[Debian-med-packaging] Bug#925733: libbpp-popgen: ftbfs with GCC-9

[Matthias Klose]

Package: src:libbpp-popgen
Version: 2.4.1-1
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-popgen_2.4.1-1_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.

[...]
+ _ZNK3bpp20AbstractCoreSequence7getNameB5cxx11Ev at Base 2.4.1-1
  _ZNK3bpp20AbstractOutputStream12getPrecisionEv at Base 2.4.1
  _ZNK3bpp20AbstractOutputStream27isScientificNotationEnabledEv at Base 2.4.1
  _ZNK3bpp20MapSequenceContainer20getNumberOfSequencesEv at Base 2.4.1
@@ -905,12 +909,14 @@
  _ZNKSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_PN3bpp23VectorSequenceContainerEESt10_Select1stISB_ESt4lessIS5_ESaISB_EE4findERS7_ at Base 2.4.1
  _ZNSt13_Bvector_baseISaIbEE13_M_deallocateEv at Base 2.4.1
  _ZNSt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEdSt4lessIS5_ESaISt4pairIKS5_dEEEixEOS5_ at Base 2.4.1
- _ZNSt3mapIidSt4lessIiESaISt4pairIKidEEEixEOi at Base 2.4.1
- _ZNSt3mapIidSt4lessIiESaISt4pairIKidEEEixERS3_ at Base 2.4.1
+#MISSING: 2.4.1-1# _ZNSt3mapIidSt4lessIiESaISt4pairIKidEEEixEOi at Base 2.4.1
+#MISSING: 2.4.1-1# _ZNSt3mapIidSt4lessIiESaISt4pairIKidEEEixERS3_ at Base 2.4.1
  _ZNSt5dequeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED1Ev at Base 2.4.1
  _ZNSt5dequeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED2Ev at Base 2.4.1
  _ZNSt6vectorIN3bpp19GeneMapperCsvExport6AlleleESaIS2_EE17_M_realloc_insertIJRKS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ at Base 2.4.1
  _ZNSt6vectorIN3bpp9LocusInfoESaIS1_EE17_M_realloc_insertIJS1_EEEvN9__gnu_cxx17__normal_iteratorIPS1_S3_EEDpOT_ at Base 2.4.1
+ _ZNSt6vectorIN3bpp9LocusInfoESaIS1_EED1Ev at Base 2.4.1-1
+ _ZNSt6vectorIN3bpp9LocusInfoESaIS1_EED2Ev at Base 2.4.1-1
  _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE12emplace_backIJS5_EEEvDpOT_ at Base 2.4.1
  _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE17_M_default_appendEm 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
@@ -953,7 +959,7 @@
  _ZNSt6vectorImSaImEE17_M_realloc_insertIJRKmEEEvN9__gnu_cxx17__normal_iteratorIPmS1_EEDpOT_ at Base 2.4.1
  _ZNSt6vectorImSaImEE17_M_realloc_insertIJmEEEvN9__gnu_cxx17__normal_iteratorIPmS1_EEDpOT_ at Base 2.4.1
  _ZNSt6vectorImSaImEE8_M_eraseEN9__gnu_cxx17__normal_iteratorIPmS1_EE at Base 2.4.1
- _ZNSt6vectorImSaImEE9push_backERKm at Base 2.4.1
+#MISSING: 2.4.1-1# _ZNSt6vectorImSaImEE9push_backERKm at Base 2.4.1
  _ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE12_M_constructIN9__gnu_cxx17__normal_iteratorIPcS4_EEEEvT_SA_St20forward_iterator_tag at Base 2.4.1
  _ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE12_M_constructIPKcEEvT_S8_St20forward_iterator_tag at Base 2.4.1
  _ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE12_M_constructIPcEEvT_S7_St20forward_iterator_tag at Base 2.4.1
@@ -983,6 +989,8 @@
  _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_mESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS8_ERS7_ at Base 2.4.1
