[Debian-med-packaging] Bug#906478: libbpp-phyl: FTBFS in buster/sid (dh_makeshlibs fails)

[Santiago Vila]

Package: src:libbpp-phyl
Version: 2.4.0-2
Severity: serious
Tags: ftbfs

Dear maintainer:

I tried to build this package in buster but it failed:

--------------------------------------------------------------------------------
[...]
 debian/rules build-arch
dh build-arch
   dh_update_autotools_config -a
   dh_autoreconf -a
   dh_auto_configure -a
	cd obj-x86_64-linux-gnu && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run "-GUnix Makefiles" ..
-- The CXX compiler identification is GNU 8.2.0
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- bpp-core 4.0.0 found:

[... snipped ...]

  _ZNSt8_Rb_treeImSt4pairIKmSt6vectorIiSaIiEEESt10_Select1stIS5_ESt4lessImESaIS5_EE7_M_copyINSB_11_Alloc_nodeEEEPSt13_Rb_tree_nodeIS5_EPKSF_PSt18_Rb_tree_node_baseRT_ at Base 2.4.0
@@ -4817,6 +4883,7 @@
  _ZNSt8_Rb_treeImSt4pairIKmiESt10_Select1stIS2_ESt4lessImESaIS2_EE24_M_get_insert_unique_posERS1_ at Base 2.4.0
  _ZNSt8_Rb_treeImSt4pairIKmiESt10_Select1stIS2_ESt4lessImESaIS2_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS2_ERS1_ at Base 2.4.0
  _ZNSt8_Rb_treeImSt4pairIKmiESt10_Select1stIS2_ESt4lessImESaIS2_EE8_M_eraseEPSt13_Rb_tree_nodeIS2_E at Base 2.4.0
+ _ZNSt8_Rb_treeImSt4pairIKmmESt10_Select1stIS2_ESt4lessImESaIS2_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJRS1_EESD_IJEEEEESt17_Rb_tree_iteratorIS2_ESt23_Rb_tree_const_iteratorIS2_EDpOT_ at Base 2.4.0-2
  _ZNSt8_Rb_treeImSt4pairIKmmESt10_Select1stIS2_ESt4lessImESaIS2_EE24_M_get_insert_unique_posERS1_ at Base 2.4.0
  _ZNSt8_Rb_treeImSt4pairIKmmESt10_Select1stIS2_ESt4lessImESaIS2_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS2_ERS1_ at Base 2.4.0
  _ZNSt8_Rb_treeImSt4pairIKmmESt10_Select1stIS2_ESt4lessImESaIS2_EE7_M_copyINS8_11_Alloc_nodeEEEPSt13_Rb_tree_nodeIS2_EPKSC_PSt18_Rb_tree_node_baseRT_ at Base 2.4.0
@@ -4848,15 +4915,21 @@
  _ZSt16__insertion_sortIN9__gnu_cxx17__normal_iteratorIPNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt6vectorIS7_SaIS7_EEEENS0_5__ops15_Iter_less_iterEEvT_SF_T0_ at Base 2.4.0
  _ZSt16__insertion_sortIN9__gnu_cxx17__normal_iteratorIPdSt6vectorIdSaIdEEEENS0_5__ops15_Iter_less_iterEEvT_S9_T0_ at Base 2.4.0
  _ZSt16__insertion_sortIN9__gnu_cxx17__normal_iteratorIPiSt6vectorIiSaIiEEEENS0_5__ops15_Iter_less_iterEEvT_S9_T0_ at Base 2.4.0
+ _ZSt16__introsort_loopIN9__gnu_cxx17__normal_iteratorIPdSt6vectorIdSaIdEEEElNS0_5__ops15_Iter_less_iterEEvT_S9_T0_T1_ at Base 2.4.0-2
+ _ZSt16__introsort_loopIN9__gnu_cxx17__normal_iteratorIPiSt6vectorIiSaIiEEEElNS0_5__ops15_Iter_less_iterEEvT_S9_T0_T1_ at Base 2.4.0-2
+ _ZSt22__final_insertion_sortIN9__gnu_cxx17__normal_iteratorIPiSt6vectorIiSaIiEEEENS0_5__ops15_Iter_less_iterEEvT_S9_T0_ at Base 2.4.0-2
  _ZSt25__unguarded_linear_insertIN9__gnu_cxx17__normal_iteratorIP12StringAndIntSt6vectorIS2_SaIS2_EEEENS0_5__ops14_Val_less_iterEEvT_T0_ at Base 2.4.0
  _ZSt25__unguarded_linear_insertIN9__gnu_cxx17__normal_iteratorIPN3bpp12SitePatterns12SortableSiteESt6vectorIS4_SaIS4_EEEENS0_5__ops14_Val_less_iterEEvT_T0_ at Base 2.4.0
