[Debian-med-packaging] Bug#925732: libbpp-phyl: ftbfs with GCC-9

[Matthias Klose]

Package: src:libbpp-phyl
Version: 2.4.1-2
Severity: normal
Tags: sid bullseye
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-9

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-9/g++-9, but succeeds to build with gcc-8/g++-8. The
severity of this report will be raised before the bullseye release,
so nothing has to be done for the buster release.

The full build log can be found at:
http://people.debian.org/~doko/logs/gcc9-20190321/libbpp-phyl_2.4.1-2_unstable_gcc9.log
The last lines of the build log are at the end of this report.

To build with GCC 9, either set CC=gcc-9 CXX=g++-9 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-9/porting_to.html

GCC 9 also passes the linker option --as-needed by default; typical
build issues are passing libraries before object files to the linker,
or underlinking of convenience libraries built from the same source.

[...]
+#MISSING: 2.4.1-2# _ZSt10__pop_heapIN9__gnu_cxx17__normal_iteratorIP12StringAndIntSt6vectorIS2_SaIS2_EEEENS0_5__ops15_Iter_less_iterEEvT_SA_SA_RT0_ at Base 2.4.1
  _ZSt10scientificRSt8ios_base at Base 2.4.1
  _ZSt11__make_heapIN9__gnu_cxx17__normal_iteratorIP12StringAndIntSt6vectorIS2_SaIS2_EEEENS0_5__ops15_Iter_less_iterEEvT_SA_RT0_ at Base 2.4.1
  _ZSt11__make_heapIN9__gnu_cxx17__normal_iteratorIPN3bpp12SitePatterns12SortableSiteESt6vectorIS4_SaIS4_EEEENS0_5__ops15_Iter_less_iterEEvT_SC_RT0_ at Base 2.4.1
@@ -4902,7 +4927,7 @@
  _ZSt5fixedRSt8ios_base at Base 2.4.1
  _ZSt9__find_ifIN9__gnu_cxx17__normal_iteratorIPNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt6vectorIS7_SaIS7_EEEENS0_5__ops16_Iter_equals_valIKS7_EEET_SH_SH_T0_St26random_access_iterator_tag at Base 2.4.1
  _ZSt9__find_ifIN9__gnu_cxx17__normal_iteratorIPPN3bpp19TreeDrawingListenerESt6vectorIS4_SaIS4_EEEENS0_5__ops16_Iter_equals_valIKS4_EEET_SE_SE_T0_St26random_access_iterator_tag at Base 2.4.1
- _ZSt9__find_ifIN9__gnu_cxx17__normal_iteratorIPPN3bpp4NodeESt6vectorIS4_SaIS4_EEEENS0_5__ops16_Iter_equals_valIKS4_EEET_SE_SE_T0_St26random_access_iterator_tag at Base 2.4.1
+#MISSING: 2.4.1-2# _ZSt9__find_ifIN9__gnu_cxx17__normal_iteratorIPPN3bpp4NodeESt6vectorIS4_SaIS4_EEEENS0_5__ops16_Iter_equals_valIKS4_EEET_SE_SE_T0_St26random_access_iterator_tag at Base 2.4.1
  _ZSt9__find_ifIN9__gnu_cxx17__normal_iteratorIPiSt6vectorIiSaIiEEEENS0_5__ops16_Iter_equals_valIKiEEET_SB_SB_T0_St26random_access_iterator_tag 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
  _ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EEOS8_PKS5_ at Base 2.4.1
@@ -6539,6 +6564,7 @@
  _ZTch0_v0_n248_NK3bpp4MG945cloneEv at Base 2.4.1
  _ZTch0_v0_n248_NK3bpp4YN985cloneEv at Base 2.4.1
  _ZTch0_v0_n280_NK3bpp13MetaOptimizer5cloneEv at Base 2.4.1
+ _ZTch0_v0_n280_NK3bpp17BrentOneDimension5cloneEv at Base 2.4.1-2