  _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_mESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE8_M_eraseEPSt13_Rb_tree_nodeIS8_E at Base 2.4.1
  _ZNSt8_Rb_treeIiSt4pairIKidESt10_Select1stIS2_ESt4lessIiESaIS2_EE14_M_insert_nodeEPSt18_Rb_tree_node_baseSA_PSt13_Rb_tree_nodeIS2_E at Base 2.4.1
+ _ZNSt8_Rb_treeIiSt4pairIKidESt10_Select1stIS2_ESt4lessIiESaIS2_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJOiEESD_IJEEEEESt17_Rb_tree_iteratorIS2_ESt23_Rb_tree_const_iteratorIS2_EDpOT_ at Base 2.4.1-1
+ _ZNSt8_Rb_treeIiSt4pairIKidESt10_Select1stIS2_ESt4lessIiESaIS2_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJRS1_EESD_IJEEEEESt17_Rb_tree_iteratorIS2_ESt23_Rb_tree_const_iteratorIS2_EDpOT_ at Base 2.4.1-1
  _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_EE8_M_eraseEPSt13_Rb_tree_nodeIS2_E at Base 2.4.1
@@ -1020,7 +1028,7 @@
  _ZSt16__introsort_loopIN9__gnu_cxx17__normal_iteratorIPmSt6vectorImSaImEEEElNS0_5__ops15_Iter_less_iterEEvT_S9_T0_T1_ at Base 2.4.1
  _ZSt25__unguarded_linear_insertIN9__gnu_cxx17__normal_iteratorIPNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt6vectorIS7_SaIS7_EEEENS0_5__ops14_Val_less_iterEEvT_T0_ at Base 2.4.1
  _ZSt5fixedRSt8ios_base at Base 2.4.1
- _ZSt9__find_ifIN9__gnu_cxx17__normal_iteratorIPmSt6vectorImSaImEEEENS0_5__ops16_Iter_equals_valIKmEEET_SB_SB_T0_St26random_access_iterator_tag at Base 2.4.1
+#MISSING: 2.4.1-1# _ZSt9__find_ifIN9__gnu_cxx17__normal_iteratorIPmSt6vectorImSaImEEEENS0_5__ops16_Iter_equals_valIKmEEET_SB_SB_T0_St26random_access_iterator_tag at Base 2.4.1
  _ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EEOS8_PKS5_ at Base 2.4.1
  _ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EEPKS5_RKS8_ at Base 2.4.1
  _ZTIN3bpp10AlleleInfoE at Base 2.4.1
@@ -1287,7 +1295,7 @@
  _ZTv0_n24_N3bpp11PopgenlibIOD0Ev at Base 2.4.1
  _ZTv0_n24_N3bpp11PopgenlibIOD1Ev at Base 2.4.1
  _ZTv0_n24_N3bpp13BasicSequenceD0Ev at Base 2.4.1
- _ZTv0_n24_N3bpp13BasicSequenceD1Ev at Base 2.4.1
+#MISSING: 2.4.1-1# _ZTv0_n24_N3bpp13BasicSequenceD1Ev at Base 2.4.1
  _ZTv0_n24_N3bpp14DistanceMatrixD0Ev at Base 2.4.1
  _ZTv0_n24_N3bpp14DistanceMatrixD1Ev at Base 2.4.1
  _ZTv0_n24_N3bpp15BasicAlleleInfoD0Ev at Base 2.4.1
@@ -1341,6 +1349,7 @@
  _ZTv0_n48_NK3bpp15DarwinVarSingle20getFormatDescriptionB5cxx11Ev at Base 2.4.1
  _ZTv0_n48_NK3bpp16AbstractCoreSite11getPositionEv at Base 2.4.1
  _ZTv0_n48_NK3bpp19GeneMapperCsvExport20getFormatDescriptionB5cxx11Ev at Base 2.4.1
+ _ZTv0_n48_NK3bpp20AbstractCoreSequence7getNameB5cxx11Ev at Base 2.4.1-1
  _ZTv0_n48_NK3bpp25AbstractSequenceContainer11getAlphabetEv at Base 2.4.1
  _ZTv0_n48_NK3bpp4Site11getPositionEv at Base 2.4.1
  _ZTv0_n48_NK3bpp7Genepop20getFormatDescriptionB5cxx11Ev at Base 2.4.1
dh_makeshlibs: failing due to earlier errors
make[1]: *** [debian/rules:13: override_dh_makeshlibs] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:8: binary-arch] Error 2
dpkg-buildpackage: error: fakeroot debian/rules binary-arch subprocess returned exit status 2