- _ZSt4fillSt13_Bit_iteratorS_RKb at Base 2.4.0
- _ZSt4findIN9__gnu_cxx17__normal_iteratorIPPN3bpp4NodeESt6vectorIS4_SaIS4_EEEES4_ET_SA_SA_RKT0_ at Base 2.4.0
+ _ZSt25__unguarded_linear_insertIN9__gnu_cxx17__normal_iteratorIPNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt6vectorIS7_SaIS7_EEEENS0_5__ops14_Val_less_iterEEvT_T0_ at Base 2.4.0-2
+#MISSING: 2.4.0-2# _ZSt4fillSt13_Bit_iteratorS_RKb at Base 2.4.0
+#MISSING: 2.4.0-2# _ZSt4findIN9__gnu_cxx17__normal_iteratorIPPN3bpp4NodeESt6vectorIS4_SaIS4_EEEES4_ET_SA_SA_RKT0_ at Base 2.4.0
  _ZSt4swapI12StringAndIntENSt9enable_ifIXsrSt6__and_IJSt6__not_ISt15__is_tuple_likeIT_EESt21is_move_constructibleIS5_ESt18is_move_assignableIS5_EEE5valueEvE4typeERS5_SF_ at Base 2.4.0
  _ZSt5fixedRSt8ios_base at Base 2.4.0
  _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 2.4.0
  _ZSt9__find_ifIN9__gnu_cxx17__normal_iteratorIPPN3bpp19TreeDrawingListenerESt6vectorIS4_SaIS4_EEEENS0_5__ops16_Iter_equals_valIKS4_EEET_SE_SE_T0_St26random_access_iterator_tag at Base 2.4.0
- _ZSteqINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EEbRKSt6vectorIT_T0_ESC_ at Base 2.4.0
+ _ZSt9__find_ifIN9__gnu_cxx17__normal_iteratorIPPN3bpp4NodeESt6vectorIS4_SaIS4_EEEENS0_5__ops16_Iter_equals_valIKS4_EEET_SE_SE_T0_St26random_access_iterator_tag at Base 2.4.0-2
+ _ZSt9__find_ifIN9__gnu_cxx17__normal_iteratorIPiSt6vectorIiSaIiEEEENS0_5__ops16_Iter_equals_valIKiEEET_SB_SB_T0_St26random_access_iterator_tag at Base 2.4.0-2
+#MISSING: 2.4.0-2# _ZSteqINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EEbRKSt6vectorIT_T0_ESC_ at Base 2.4.0
  _ZSteqIcEN9__gnu_cxx11__enable_ifIXsrSt9__is_charIT_E7__valueEbE6__typeERKNSt7__cxx1112basic_stringIS3_St11char_traitsIS3_ESaIS3_EEESE_ at Base 2.4.0
  _ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EEOS8_PKS5_ at Base 2.4.0
  _ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EEOS8_RKS8_ at Base 2.4.0
@@ -8080,6 +8153,7 @@
  _ZTv0_n24_N3bpp16BranchLikelihoodD1Ev at Base 2.4.0
  _ZTv0_n24_N3bpp16GCFrequenciesSetD0Ev at Base 2.4.0
  _ZTv0_n24_N3bpp16GCFrequenciesSetD1Ev at Base 2.4.0
+ _ZTv0_n24_N3bpp17BrentOneDimensionD0Ev at Base 2.4.0-2
  _ZTv0_n24_N3bpp17CanonicalStateMapD0Ev at Base 2.4.0
  _ZTv0_n24_N3bpp17CanonicalStateMapD1Ev at Base 2.4.0
  _ZTv0_n24_N3bpp17MvaFrequenciesSetD0Ev at Base 2.4.0
dh_makeshlibs: failing due to earlier errors
make[1]: *** [debian/rules:15: override_dh_makeshlibs] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:10: binary-arch] Error 2
dpkg-buildpackage: error: fakeroot debian/rules binary-arch subprocess returned exit status 2
--------------------------------------------------------------------------------

The build was made with "dpkg-buildpackage -B" in my autobuilder.
Most probably, it also fails here in reproducible builds:

https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/libbpp-phyl.html

where you can get a full build log if you need it.

If this is really a bug in one of the build-depends, please use reassign and affects,
so that this is still visible in the BTS web page for this package.

Thanks.