[Debian-med-packaging] Bug#1037718: libbpp-phyl: ftbfs with GCC-13

Wed Jun 14 10:26:30 BST 2023

Package: src:libbpp-phyl
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-phyl_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

[...]
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+#MISSING: 2.4.1-8# _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_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# _ZNSt8_Rb_treeImSt4pairIKmPN3bpp4NodeEESt10_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: 2.4.1-8# _ZNSt8_Rb_treeImSt4pairIKmPN3bpp4NodeEESt10_Select1stIS5_ESt4lessImESaIS5_EE24_M_get_insert_unique_posERS1_ at Base 2.4.1
+#MISSING: 2.4.1-8# _ZNSt8_Rb_treeImSt4pairIKmPN3bpp4NodeEESt10_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_treeImSt4pairIKmSt3mapImSt6vectorImSaImEESt4lessImESaIS0_IS1_S5_EEEESt10_Select1stISB_ES7_SaISB_EE24_M_get_insert_unique_posERS1_ at Base 2.4.1
+#MISSING: 2.4.1-8# _ZNSt8_Rb_treeImSt4pairIKmSt3mapImSt6vectorImSaImEESt4lessImESaIS0_IS1_S5_EEEESt10_Select1stISB_ES7_SaISB_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorISB_ERS1_ at Base 2.4.1
+#MISSING: 2.4.1-8# _ZNSt8_Rb_treeImSt4pairIKmSt6vectorIdSaIdEEESt10_Select1stIS5_ESt4lessImESaIS5_EE24_M_get_insert_unique_posERS1_ at Base 2.4.1
+#MISSING: 2.4.1-8# _ZNSt8_Rb_treeImSt4pairIKmSt6vectorIdSaIdEEESt10_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_treeImSt4pairIKmSt6vectorIiSaIiEEESt10_Select1stIS5_ESt4lessImESaIS5_EE20_Reuse_or_alloc_nodeclIRKS5_EEPSt13_Rb_tree_nodeIS5_EOT_ at Base 2.4.1
+#MISSING: 2.4.1-8# _ZNSt8_Rb_treeImSt4pairIKmSt6vectorIiSaIiEEESt10_Select1stIS5_ESt4lessImESaIS5_EE24_M_get_insert_unique_posERS1_ at Base 2.4.1
+#MISSING: 2.4.1-8# _ZNSt8_Rb_treeImSt4pairIKmSt6vectorIiSaIiEEESt10_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_treeImSt4pairIKmSt6vectorImSaImEEESt10_Select1stIS5_ESt4lessImESaIS5_EE24_M_get_insert_unique_posERS1_ at Base 2.4.1
+#MISSING: 2.4.1-8# _ZNSt8_Rb_treeImSt4pairIKmSt6vectorImSaImEEESt10_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_treeImSt4pairIKmiESt10_Select1stIS2_ESt4lessImESaIS2_EE24_M_get_insert_unique_posERS1_ at Base 2.4.1
+#MISSING: 2.4.1-8# _ZNSt8_Rb_treeImSt4pairIKmiESt10_Select1stIS2_ESt4lessImESaIS2_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS2_ERS1_ at Base 2.4.1
+#MISSING: 2.4.1-8# _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: 2.4.1-8# _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
  _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
@@ -4894,17 +4973,20 @@
  _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
  _ZSt16__insertion_sortIN9__gnu_cxx17__normal_iteratorIP12StringAndIntSt6vectorIS2_SaIS2_EEEENS0_5__ops15_Iter_less_iterEEvT_SA_T0_ at Base 2.4.1
+ _ZSt18__do_uninit_fill_nIPN3bpp18UserAlphabetIndex1EmS1_ET_S3_T0_RKT1_ at Base 2.4.1-8
  _ZSt18__do_uninit_fill_nIPNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEmS5_ET_S7_T0_RKT1_ at Base 2.4.1
- _ZSt19piecewise_construct at Base 2.4.1
+#MISSING: 2.4.1-8# _ZSt19piecewise_construct 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
+ _ZSteqIcSt11char_traitsIcESaIcEEbRKNSt7__cxx1112basic_stringIT_T0_T1_EEPKS5_ at Base 2.4.1-8
+ _ZSteqIcSt11char_traitsIcESaIcEEbRKNSt7__cxx1112basic_stringIT_T0_T1_EESA_ at Base 2.4.1-8
  _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
- _ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EEPKS5_RKS8_ at Base 2.4.1
- _ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EERKS8_PKS5_ at Base 2.4.1
- _ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EERKS8_SA_ at Base 2.4.1
+#MISSING: 2.4.1-8# _ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EEPKS5_RKS8_ at Base 2.4.1
+#MISSING: 2.4.1-8# _ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EERKS8_PKS5_ at Base 2.4.1
+#MISSING: 2.4.1-8# _ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EERKS8_SA_ at Base 2.4.1
  _ZTIN3bpp10BppBooleanE at Base 2.4.1
  _ZTIN3bpp10BppNumberIE at Base 2.4.1
  _ZTIN3bpp10ConstraintE at Base 2.4.1
@@ -8249,6 +8331,7 @@
  _ZTv0_n24_N3bpp26RHomogeneousTreeLikelihoodD0Ev at Base 2.4.1
  _ZTv0_n24_N3bpp26RHomogeneousTreeLikelihoodD1Ev at Base 2.4.1
  _ZTv0_n24_N3bpp26SimpleDiscreteDistributionD0Ev at Base 2.4.1
+ _ZTv0_n24_N3bpp26SimpleDiscreteDistributionD1Ev at Base 2.4.1-8
  _ZTv0_n24_N3bpp27BppOSubstitutionModelFormatD0Ev at Base 2.4.1
  _ZTv0_n24_N3bpp27BppOSubstitutionModelFormatD1Ev at Base 2.4.1
  _ZTv0_n24_N3bpp27CodonAdHocSubstitutionModelD0Ev at Base 2.4.1
@@ -9413,6 +9496,6 @@
  _ZTv0_n96_NK3bpp24DRASDRTreeLikelihoodData24getNumberOfDistinctSitesEv at Base 2.4.1
  _ZTv0_n96_NK3bpp26TreeDrawingListenerAdapter12isAutonomousEv at Base 2.4.1
  _ZTv0_n96_NK3bpp28NNIHomogeneousTreeLikelihood16getTopologyValueEv 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
  _Zlt12StringAndIntS_ at Base 2.4.1
  _Zlt9IntAndIntS_ at Base 2.4.1
dh_makeshlibs: error: failing due to earlier errors
make: *** [debian/rules:10: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2

