[Debian-med-packaging] Bug#1075149: libbpp-phyl-omics: ftbfs with GCC-14

[Matthias Klose]

Package: src:libbpp-phyl-omics
Version: 2.4.1-6
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-omics_2.4.1-6_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

[...]
- _ZNSt12_Vector_baseINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED2Ev at Base 2.4.1
- _ZNSt12_Vector_baseISt6vectorIdSaIdEESaIS2_EED1Ev at Base 2.4.1
- _ZNSt12_Vector_baseISt6vectorIdSaIdEESaIS2_EED2Ev at Base 2.4.1
+#MISSING: 2.4.1-6# _ZNSt12_Vector_baseINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED1Ev at Base 2.4.1
+#MISSING: 2.4.1-6# _ZNSt12_Vector_baseINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED2Ev at Base 2.4.1
+#MISSING: 2.4.1-6# _ZNSt12_Vector_baseISt6vectorIdSaIdEESaIS2_EED1Ev at Base 2.4.1
+#MISSING: 2.4.1-6# _ZNSt12_Vector_baseISt6vectorIdSaIdEESaIS2_EED2Ev at Base 2.4.1
  _ZNSt15_Sp_counted_ptrIDnLN9__gnu_cxx12_Lock_policyE2EE10_M_disposeEv at Base 2.4.1
  _ZNSt16_Sp_counted_baseILN9__gnu_cxx12_Lock_policyE2EE10_M_destroyEv at Base 2.4.1
  _ZNSt16_Sp_counted_baseILN9__gnu_cxx12_Lock_policyE2EE24_M_release_last_use_coldEv at Base 2.4.1
  _ZNSt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEPN3bpp10BppNumberIESt4lessIS5_ESaISt4pairIKS5_S8_EEEixERSC_ at Base 2.4.1
  _ZNSt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEPN3bpp8ClonableESt4lessIS5_ESaISt4pairIKS5_S8_EEEixERSC_ at Base 2.4.1
- _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE17_M_realloc_insertIJRKS5_EEEvN9__gnu_cxx17__normal_iteratorIPS5_S7_EEDpOT_ at Base 2.4.1
- _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE17_M_realloc_insertIJS5_EEEvN9__gnu_cxx17__normal_iteratorIPS5_S7_EEDpOT_ at Base 2.4.1-6~
+ _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE17_M_realloc_appendIJRKS5_EEEvDpOT_ at Base 2.4.1-6
+ _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE17_M_realloc_appendIJS5_EEEvDpOT_ at Base 2.4.1-6
+#MISSING: 2.4.1-6# _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE17_M_realloc_insertIJRKS5_EEEvN9__gnu_cxx17__normal_iteratorIPS5_S7_EEDpOT_ at Base 2.4.1
+#MISSING: 2.4.1-6# _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE17_M_realloc_insertIJS5_EEEvN9__gnu_cxx17__normal_iteratorIPS5_S7_EEDpOT_ at Base 2.4.1-6~
  _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED1Ev at Base 2.4.1
  _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED2Ev at Base 2.4.1
- _ZNSt6vectorIPKN3bpp4NodeESaIS3_EE17_M_realloc_insertIJS3_EEEvN9__gnu_cxx17__normal_iteratorIPS3_S5_EEDpOT_ at Base 2.4.1
- _ZNSt6vectorIPKN3bpp4NodeESaIS3_EED1Ev at Base 2.4.1-6~
- _ZNSt6vectorIPKN3bpp4NodeESaIS3_EED2Ev at Base 2.4.1-6~
- _ZNSt6vectorIPN3bpp17IterationListenerESaIS2_EE17_M_realloc_insertIJRKS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ at Base 2.4.1
- _ZNSt6vectorIPN3bpp4NodeESaIS2_EE17_M_realloc_insertIJS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ at Base 2.4.1
- _ZNSt6vectorIPN3bpp4NodeESaIS2_EED1Ev at Base 2.4.1-6~
- _ZNSt6vectorIPN3bpp4NodeESaIS2_EED2Ev at Base 2.4.1-6~
+ _ZNSt6vectorIPKN3bpp4NodeESaIS3_EE12emplace_backIJS3_EEEvDpOT_ at Base 2.4.1-6
+#MISSING: 2.4.1-6# _ZNSt6vectorIPKN3bpp4NodeESaIS3_EE17_M_realloc_insertIJS3_EEEvN9__gnu_cxx17__normal_iteratorIPS3_S5_EEDpOT_ at Base 2.4.1
+#MISSING: 2.4.1-6# _ZNSt6vectorIPKN3bpp4NodeESaIS3_EED1Ev at Base 2.4.1-6~
+#MISSING: 2.4.1-6# _ZNSt6vectorIPKN3bpp4NodeESaIS3_EED2Ev at Base 2.4.1-6~