  _ZTch0_v0_n280_NK3bpp21PseudoNewtonOptimizer5cloneEv at Base 2.4.1
  _ZTch0_v0_n40_N3bpp26RHomogeneousTreeLikelihood17getLikelihoodDataEv at Base 2.4.1
  _ZTch0_v0_n40_N3bpp27DRHomogeneousTreeLikelihood17getLikelihoodDataEv at Base 2.4.1
@@ -6566,6 +6592,7 @@
  _ZTch0_v0_n40_NK3bpp15StlOutputStream5cloneEv at Base 2.4.1
  _ZTch0_v0_n40_NK3bpp16BranchLikelihood5cloneEv at Base 2.4.1
  _ZTch0_v0_n40_NK3bpp16GCFrequenciesSet5cloneEv at Base 2.4.1
+ _ZTch0_v0_n40_NK3bpp17BrentOneDimension5cloneEv at Base 2.4.1-2
  _ZTch0_v0_n40_NK3bpp17CanonicalStateMap5cloneEv at Base 2.4.1
  _ZTch0_v0_n40_NK3bpp17MvaFrequenciesSet5cloneEv at Base 2.4.1
  _ZTch0_v0_n40_NK3bpp17OptimizationTools13ScaleFunction5cloneEv at Base 2.4.1
@@ -7190,6 +7217,7 @@
  _ZTcv0_n32_v0_n248_NK3bpp4MG945cloneEv at Base 2.4.1
  _ZTcv0_n32_v0_n248_NK3bpp4YN985cloneEv at Base 2.4.1
  _ZTcv0_n32_v0_n280_NK3bpp13MetaOptimizer5cloneEv at Base 2.4.1
+ _ZTcv0_n32_v0_n280_NK3bpp17BrentOneDimension5cloneEv at Base 2.4.1-2
  _ZTcv0_n32_v0_n280_NK3bpp21PseudoNewtonOptimizer5cloneEv at Base 2.4.1
  _ZTcv0_n32_v0_n40_NK3bpp10BppBoolean5cloneEv at Base 2.4.1
  _ZTcv0_n32_v0_n40_NK3bpp11LG10_EX_EHO13EmbeddedModel5cloneEv at Base 2.4.1
@@ -7213,6 +7241,7 @@
  _ZTcv0_n32_v0_n40_NK3bpp15StlOutputStream5cloneEv at Base 2.4.1
  _ZTcv0_n32_v0_n40_NK3bpp16BranchLikelihood5cloneEv at Base 2.4.1
  _ZTcv0_n32_v0_n40_NK3bpp16GCFrequenciesSet5cloneEv at Base 2.4.1
+ _ZTcv0_n32_v0_n40_NK3bpp17BrentOneDimension5cloneEv at Base 2.4.1-2
  _ZTcv0_n32_v0_n40_NK3bpp17CanonicalStateMap5cloneEv at Base 2.4.1
  _ZTcv0_n32_v0_n40_NK3bpp17MvaFrequenciesSet5cloneEv at Base 2.4.1
  _ZTcv0_n32_v0_n40_NK3bpp17OptimizationTools13ScaleFunction5cloneEv at Base 2.4.1
@@ -8198,10 +8227,11 @@
  _ZTv0_n24_N3bpp23FullCodonFrequenciesSetD1Ev at Base 2.4.1
  _ZTv0_n24_N3bpp23MarkovModulatedStateMapD0Ev at Base 2.4.1
  _ZTv0_n24_N3bpp23MarkovModulatedStateMapD1Ev at Base 2.4.1
- _ZTv0_n24_N3bpp23ParametersStopConditionD1Ev at Base 2.4.1
+#MISSING: 2.4.1-2# _ZTv0_n24_N3bpp23ParametersStopConditionD1Ev at Base 2.4.1
  _ZTv0_n24_N3bpp23VectorSequenceContainerD1Ev at Base 2.4.1
  _ZTv0_n24_N3bpp24BppOFrequenciesSetFormatD0Ev at Base 2.4.1
  _ZTv0_n24_N3bpp24BppOFrequenciesSetFormatD1Ev at Base 2.4.1
+ _ZTv0_n24_N3bpp24BppOParametrizableFormatD0Ev at Base 2.4.1-2
  _ZTv0_n24_N3bpp24ConstantRateDistributionD0Ev at Base 2.4.1
  _ZTv0_n24_N3bpp24ConstantRateDistributionD1Ev at Base 2.4.1
  _ZTv0_n24_N3bpp24DRASDRTreeLikelihoodDataD0Ev at Base 2.4.1
@@ -8253,7 +8283,7 @@
  _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: 2.4.1-2# _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: failing due to earlier errors
make: *** [debian/rules:10: binary-arch] Error 2
dpkg-buildpackage: error: fakeroot debian/rules binary-arch subprocess returned exit status 2