[Debian-med-packaging] Bug#1075151: libbpp-popgen: ftbfs with GCC-14

Wed Jul 3 13:32:40 BST 2024

Package: src:libbpp-popgen
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-popgen_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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- _ZNSt6vectorIdSaIdEE17_M_realloc_insertIJdEEEvN9__gnu_cxx17__normal_iteratorIPdS1_EEDpOT_ at Base 2.4.1
- _ZNSt6vectorIdSaIdEED1Ev at Base 2.4.1
- _ZNSt6vectorIdSaIdEED2Ev at Base 2.4.1
+ _ZNSt6vectorIdSaIdEE17_M_realloc_appendIJRKdEEEvDpOT_ at Base 2.4.1-10
+ _ZNSt6vectorIdSaIdEE17_M_realloc_appendIJdEEEvDpOT_ at Base 2.4.1-10
+#MISSING: 2.4.1-10# _ZNSt6vectorIdSaIdEE17_M_realloc_insertIJRKdEEEvN9__gnu_cxx17__normal_iteratorIPdS1_EEDpOT_ at Base 2.4.1
+#MISSING: 2.4.1-10# _ZNSt6vectorIdSaIdEE17_M_realloc_insertIJdEEEvN9__gnu_cxx17__normal_iteratorIPdS1_EEDpOT_ at Base 2.4.1
+#MISSING: 2.4.1-10# _ZNSt6vectorIdSaIdEED1Ev at Base 2.4.1
+#MISSING: 2.4.1-10# _ZNSt6vectorIdSaIdEED2Ev at Base 2.4.1
  _ZNSt6vectorIjSaIjEE17_M_default_appendEm at Base 2.4.1
- _ZNSt6vectorIjSaIjEE17_M_realloc_insertIJRKjEEEvN9__gnu_cxx17__normal_iteratorIPjS1_EEDpOT_ at Base 2.4.1
- _ZNSt6vectorIjSaIjEED1Ev at Base 2.4.1
- _ZNSt6vectorIjSaIjEED2Ev at Base 2.4.1
+#MISSING: 2.4.1-10# _ZNSt6vectorIjSaIjEE17_M_realloc_insertIJRKjEEEvN9__gnu_cxx17__normal_iteratorIPjS1_EEDpOT_ at Base 2.4.1
+#MISSING: 2.4.1-10# _ZNSt6vectorIjSaIjEED1Ev at Base 2.4.1
+#MISSING: 2.4.1-10# _ZNSt6vectorIjSaIjEED2Ev at Base 2.4.1
  _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
- _ZNSt6vectorImSaImEED1Ev at Base 2.4.1
- _ZNSt6vectorImSaImEED2Ev at Base 2.4.1
+ _ZNSt6vectorImSaImEE17_M_realloc_appendIJRKmEEEvDpOT_ at Base 2.4.1-10
+ _ZNSt6vectorImSaImEE17_M_realloc_appendIJmEEEvDpOT_ at Base 2.4.1-10
+#MISSING: 2.4.1-10# _ZNSt6vectorImSaImEE17_M_realloc_insertIJRKmEEEvN9__gnu_cxx17__normal_iteratorIPmS1_EEDpOT_ at Base 2.4.1
+#MISSING: 2.4.1-10# _ZNSt6vectorImSaImEE17_M_realloc_insertIJmEEEvN9__gnu_cxx17__normal_iteratorIPmS1_EEDpOT_ at Base 2.4.1
+#MISSING: 2.4.1-10# _ZNSt6vectorImSaImEED1Ev at Base 2.4.1
+#MISSING: 2.4.1-10# _ZNSt6vectorImSaImEED2Ev at Base 2.4.1
  _ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED0Ev at Base 2.4.1
  _ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED1Ev at Base 2.4.1
  _ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED2Ev at Base 2.4.1
  _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES5_St9_IdentityIS5_ESt4lessIS5_ESaIS5_EE16_M_insert_uniqueIRKS5_EESt4pairISt17_Rb_tree_iteratorIS5_EbEOT_ at Base 2.4.1
- _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_PN3bpp23VectorSequenceContainerEESt10_Select1stISB_ESt4lessIS5_ESaISB_EE24_M_get_insert_unique_posERS7_ at Base 2.4.1
- _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_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_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
+#MISSING: 2.4.1-10# _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_PN3bpp23VectorSequenceContainerEESt10_Select1stISB_ESt4lessIS5_ESaISB_EE24_M_get_insert_unique_posERS7_ at Base 2.4.1
+#MISSING: 2.4.1-10# _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
+#MISSING: 2.4.1-10# _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_St3setIS5_St4lessIS5_ESaIS5_EEESt10_Select1stISD_ESA_SaISD_EE24_M_get_insert_unique_posERS7_ at Base 2.4.1
+#MISSING: 2.4.1-10# _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_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
+#MISSING: 2.4.1-10# _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_iESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE24_M_get_insert_unique_posERS7_ at Base 2.4.1
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+#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_treeImSt4pairIKmN3bpp28MultilocusGenotypeStatistics6FstatsEESt10_Select1stIS5_ESt4lessImESaIS5_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJRS1_EESG_IJEEEEESt17_Rb_tree_iteratorIS5_ESt23_Rb_tree_const_iteratorIS5_EDpOT_ at Base 2.4.1-10
+ _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
  _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
  _ZSt16__do_uninit_copyIN9__gnu_cxx17__normal_iteratorIPKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt6vectorIS7_SaIS7_EEEEPS7_ET0_T_SG_SF_ at Base 2.4.1
  _ZSt16__do_uninit_copyIN9__gnu_cxx17__normal_iteratorIPKSt6vectorIdSaIdEES2_IS4_SaIS4_EEEEPS4_ET0_T_SC_SB_ at Base 2.4.1
- _ZSt16__do_uninit_copyIPKN3bpp9LocusInfoEPS1_ET0_T_S6_S5_ at Base 2.4.1
+#MISSING: 2.4.1-10# _ZSt16__do_uninit_copyIPKN3bpp9LocusInfoEPS1_ET0_T_S6_S5_ at Base 2.4.1
  _ZSt5fixedRSt8ios_base at Base 2.4.1
- _ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EEOS8_S9_ at Base 2.4.1
+#MISSING: 2.4.1-10# _ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EEOS8_S9_ at Base 2.4.1
  _ZTIN3bpp10AlleleInfoE at Base 2.4.1
  _ZTIN3bpp10IndividualE at Base 2.4.1
  _ZTIN3bpp10SymbolListE 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