[Debian-med-packaging] Bug#1012968: libbpp-phyl: ftbfs with GCC-12

Thu Jun 16 13:10:35 BST 2022

Package: src:libbpp-phyl
Version: 2.4.1-6
Severity: normal
Tags: sid bookworm
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-12

[This bug is targeted to the upcoming bookworm 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-12/g++-12, but succeeds to build with gcc-11/g++-11. The
severity of this report will be raised before the bookworm release.

The full build log can be found at:
http://qa-logs.debian.net/2022/06/09/gcc12/libbpp-phyl_2.4.1-6_unstable_gcc12.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_treeImSt4pairIKmmESt10_Select1stIS2_ESt4lessImESaIS2_EE24_M_get_insert_unique_posERS1_ at Base 2.4.1
  _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
- _ZNSt8_Rb_treeIsSt4pairIKsNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEESt10_Select1stIS8_ESt4lessIsESaIS8_EE8_M_eraseEPSt13_Rb_tree_nodeIS8_E at Base 2.4.1
+#MISSING: 2.4.1-6# _ZNSt8_Rb_treeIsSt4pairIKsNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEESt10_Select1stIS8_ESt4lessIsESaIS8_EE8_M_eraseEPSt13_Rb_tree_nodeIS8_E 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
  _ZSt13__adjust_heapIN9__gnu_cxx17__normal_iteratorIP12StringAndIntSt6vectorIS2_SaIS2_EEEElS2_NS0_5__ops15_Iter_less_iterEEvT_T0_SB_T1_T2_ 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 2.4.1-6
+ _ZSt16__do_uninit_copyIN9__gnu_cxx17__normal_iteratorIPKN3bpp13ParameterListESt6vectorIS3_SaIS3_EEEEPS3_ET0_T_SC_SB_ at Base 2.4.1-6
+ _ZSt16__do_uninit_copyIN9__gnu_cxx17__normal_iteratorIPKN3bpp7SimplexESt6vectorIS3_SaIS3_EEEEPS3_ET0_T_SC_SB_ at Base 2.4.1-6
+ _ZSt16__do_uninit_copyIN9__gnu_cxx17__normal_iteratorIPKN3bpp9RowMatrixIdEESt6vectorIS4_SaIS4_EEEEPS4_ET0_T_SD_SC_ at Base 2.4.1-6
+ _ZSt16__do_uninit_copyIN9__gnu_cxx17__normal_iteratorIPKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt6vectorIS7_SaIS7_EEEEPS7_ET0_T_SG_SF_ at Base 2.4.1-6
+ _ZSt16__do_uninit_copyIN9__gnu_cxx17__normal_iteratorIPKSt3setImSt4lessImESaImEESt6vectorIS6_SaIS6_EEEEPS6_ET0_T_SF_SE_ at Base 2.4.1-6
+ _ZSt16__do_uninit_copyIN9__gnu_cxx17__normal_iteratorIPKSt6vectorIS2_IdSaIdEESaIS4_EES2_IS6_SaIS6_EEEEPS6_ET0_T_SE_SD_ at Base 2.4.1-6
+ _ZSt16__do_uninit_copyIN9__gnu_cxx17__normal_iteratorIPKSt6vectorIS2_IjSaIjEESaIS4_EES2_IS6_SaIS6_EEEEPS6_ET0_T_SE_SD_ at Base 2.4.1-6
+ _ZSt16__do_uninit_copyIN9__gnu_cxx17__normal_iteratorIPKSt6vectorIbSaIbEES2_IS4_SaIS4_EEEEPS4_ET0_T_SC_SB_ at Base 2.4.1-6
+ _ZSt16__do_uninit_copyIN9__gnu_cxx17__normal_iteratorIPKSt6vectorIdSaIdEES2_IS4_SaIS4_EEEEPS4_ET0_T_SC_SB_ at Base 2.4.1-6
+ _ZSt16__do_uninit_copyIN9__gnu_cxx17__normal_iteratorIPKSt6vectorIjSaIjEES2_IS4_SaIS4_EEEEPS4_ET0_T_SC_SB_ at Base 2.4.1-6
+ _ZSt16__do_uninit_copyIN9__gnu_cxx17__normal_iteratorIPNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt6vectorIS7_SaIS7_EEEES8_ET0_T_SE_SD_ at Base 2.4.1-6
