[Debian-med-packaging] Bug#1015475: libbpp-phyl: ftbfs with LTO (link time optimization) enabled

[Matthias Klose]

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

This package currently fails to build (at least on the amd64
architecture) with link time optimizations enabled.  For a background
for LTO please see

https://wiki.debian.org/ToolChain/LTO

The goal is to enable this optimization by default in an upcoming
Debian release in dpkg-buildflags for 64bit architectures.  The goal
is to get this package to build with link time optimizations, or to
explicitly disable link time optimizations for this package build.

To reproduce the build failure, enable the lto optimization in
testing/unstable by adding "optimize=+lto" to DEB_BUILD_MAINT_OPTIONS
in the debian/rules file, or if this macro is unset, just set it:

export DEB_BUILD_MAINT_OPTIONS = optimize=+lto

Please try to fix the build with lto enabled, fixing the packaging or
forwarding the issue upstream. If the issue cannot be fixed,
explicitly disallow building the package with lto by adding to your
rules file:

export DEB_BUILD_MAINT_OPTIONS = optimize=-lto

or adding that string to your existing setting of DEB_BUILD_MAINT_OPTIONS.

The full build log can be found at:
http://qa-logs.debian.net/2022/06/09/dpkglto/libbpp-phyl_2.4.1-6_unstable_dpkglto.log
The last lines of the build log are at the end of this report.

