[Debian-med-packaging] Bug#984089: libbpp-phyl: ftbfs with GCC-11

Matthias Klose doko at debian.org
Wed Mar 3 16:14:02 GMT 2021


Package: src:libbpp-phyl
Version: 2.4.1-4
Severity: normal
Tags: sid bookworm
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-11

[This bug is not targeted to the upcoming bullseye 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-11/g++-11, but succeeds to build with gcc-10/g++-10. The
severity of this report will be raised before the bookworm release,
so nothing has to be done for the bullseye release.

The full build log can be found at:
http://people.debian.org/~doko/logs/20210228/filtered/gcc11/libbpp-phyl_2.4.1-4_unstable_gcc11.log
The last lines of the build log are at the end of this report.

To build with GCC 11, either set CC=gcc-11 CXX=g++-11 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-11/porting_to.html

GCC 11 defaults to the GNU++17 standard.  If your package installs
header files in /usr/include, please don't work around C++17 issues
by choosing a lower C++ standard for the package build, but fix these
issues to build with the C++17 standard.

[...]
  _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_S5_ESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EEC2ERKSE_ at Base 2.4.1
@@ -4855,14 +4872,16 @@
  _ZNSt8_Rb_treeIiSt4pairIKiN3bpp23DRTreeParsimonyLeafDataEESt10_Select1stIS4_ESt4lessIiESaIS4_EE20_Reuse_or_alloc_nodeclIRKS4_EEPSt13_Rb_tree_nodeIS4_EOT_ at Base 2.4.1
  _ZNSt8_Rb_treeIiSt4pairIKiN3bpp23DRTreeParsimonyLeafDataEESt10_Select1stIS4_ESt4lessIiESaIS4_EE24_M_get_insert_unique_posERS1_ at Base 2.4.1
  _ZNSt8_Rb_treeIiSt4pairIKiN3bpp23DRTreeParsimonyLeafDataEESt10_Select1stIS4_ESt4lessIiESaIS4_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS4_ERS1_ at Base 2.4.1
- _ZNSt8_Rb_treeIiSt4pairIKiN3bpp23DRTreeParsimonyLeafDataEESt10_Select1stIS4_ESt4lessIiESaIS4_EE7_M_copyINSA_20_Reuse_or_alloc_nodeEEEPSt13_Rb_tree_nodeIS4_EPKSE_PSt18_Rb_tree_node_baseRT_ at Base 2.4.1
+ _ZNSt8_Rb_treeIiSt4pairIKiN3bpp23DRTreeParsimonyLeafDataEESt10_Select1stIS4_ESt4lessIiESaIS4_EE7_M_copyILb0ENSA_20_Reuse_or_alloc_nodeEEEPSt13_Rb_tree_nodeIS4_ESF_PSt18_Rb_tree_node_baseRT0_ at Base 2.4.1-4
+#MISSING: 2.4.1-4# _ZNSt8_Rb_treeIiSt4pairIKiN3bpp23DRTreeParsimonyLeafDataEESt10_Select1stIS4_ESt4lessIiESaIS4_EE7_M_copyINSA_20_Reuse_or_alloc_nodeEEEPSt13_Rb_tree_nodeIS4_EPKSE_PSt18_Rb_tree_node_baseRT_ at Base 2.4.1