+ _ZSt16__do_uninit_copyIPKN3bpp12MutationPathEPS1_ET0_T_S6_S5_ at Base 2.4.1-6
+ _ZSt16__do_uninit_copyIPKN3bpp13ParameterListEPS1_ET0_T_S6_S5_ at Base 2.4.1-6
+ _ZSt16__do_uninit_copyIPKN3bpp22AbstractTreeLikelihood36ConstNoPartitionSiteModelDescriptionEPS2_ET0_T_S7_S6_ at Base 2.4.1-6
+ _ZSt16__do_uninit_copyIPKN3bpp7SimplexEPS1_ET0_T_S6_S5_ at Base 2.4.1-6
  _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_nIPNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEmS5_ET_S7_T0_RKT1_ at Base 2.4.1-6
+ _ZSt19piecewise_construct at Base 2.4.1-6
  _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
- _ZSteqIcEN9__gnu_cxx11__enable_ifIXsrSt9__is_charIT_E7__valueEbE6__typeERKNSt7__cxx1112basic_stringIS3_St11char_traitsIS3_ESaIS3_EEESE_ at Base 2.4.1
+#MISSING: 2.4.1-6# _ZSteqIcEN9__gnu_cxx11__enable_ifIXsrSt9__is_charIT_E7__valueEbE6__typeERKNSt7__cxx1112basic_stringIS3_St11char_traitsIS3_ESaIS3_EEESE_ at Base 2.4.1
  _ZStmiRKSt15_Deque_iteratorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERS5_PS5_ESA_ at Base 2.4.1
- _ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EEOS8_PKS5_ at Base 2.4.1
- _ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EEOS8_RKS8_ at Base 2.4.1
+#MISSING: 2.4.1-6# _ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EEOS8_PKS5_ at Base 2.4.1
+#MISSING: 2.4.1-6# _ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EEOS8_RKS8_ 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
@@ -8138,7 +8175,7 @@
  _ZTv0_n24_N3bpp12TreeTemplateINS_12NodeTemplateINS_9PGMAInfosEEEED1Ev at Base 2.4.1
  _ZTv0_n24_N3bpp12TreeTemplateINS_4NodeEED0Ev at Base 2.4.1
  _ZTv0_n24_N3bpp12TreeTemplateINS_4NodeEED1Ev at Base 2.4.1
- _ZTv0_n24_N3bpp12WordAlphabetD0Ev at Base 2.4.1
+#MISSING: 2.4.1-6# _ZTv0_n24_N3bpp12WordAlphabetD0Ev at Base 2.4.1
  _ZTv0_n24_N3bpp13AlphabetStateD0Ev at Base 2.4.1
  _ZTv0_n24_N3bpp13AlphabetStateD1Ev at Base 2.4.1
  _ZTv0_n24_N3bpp13BasicSequenceD0Ev at Base 2.4.1
@@ -8240,7 +8277,7 @@
  _ZTv0_n24_N3bpp24BppOFrequenciesSetFormatD0Ev at Base 2.4.1
  _ZTv0_n24_N3bpp24BppOFrequenciesSetFormatD1Ev at Base 2.4.1
  _ZTv0_n24_N3bpp24BppOParametrizableFormatD0Ev at Base 2.4.1
- _ZTv0_n24_N3bpp24BppOParametrizableFormatD1Ev at Base 2.4.1
+#MISSING: 2.4.1-6# _ZTv0_n24_N3bpp24BppOParametrizableFormatD1Ev at Base 2.4.1
  _ZTv0_n24_N3bpp24ConstantRateDistributionD0Ev at Base 2.4.1
  _ZTv0_n24_N3bpp24ConstantRateDistributionD1Ev at Base 2.4.1
  _ZTv0_n24_N3bpp24DRASDRTreeLikelihoodDataD0Ev at Base 2.4.1
@@ -8292,7 +8329,7 @@
  _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
+#MISSING: 2.4.1-6# _ZTv0_n24_N3bpp26SimpleDiscreteDistributionD1Ev at Base 2.4.1
  _ZTv0_n24_N3bpp27BppOSubstitutionModelFormatD0Ev at Base 2.4.1
  _ZTv0_n24_N3bpp27BppOSubstitutionModelFormatD1Ev at Base 2.4.1
  _ZTv0_n24_N3bpp27CodonAdHocSubstitutionModelD0Ev 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