+ _ZNSt6vectorIPN3bpp17IterationListenerESaIS2_EE17_M_realloc_appendIJRKS2_EEEvDpOT_ at Base 2.4.1-6
+#MISSING: 2.4.1-6# _ZNSt6vectorIPN3bpp17IterationListenerESaIS2_EE17_M_realloc_insertIJRKS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ at Base 2.4.1
+ _ZNSt6vectorIPN3bpp4NodeESaIS2_EE12emplace_backIJS2_EEEvDpOT_ at Base 2.4.1-6
+#MISSING: 2.4.1-6# _ZNSt6vectorIPN3bpp4NodeESaIS2_EE17_M_realloc_insertIJS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ at Base 2.4.1
+#MISSING: 2.4.1-6# _ZNSt6vectorIPN3bpp4NodeESaIS2_EED1Ev at Base 2.4.1-6~
+#MISSING: 2.4.1-6# _ZNSt6vectorIPN3bpp4NodeESaIS2_EED2Ev at Base 2.4.1-6~
  _ZNSt6vectorIS_IdSaIdEESaIS1_EE17_M_default_appendEm at Base 2.4.1
  _ZNSt6vectorIS_IdSaIdEESaIS1_EED1Ev at Base 2.4.1
  _ZNSt6vectorIS_IdSaIdEESaIS1_EED2Ev at Base 2.4.1
  _ZNSt6vectorIdSaIdEE17_M_default_appendEm at Base 2.4.1
- _ZNSt6vectorIdSaIdEED1Ev at Base 2.4.1-6~
- _ZNSt6vectorIdSaIdEED2Ev at Base 2.4.1-6~
+#MISSING: 2.4.1-6# _ZNSt6vectorIdSaIdEED1Ev at Base 2.4.1-6~
+#MISSING: 2.4.1-6# _ZNSt6vectorIdSaIdEED2Ev at Base 2.4.1-6~
  _ZNSt6vectorIiSaIiEE12emplace_backIJiEEEvDpOT_ at Base 2.4.1-6~
- _ZNSt6vectorIiSaIiEE17_M_realloc_insertIJiEEEvN9__gnu_cxx17__normal_iteratorIPiS1_EEDpOT_ at Base 2.4.1
- _ZNSt6vectorIiSaIiEED1Ev at Base 2.4.1-6~
- _ZNSt6vectorIiSaIiEED2Ev at Base 2.4.1-6~
- _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_PN3bpp10BppNumberIEESt10_Select1stISB_ESt4lessIS5_ESaISB_EE24_M_get_insert_unique_posERS7_ at Base 2.4.1
- _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_PN3bpp10BppNumberIEESt10_Select1stISB_ESt4lessIS5_ESaISB_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorISB_ERS7_ at Base 2.4.1
+#MISSING: 2.4.1-6# _ZNSt6vectorIiSaIiEE17_M_realloc_insertIJiEEEvN9__gnu_cxx17__normal_iteratorIPiS1_EEDpOT_ at Base 2.4.1
+#MISSING: 2.4.1-6# _ZNSt6vectorIiSaIiEED1Ev at Base 2.4.1-6~
+#MISSING: 2.4.1-6# _ZNSt6vectorIiSaIiEED2Ev at Base 2.4.1-6~
+ _ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED0Ev at Base 2.4.1-6
+ _ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED1Ev at Base 2.4.1-6
+ _ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED2Ev at Base 2.4.1-6
+#MISSING: 2.4.1-6# _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_PN3bpp10BppNumberIEESt10_Select1stISB_ESt4lessIS5_ESaISB_EE24_M_get_insert_unique_posERS7_ at Base 2.4.1
+#MISSING: 2.4.1-6# _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_PN3bpp10BppNumberIEESt10_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_PN3bpp10BppNumberIEESt10_Select1stISB_ESt4lessIS5_ESaISB_EE4findERS7_ at Base 2.4.1
- _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_PN3bpp8ClonableEESt10_Select1stISB_ESt4lessIS5_ESaISB_EE24_M_get_insert_unique_posERS7_ at Base 2.4.1
- _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_PN3bpp8ClonableEESt10_Select1stISB_ESt4lessIS5_ESaISB_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorISB_ERS7_ at Base 2.4.1
+#MISSING: 2.4.1-6# _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_PN3bpp8ClonableEESt10_Select1stISB_ESt4lessIS5_ESaISB_EE24_M_get_insert_unique_posERS7_ at Base 2.4.1
+#MISSING: 2.4.1-6# _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_PN3bpp8ClonableEESt10_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_PN3bpp8ClonableEESt10_Select1stISB_ESt4lessIS5_ESaISB_EE4findERS7_ 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
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