  _ZNSt8_Rb_treeIiSt4pairIKiN3bpp23DRTreeParsimonyLeafDataEESt10_Select1stIS4_ESt4lessIiESaIS4_EE8_M_eraseEPSt13_Rb_tree_nodeIS4_E at Base 2.4.1
  _ZNSt8_Rb_treeIiSt4pairIKiN3bpp23DRTreeParsimonyLeafDataEESt10_Select1stIS4_ESt4lessIiESaIS4_EEC1ERKSA_ at Base 2.4.1
  _ZNSt8_Rb_treeIiSt4pairIKiN3bpp23DRTreeParsimonyLeafDataEESt10_Select1stIS4_ESt4lessIiESaIS4_EEC2ERKSA_ at Base 2.4.1
  _ZNSt8_Rb_treeIiSt4pairIKiN3bpp23DRTreeParsimonyNodeDataEESt10_Select1stIS4_ESt4lessIiESaIS4_EE20_Reuse_or_alloc_nodeclIRKS4_EEPSt13_Rb_tree_nodeIS4_EOT_ at Base 2.4.1
  _ZNSt8_Rb_treeIiSt4pairIKiN3bpp23DRTreeParsimonyNodeDataEESt10_Select1stIS4_ESt4lessIiESaIS4_EE24_M_get_insert_unique_posERS1_ at Base 2.4.1
  _ZNSt8_Rb_treeIiSt4pairIKiN3bpp23DRTreeParsimonyNodeDataEESt10_Select1stIS4_ESt4lessIiESaIS4_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS4_ERS1_ at Base 2.4.1
- _ZNSt8_Rb_treeIiSt4pairIKiN3bpp23DRTreeParsimonyNodeDataEESt10_Select1stIS4_ESt4lessIiESaIS4_EE7_M_copyINSA_20_Reuse_or_alloc_nodeEEEPSt13_Rb_tree_nodeIS4_EPKSE_PSt18_Rb_tree_node_baseRT_ at Base 2.4.1
+ _ZNSt8_Rb_treeIiSt4pairIKiN3bpp23DRTreeParsimonyNodeDataEESt10_Select1stIS4_ESt4lessIiESaIS4_EE7_M_copyILb0ENSA_20_Reuse_or_alloc_nodeEEEPSt13_Rb_tree_nodeIS4_ESF_PSt18_Rb_tree_node_baseRT0_ at Base 2.4.1-4
+#MISSING: 2.4.1-4# _ZNSt8_Rb_treeIiSt4pairIKiN3bpp23DRTreeParsimonyNodeDataEESt10_Select1stIS4_ESt4lessIiESaIS4_EE7_M_copyINSA_20_Reuse_or_alloc_nodeEEEPSt13_Rb_tree_nodeIS4_EPKSE_PSt18_Rb_tree_node_baseRT_ at Base 2.4.1
  _ZNSt8_Rb_treeIiSt4pairIKiN3bpp23DRTreeParsimonyNodeDataEESt10_Select1stIS4_ESt4lessIiESaIS4_EE8_M_eraseEPSt13_Rb_tree_nodeIS4_E at Base 2.4.1
  _ZNSt8_Rb_treeIiSt4pairIKiN3bpp23DRTreeParsimonyNodeDataEESt10_Select1stIS4_ESt4lessIiESaIS4_EEC1ERKSA_ at Base 2.4.1
  _ZNSt8_Rb_treeIiSt4pairIKiN3bpp23DRTreeParsimonyNodeDataEESt10_Select1stIS4_ESt4lessIiESaIS4_EEC2ERKSA_ at Base 2.4.1
@@ -4913,7 +4932,8 @@
  _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_EE24_M_get_insert_unique_posERS1_ at Base 2.4.1
  _ZNSt8_Rb_treeIiSt4pairIKiSt6vectorIiSaIiEEESt10_Select1stIS5_ESt4lessIiESaIS5_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS5_ERS1_ at Base 2.4.1
- _ZNSt8_Rb_treeIiSt4pairIKiSt6vectorIiSaIiEEESt10_Select1stIS5_ESt4lessIiESaIS5_EE7_M_copyINSB_20_Reuse_or_alloc_nodeEEEPSt13_Rb_tree_nodeIS5_EPKSF_PSt18_Rb_tree_node_baseRT_ at Base 2.4.1
