_uninit_copyIPKN3bpp9LocusInfoEPS1_ET0_T_S6_S5_ at Base 2.4.1
- (optional)_ZSt19piecewise_construct at Base 2.4.1
+#MISSING: 2.4.1-8# (optional)_ZSt19piecewise_construct at Base 2.4.1
  _ZSt5fixedRSt8ios_base at Base 2.4.1
- (optional)_ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EEOS8_PKS5_ at Base 2.4.1
+#MISSING: 2.4.1-8# (optional)_ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EEOS8_PKS5_ at Base 2.4.1
  (optional)_ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EEOS8_S9_ at Base 2.4.1
- _ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EEPKS5_RKS8_ at Base 2.4.1
+#MISSING: 2.4.1-8# _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
  _ZTIN3bpp10SymbolListE at Base 2.4.1
@@ -1371,4 +1386,4 @@
  _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
+#MISSING: 2.4.1-8# _ZZNSt8__detail18__to_chars_10_implImEEvPcjT_E8__digits 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

