[Debian-med-packaging] Bug#1075148: libbpp-phyl: ftbfs with GCC-14

Wed Jul 3 13:32:37 BST 2024

Package: src:libbpp-phyl
Version: 2.4.1-10
Severity: important
Tags: sid trixie
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-14

[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-14/g++-14, but succeeds to build with gcc-13/g++-13. 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/2024/07/01/libbpp-phyl_2.4.1-10_unstable_gccexp.log
The last lines of the build log are at the end of this report.

To build with GCC 14, either set CC=gcc-14 CXX=g++-14 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-14/porting_to.html

[...]
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+#MISSING: 2.4.1-10# _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_bESt10_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_dESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJOS5_EESJ_IJEEEEESt17_Rb_tree_iteratorIS8_ESt23_Rb_tree_const_iteratorIS8_EDpOT_ at Base 2.4.1-10
+#MISSING: 2.4.1-10# _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_dESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE24_M_get_insert_unique_posERS7_ at Base 2.4.1
+#MISSING: 2.4.1-10# _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_mESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJOS5_EESJ_IJEEEEESt17_Rb_tree_iteratorIS8_ESt23_Rb_tree_const_iteratorIS8_EDpOT_ at Base 2.4.1-10
+#MISSING: 2.4.1-10# _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_mESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE24_M_get_insert_unique_posERS7_ at Base 2.4.1
+#MISSING: 2.4.1-10# _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_EE4findERS7_ at Base 2.4.1
+ _ZNSt8_Rb_treeIPKN3bpp4NodeESt4pairIKS3_St6vectorIS4_INSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEdESaISD_EEESt10_Select1stISG_ESt4lessIS3_ESaISG_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJOS3_EESR_IJEEEEESt17_Rb_tree_iteratorISG_ESt23_Rb_tree_const_iteratorISG_EDpOT_ at Base 2.4.1-10
+ _ZNSt8_Rb_treeIPKN3bpp4NodeESt4pairIKS3_St6vectorIS4_INSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEdESaISD_EEESt10_Select1stISG_ESt4lessIS3_ESaISG_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJRS5_EESR_IJEEEEESt17_Rb_tree_iteratorISG_ESt23_Rb_tree_const_iteratorISG_EDpOT_ at Base 2.4.1-10
  _ZNSt8_Rb_treeIiSt4pairIKiN3bpp23DRTreeParsimonyLeafDataEESt10_Select1stIS4_ESt4lessIiESaIS4_EE20_Reuse_or_alloc_nodeclIRKS4_EEPSt13_Rb_tree_nodeIS4_EOT_ at Base 2.4.1
- _ZNSt8_Rb_treeIiSt4pairIKiSt6vectorIS2_IS2_IdSaIdEESaIS4_EESaIS6_EEESt10_Select1stIS9_ESt4lessIiESaIS9_EE12_M_erase_auxESt23_Rb_tree_const_iteratorIS9_ESH_ at Base 2.4.1
+ _ZNSt8_Rb_treeIiSt4pairIKiSt6vectorIPN3bpp34RNonHomogeneousMixedTreeLikelihoodESaIS5_EEESt10_Select1stIS8_ESt4lessIiESaIS8_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJOiEESJ_IJEEEEESt17_Rb_tree_iteratorIS8_ESt23_Rb_tree_const_iteratorIS8_EDpOT_ at Base 2.4.1-10
+ _ZNSt8_Rb_treeIiSt4pairIKiSt6vectorIPN3bpp34RNonHomogeneousMixedTreeLikelihoodESaIS5_EEESt10_Select1stIS8_ESt4lessIiESaIS8_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJRS1_EESJ_IJEEEEESt17_Rb_tree_iteratorIS8_ESt23_Rb_tree_const_iteratorIS8_EDpOT_ at Base 2.4.1-10