[...]
- _ZTv0_n88_NK3bpp17AbstractOptimizer16getFunctionValueEv at Base 2.4.1
- _ZTv0_n88_NK3bpp20DRTreeParsimonyScore11getTopologyEv at Base 2.4.1
- _ZTv0_n88_NK3bpp21PseudoNewtonOptimizer16getFunctionValueEv at Base 2.4.1
- _ZTv0_n88_NK3bpp22SWSubstitutionRegister11getTypeNameB5cxx11Em at Base 2.4.1
- _ZTv0_n88_NK3bpp24DnDsSubstitutionRegister11getTypeNameB5cxx11Em at Base 2.4.1
- _ZTv0_n88_NK3bpp24KrKcSubstitutionRegister11getTypeNameB5cxx11Em at Base 2.4.1
- _ZTv0_n88_NK3bpp24TsTvSubstitutionRegister11getTypeNameB5cxx11Em at Base 2.4.1
- _ZTv0_n88_NK3bpp25TotalSubstitutionRegister11getTypeNameB5cxx11Em at Base 2.4.1
- _ZTv0_n88_NK3bpp27GeneralSubstitutionRegister11getTypeNameB5cxx11Em at Base 2.4.1
- _ZTv0_n88_NK3bpp27VectorOfSubstitionRegisters11getTypeNameB5cxx11Em at Base 2.4.1
- _ZTv0_n88_NK3bpp28CategorySubstitutionRegister11getTypeNameB5cxx11Em at Base 2.4.1
- _ZTv0_n88_NK3bpp28NNIHomogeneousTreeLikelihood11getTopologyEv at Base 2.4.1
- _ZTv0_n88_NK3bpp28SelectedSubstitutionRegister11getTypeNameB5cxx11Em at Base 2.4.1
- _ZTv0_n88_NK3bpp30AAExteriorSubstitutionRegister11getTypeNameB5cxx11Em at Base 2.4.1
- _ZTv0_n88_NK3bpp30AAInteriorSubstitutionRegister11getTypeNameB5cxx11Em at Base 2.4.1
- _ZTv0_n88_NK3bpp32GCSynonymousSubstitutionRegister11getTypeNameB5cxx11Em at Base 2.4.1
- _ZTv0_n88_NK3bpp33AbstractOptimizationStopCondition12getToleranceEv at Base 2.4.1
- _ZTv0_n88_NK3bpp35AbstractAgglomerativeDistanceMethod9isVerboseEv at Base 2.4.1
- _ZTv0_n96_N3bpp21ParametrizableAdapter19setParametersValuesERKNS_13ParameterListE at Base 2.4.1
- _ZTv0_n96_N3bpp22AbstractParametrizable19setParametersValuesERKNS_13ParameterListE at Base 2.4.1
- _ZTv0_n96_N3bpp6StdErrlsERKm at Base 2.4.1
- _ZTv0_n96_NK3bpp15AbstractMapping12getNodeIndexEi at Base 2.4.1
- _ZTv0_n96_NK3bpp16AbstractStateMap14getModelStatesERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 2.4.1
- _ZTv0_n96_NK3bpp19AbstractTreeDrawing8getXUnitEv at Base 2.4.1
+#MISSING: 2.4.1-6# _ZTv0_n88_N3bpp6StdErrlsERKl at Base 2.4.1
+#MISSING: 2.4.1-6# _ZTv0_n88_NK3bpp15AbstractMapping16getBranchLengthsEv at Base 2.4.1
+#MISSING: 2.4.1-6# _ZTv0_n88_NK3bpp16AbstractStateMap21getAlphabetStateAsIntEm at Base 2.4.1
+#MISSING: 2.4.1-6# _ZTv0_n88_NK3bpp17AbstractOptimizer16getFunctionValueEv at Base 2.4.1
+#MISSING: 2.4.1-6# _ZTv0_n88_NK3bpp20DRTreeParsimonyScore11getTopologyEv at Base 2.4.1
+#MISSING: 2.4.1-6# _ZTv0_n88_NK3bpp21PseudoNewtonOptimizer16getFunctionValueEv at Base 2.4.1
+#MISSING: 2.4.1-6# _ZTv0_n88_NK3bpp22SWSubstitutionRegister11getTypeNameB5cxx11Em at Base 2.4.1
+#MISSING: 2.4.1-6# _ZTv0_n88_NK3bpp24DnDsSubstitutionRegister11getTypeNameB5cxx11Em at Base 2.4.1
+#MISSING: 2.4.1-6# _ZTv0_n88_NK3bpp24KrKcSubstitutionRegister11getTypeNameB5cxx11Em at Base 2.4.1
+#MISSING: 2.4.1-6# _ZTv0_n88_NK3bpp24TsTvSubstitutionRegister11getTypeNameB5cxx11Em at Base 2.4.1
+#MISSING: 2.4.1-6# _ZTv0_n88_NK3bpp25TotalSubstitutionRegister11getTypeNameB5cxx11Em at Base 2.4.1
+#MISSING: 2.4.1-6# _ZTv0_n88_NK3bpp27GeneralSubstitutionRegister11getTypeNameB5cxx11Em at Base 2.4.1
+#MISSING: 2.4.1-6# _ZTv0_n88_NK3bpp27VectorOfSubstitionRegisters11getTypeNameB5cxx11Em at Base 2.4.1
+#MISSING: 2.4.1-6# _ZTv0_n88_NK3bpp28CategorySubstitutionRegister11getTypeNameB5cxx11Em at Base 2.4.1
+#MISSING: 2.4.1-6# _ZTv0_n88_NK3bpp28NNIHomogeneousTreeLikelihood11getTopologyEv at Base 2.4.1
+#MISSING: 2.4.1-6# _ZTv0_n88_NK3bpp28SelectedSubstitutionRegister11getTypeNameB5cxx11Em at Base 2.4.1
+#MISSING: 2.4.1-6# _ZTv0_n88_NK3bpp30AAExteriorSubstitutionRegister11getTypeNameB5cxx11Em at Base 2.4.1
+#MISSING: 2.4.1-6# _ZTv0_n88_NK3bpp30AAInteriorSubstitutionRegister11getTypeNameB5cxx11Em at Base 2.4.1
+#MISSING: 2.4.1-6# _ZTv0_n88_NK3bpp32GCSynonymousSubstitutionRegister11getTypeNameB5cxx11Em at Base 2.4.1
+#MISSING: 2.4.1-6# _ZTv0_n88_NK3bpp33AbstractOptimizationStopCondition12getToleranceEv at Base 2.4.1
+#MISSING: 2.4.1-6# _ZTv0_n88_NK3bpp35AbstractAgglomerativeDistanceMethod9isVerboseEv at Base 2.4.1
+#MISSING: 2.4.1-6# _ZTv0_n96_N3bpp21ParametrizableAdapter19setParametersValuesERKNS_13ParameterListE at Base 2.4.1
+#MISSING: 2.4.1-6# _ZTv0_n96_N3bpp22AbstractParametrizable19setParametersValuesERKNS_13ParameterListE at Base 2.4.1
+#MISSING: 2.4.1-6# _ZTv0_n96_N3bpp6StdErrlsERKm at Base 2.4.1
+#MISSING: 2.4.1-6# _ZTv0_n96_NK3bpp15AbstractMapping12getNodeIndexEi at Base 2.4.1
+#MISSING: 2.4.1-6# _ZTv0_n96_NK3bpp16AbstractStateMap14getModelStatesERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 2.4.1
+#MISSING: 2.4.1-6# _ZTv0_n96_NK3bpp19AbstractTreeDrawing8getXUnitEv at Base 2.4.1
  _ZTv0_n96_NK3bpp19DecompositionReward9getRewardEmmd at Base 2.4.1
- _ZTv0_n96_NK3bpp20DRTreeParsimonyScore16getTopologyValueEv at Base 2.4.1
+#MISSING: 2.4.1-6# _ZTv0_n96_NK3bpp20DRTreeParsimonyScore16getTopologyValueEv at Base 2.4.1
  _ZTv0_n96_NK3bpp21PseudoNewtonOptimizer15PNStopCondition19getCurrentToleranceEv at Base 2.4.1
- _ZTv0_n96_NK3bpp23DRASRTreeLikelihoodData24getNumberOfDistinctSitesEv at Base 2.4.1
- _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: 2.4.1-6# _ZTv0_n96_NK3bpp23DRASRTreeLikelihoodData24getNumberOfDistinctSitesEv at Base 2.4.1
+#MISSING: 2.4.1-6# _ZTv0_n96_NK3bpp24DRASDRTreeLikelihoodData24getNumberOfDistinctSitesEv at Base 2.4.1
+#MISSING: 2.4.1-6# _ZTv0_n96_NK3bpp26TreeDrawingListenerAdapter12isAutonomousEv at Base 2.4.1
+#MISSING: 2.4.1-6# _ZTv0_n96_NK3bpp28NNIHomogeneousTreeLikelihood16getTopologyValueEv at Base 2.4.1
+#MISSING: 2.4.1-6# _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