+ _ZNSt8_Rb_treeIiSt4pairIKiSt6vectorIiSaIiEEESt10_Select1stIS5_ESt4lessIiESaIS5_EE7_M_copyILb0ENSB_20_Reuse_or_alloc_nodeEEEPSt13_Rb_tree_nodeIS5_ESG_PSt18_Rb_tree_node_baseRT0_ at Base 2.4.1-4
+#MISSING: 2.4.1-4# _ZNSt8_Rb_treeIiSt4pairIKiSt6vectorIiSaIiEEESt10_Select1stIS5_ESt4lessIiESaIS5_EE7_M_copyINSB_20_Reuse_or_alloc_nodeEEEPSt13_Rb_tree_nodeIS5_EPKSF_PSt18_Rb_tree_node_baseRT_ at Base 2.4.1
  _ZNSt8_Rb_treeIiSt4pairIKiSt6vectorIiSaIiEEESt10_Select1stIS5_ESt4lessIiESaIS5_EE8_M_eraseEPSt13_Rb_tree_nodeIS5_E at Base 2.4.1
  _ZNSt8_Rb_treeIiSt4pairIKiSt6vectorIiSaIiEEESt10_Select1stIS5_ESt4lessIiESaIS5_EEC1ERKSB_ at Base 2.4.1
  _ZNSt8_Rb_treeIiSt4pairIKiSt6vectorIiSaIiEEESt10_Select1stIS5_ESt4lessIiESaIS5_EEC2ERKSB_ at Base 2.4.1
@@ -4929,14 +4949,16 @@
  _ZNSt8_Rb_treeIiSt4pairIKiSt6vectorImSaImEEESt10_Select1stIS5_ESt4lessIiESaIS5_EEC2ERKSB_ 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
- _ZNSt8_Rb_treeIiSt4pairIKidESt10_Select1stIS2_ESt4lessIiESaIS2_EE7_M_copyINS8_20_Reuse_or_alloc_nodeEEEPSt13_Rb_tree_nodeIS2_EPKSC_PSt18_Rb_tree_node_baseRT_ at Base 2.4.1
+ _ZNSt8_Rb_treeIiSt4pairIKidESt10_Select1stIS2_ESt4lessIiESaIS2_EE7_M_copyILb0ENS8_20_Reuse_or_alloc_nodeEEEPSt13_Rb_tree_nodeIS2_ESD_PSt18_Rb_tree_node_baseRT0_ at Base 2.4.1-4
+#MISSING: 2.4.1-4# _ZNSt8_Rb_treeIiSt4pairIKidESt10_Select1stIS2_ESt4lessIiESaIS2_EE7_M_copyINS8_20_Reuse_or_alloc_nodeEEEPSt13_Rb_tree_nodeIS2_EPKSC_PSt18_Rb_tree_node_baseRT_ at Base 2.4.1
  _ZNSt8_Rb_treeIiSt4pairIKidESt10_Select1stIS2_ESt4lessIiESaIS2_EE8_M_eraseEPSt13_Rb_tree_nodeIS2_E at Base 2.4.1
  _ZNSt8_Rb_treeIiSt4pairIKiiESt10_Select1stIS2_ESt4lessIiESaIS2_EE24_M_get_insert_unique_posERS1_ at Base 2.4.1
  _ZNSt8_Rb_treeIiSt4pairIKiiESt10_Select1stIS2_ESt4lessIiESaIS2_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS2_ERS1_ at Base 2.4.1
  _ZNSt8_Rb_treeIiSt4pairIKiiESt10_Select1stIS2_ESt4lessIiESaIS2_EE8_M_eraseEPSt13_Rb_tree_nodeIS2_E 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_treeIiSt4pairIKimESt10_Select1stIS2_ESt4lessIiESaIS2_EE7_M_copyINS8_20_Reuse_or_alloc_nodeEEEPSt13_Rb_tree_nodeIS2_EPKSC_PSt18_Rb_tree_node_baseRT_ at Base 2.4.1
+ _ZNSt8_Rb_treeIiSt4pairIKimESt10_Select1stIS2_ESt4lessIiESaIS2_EE7_M_copyILb0ENS8_20_Reuse_or_alloc_nodeEEEPSt13_Rb_tree_nodeIS2_ESD_PSt18_Rb_tree_node_baseRT0_ at Base 2.4.1-4
+#MISSING: 2.4.1-4# _ZNSt8_Rb_treeIiSt4pairIKimESt10_Select1stIS2_ESt4lessIiESaIS2_EE7_M_copyINS8_20_Reuse_or_alloc_nodeEEEPSt13_Rb_tree_nodeIS2_EPKSC_PSt18_Rb_tree_node_baseRT_ at Base 2.4.1