+#MISSING: 2.4.1-10# _ZNSt8_Rb_treeIiSt4pairIKiSt6vectorIS2_IS2_IdSaIdEESaIS4_EESaIS6_EEESt10_Select1stIS9_ESt4lessIiESaIS9_EE12_M_erase_auxESt23_Rb_tree_const_iteratorIS9_ESH_ at Base 2.4.1
  _ZNSt8_Rb_treeIiSt4pairIKiSt6vectorIS2_IS2_IdSaIdEESaIS4_EESaIS6_EEESt10_Select1stIS9_ESt4lessIiESaIS9_EE20_Reuse_or_alloc_nodeclIRKS9_EEPSt13_Rb_tree_nodeIS9_EOT_ at Base 2.4.1
+ _ZNSt8_Rb_treeIiSt4pairIKiSt6vectorIS2_IS2_IdSaIdEESaIS4_EESaIS6_EEESt10_Select1stIS9_ESt4lessIiESaIS9_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJOiEESK_IJEEEEESt17_Rb_tree_iteratorIS9_ESt23_Rb_tree_const_iteratorIS9_EDpOT_ at Base 2.4.1-10
+ _ZNSt8_Rb_treeIiSt4pairIKiSt6vectorIS2_IS2_IdSaIdEESaIS4_EESaIS6_EEESt10_Select1stIS9_ESt4lessIiESaIS9_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJRS1_EESK_IJEEEEESt17_Rb_tree_iteratorIS9_ESt23_Rb_tree_const_iteratorIS9_EDpOT_ at Base 2.4.1-10
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+ _ZNSt8_Rb_treeIiSt4pairIKiSt6vectorISt6bitsetILm21EESaIS4_EEESt10_Select1stIS7_ESt4lessIiESaIS7_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJRS1_EESI_IJEEEEESt17_Rb_tree_iteratorIS7_ESt23_Rb_tree_const_iteratorIS7_EDpOT_ at Base 2.4.1-10
+ _ZNSt8_Rb_treeIiSt4pairIKiSt6vectorIdSaIdEEESt10_Select1stIS5_ESt4lessIiESaIS5_EE20_Reuse_or_alloc_nodeclIRKS5_EEPSt13_Rb_tree_nodeIS5_EOT_ at Base 2.4.1-10
+ _ZNSt8_Rb_treeIiSt4pairIKiSt6vectorIdSaIdEEESt10_Select1stIS5_ESt4lessIiESaIS5_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJRS1_EESG_IJEEEEESt17_Rb_tree_iteratorIS5_ESt23_Rb_tree_const_iteratorIS5_EDpOT_ at Base 2.4.1-10
  (optional)_ZNSt8_Rb_treeIiSt4pairIKiSt6vectorIiSaIiEEESt10_Select1stIS5_ESt4lessIiESaIS5_EE20_Reuse_or_alloc_nodeclIRKS5_EEPSt13_Rb_tree_nodeIS5_EOT_ at Base 2.4.1
+ _ZNSt8_Rb_treeIiSt4pairIKiSt6vectorIiSaIiEEESt10_Select1stIS5_ESt4lessIiESaIS5_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJRS1_EESG_IJEEEEESt17_Rb_tree_iteratorIS5_ESt23_Rb_tree_const_iteratorIS5_EDpOT_ at Base 2.4.1-10
+ _ZNSt8_Rb_treeIiSt4pairIKiSt6vectorIjSaIjEEESt10_Select1stIS5_ESt4lessIiESaIS5_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJRS1_EESG_IJEEEEESt17_Rb_tree_iteratorIS5_ESt23_Rb_tree_const_iteratorIS5_EDpOT_ at Base 2.4.1-10
+ _ZNSt8_Rb_treeIiSt4pairIKiSt6vectorImSaImEEESt10_Select1stIS5_ESt4lessIiESaIS5_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJOiEESG_IJEEEEESt17_Rb_tree_iteratorIS5_ESt23_Rb_tree_const_iteratorIS5_EDpOT_ at Base 2.4.1-10
+ _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 2.4.1-10
  (optional)_ZNSt8_Rb_treeImSt4pairIKmSt6vectorIiSaIiEEESt10_Select1stIS5_ESt4lessImESaIS5_EE20_Reuse_or_alloc_nodeclIRKS5_EEPSt13_Rb_tree_nodeIS5_EOT_ at Base 2.4.1
+ _ZNSt8_Rb_treeImSt4pairIKmSt6vectorIiSaIiEEESt10_Select1stIS5_ESt4lessImESaIS5_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJRS1_EESG_IJEEEEESt17_Rb_tree_iteratorIS5_ESt23_Rb_tree_const_iteratorIS5_EDpOT_ at Base 2.4.1-10
  _ZNSt8_Rb_treeImmSt9_IdentityImESt4lessImESaImEE16_M_insert_uniqueImEESt4pairISt17_Rb_tree_iteratorImEbEOT_ at Base 2.4.1
  _ZSt10scientificRSt8ios_base at Base 2.4.1
  _ZSt11__remove_ifIN9__gnu_cxx17__normal_iteratorIPcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEENS0_5__ops16_Iter_equals_valIKcEEET_SE_SE_T0_ at Base 2.4.1
@@ -4829,19 +4912,19 @@
  _ZSt16__do_uninit_copyIN9__gnu_cxx17__normal_iteratorIPKSt6vectorIdSaIdEES2_IS4_SaIS4_EEEEPS4_ET0_T_SC_SB_ at Base 2.4.1
  _ZSt16__do_uninit_copyIN9__gnu_cxx17__normal_iteratorIPKSt6vectorIjSaIjEES2_IS4_SaIS4_EEEEPS4_ET0_T_SC_SB_ at Base 2.4.1
  _ZSt16__do_uninit_copyIN9__gnu_cxx17__normal_iteratorIPNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt6vectorIS7_SaIS7_EEEES8_ET0_T_SE_SD_ at Base 2.4.1
- _ZSt16__do_uninit_copyIPKN3bpp12MutationPathEPS1_ET0_T_S6_S5_ at Base 2.4.1
- _ZSt16__do_uninit_copyIPKN3bpp13ParameterListEPS1_ET0_T_S6_S5_ at Base 2.4.1
- _ZSt16__do_uninit_copyIPKN3bpp22AbstractTreeLikelihood36ConstNoPartitionSiteModelDescriptionEPS2_ET0_T_S7_S6_ at Base 2.4.1
- _ZSt16__do_uninit_copyIPKN3bpp7SimplexEPS1_ET0_T_S6_S5_ at Base 2.4.1
+#MISSING: 2.4.1-10# _ZSt16__do_uninit_copyIPKN3bpp12MutationPathEPS1_ET0_T_S6_S5_ at Base 2.4.1
+#MISSING: 2.4.1-10# _ZSt16__do_uninit_copyIPKN3bpp13ParameterListEPS1_ET0_T_S6_S5_ at Base 2.4.1
+#MISSING: 2.4.1-10# _ZSt16__do_uninit_copyIPKN3bpp22AbstractTreeLikelihood36ConstNoPartitionSiteModelDescriptionEPS2_ET0_T_S7_S6_ at Base 2.4.1
+#MISSING: 2.4.1-10# _ZSt16__do_uninit_copyIPKN3bpp7SimplexEPS1_ET0_T_S6_S5_ at Base 2.4.1
  _ZSt16__insertion_sortIN9__gnu_cxx17__normal_iteratorIP12StringAndIntSt6vectorIS2_SaIS2_EEEENS0_5__ops15_Iter_less_iterEEvT_SA_T0_ at Base 2.4.1
- (optional)_ZSt18__do_uninit_fill_nIPN3bpp18UserAlphabetIndex1EmS1_ET_S3_T0_RKT1_ at Base 2.4.1
+#MISSING: 2.4.1-10# (optional)_ZSt18__do_uninit_fill_nIPN3bpp18UserAlphabetIndex1EmS1_ET_S3_T0_RKT1_ at Base 2.4.1
  _ZSt18__do_uninit_fill_nIPNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEmS5_ET_S7_T0_RKT1_ at Base 2.4.1
  _ZSt25__unguarded_linear_insertIN9__gnu_cxx17__normal_iteratorIP12StringAndIntSt6vectorIS2_SaIS2_EEEENS0_5__ops14_Val_less_iterEEvT_T0_ at Base 2.4.1
  _ZSt4swapI12StringAndIntENSt9enable_ifIXsrSt6__and_IJSt6__not_ISt15__is_tuple_likeIT_EESt21is_move_constructibleIS5_ESt18is_move_assignableIS5_EEE5valueEvE4typeERS5_SF_ at Base 2.4.1
  _ZSt5fixedRSt8ios_base at Base 2.4.1
  (optional)_ZSteqIcSt11char_traitsIcESaIcEEbRKNSt7__cxx1112basic_stringIT_T0_T1_EEPKS5_ at Base 2.4.1
  (optional)_ZSteqIcSt11char_traitsIcESaIcEEbRKNSt7__cxx1112basic_stringIT_T0_T1_EESA_ at Base 2.4.1
- _ZStmiRKSt15_Deque_iteratorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERS5_PS5_ESA_ at Base 2.4.1
+#MISSING: 2.4.1-10# _ZStmiRKSt15_Deque_iteratorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERS5_PS5_ESA_ 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
  _ZTIN3bpp10BppBooleanE at Base 2.4.1
@@ -9358,5 +9441,7 @@
  _ZTv0_n96_NK3bpp24DRASDRTreeLikelihoodData24getNumberOfDistinctSitesEv at Base 2.4.1
  _ZTv0_n96_NK3bpp26TreeDrawingListenerAdapter12isAutonomousEv at Base 2.4.1
  _ZTv0_n96_NK3bpp28NNIHomogeneousTreeLikelihood16getTopologyValueEv at Base 2.4.1
+ _ZZNSt6vectorIN3bpp7SimplexESaIS1_EE17_M_realloc_appendIJS1_EEEvDpOT_EN11_Guard_eltsD1Ev at Base 2.4.1-10
+ _ZZNSt6vectorIN3bpp7SimplexESaIS1_EE17_M_realloc_appendIJS1_EEEvDpOT_EN11_Guard_eltsD2Ev at Base 2.4.1-10
  _Zlt12StringAndIntS_ at Base 2.4.1
  _Zlt9IntAndIntS_ 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