  _ZNSt8_Rb_treeIiSt4pairIKimESt10_Select1stIS2_ESt4lessIiESaIS2_EE8_M_eraseEPSt13_Rb_tree_nodeIS2_E at Base 2.4.1
  _ZNSt8_Rb_treeIiSt4pairIKimESt10_Select1stIS2_ESt4lessIiESaIS2_EEC1ERKS8_ at Base 2.4.1
  _ZNSt8_Rb_treeIiSt4pairIKimESt10_Select1stIS2_ESt4lessIiESaIS2_EEC2ERKS8_ at Base 2.4.1
@@ -4960,7 +4982,8 @@
  _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_EE24_M_get_insert_unique_posERS1_ at Base 2.4.1
  _ZNSt8_Rb_treeImSt4pairIKmSt6vectorIiSaIiEEESt10_Select1stIS5_ESt4lessImESaIS5_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS5_ERS1_ at Base 2.4.1
- _ZNSt8_Rb_treeImSt4pairIKmSt6vectorIiSaIiEEESt10_Select1stIS5_ESt4lessImESaIS5_EE7_M_copyINSB_20_Reuse_or_alloc_nodeEEEPSt13_Rb_tree_nodeIS5_EPKSF_PSt18_Rb_tree_node_baseRT_ at Base 2.4.1
+ _ZNSt8_Rb_treeImSt4pairIKmSt6vectorIiSaIiEEESt10_Select1stIS5_ESt4lessImESaIS5_EE7_M_copyILb0ENSB_20_Reuse_or_alloc_nodeEEEPSt13_Rb_tree_nodeIS5_ESG_PSt18_Rb_tree_node_baseRT0_ at Base 2.4.1-4
+#MISSING: 2.4.1-4# _ZNSt8_Rb_treeImSt4pairIKmSt6vectorIiSaIiEEESt10_Select1stIS5_ESt4lessImESaIS5_EE7_M_copyINSB_20_Reuse_or_alloc_nodeEEEPSt13_Rb_tree_nodeIS5_EPKSF_PSt18_Rb_tree_node_baseRT_ at Base 2.4.1
  _ZNSt8_Rb_treeImSt4pairIKmSt6vectorIiSaIiEEESt10_Select1stIS5_ESt4lessImESaIS5_EE8_M_eraseEPSt13_Rb_tree_nodeIS5_E at Base 2.4.1
  _ZNSt8_Rb_treeImSt4pairIKmSt6vectorIiSaIiEEESt10_Select1stIS5_ESt4lessImESaIS5_EEC1ERKSB_ at Base 2.4.1
  _ZNSt8_Rb_treeImSt4pairIKmSt6vectorIiSaIiEEESt10_Select1stIS5_ESt4lessImESaIS5_EEC2ERKSB_ at Base 2.4.1
@@ -4981,6 +5004,7 @@
  _ZNSt8_Rb_treeIsSt4pairIKsNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEESt10_Select1stIS8_ESt4lessIsESaIS8_EEC1ERKSE_ at Base 2.4.1
  _ZNSt8_Rb_treeIsSt4pairIKsNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEESt10_Select1stIS8_ESt4lessIsESaIS8_EEC2ERKSE_ 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 2.4.1-4
  _ZSt13__adjust_heapIN9__gnu_cxx17__normal_iteratorIP12StringAndIntSt6vectorIS2_SaIS2_EEEElS2_NS0_5__ops15_Iter_less_iterEEvT_T0_SB_T1_T2_ 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
  _ZSt25__unguarded_linear_insertIN9__gnu_cxx17__normal_iteratorIP12StringAndIntSt6vectorIS2_SaIS2_EEEENS0_5__ops14_Val_less_iterEEvT_T0_ 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



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