[Debian-med-packaging] Bug#897781: libbpp-phyl-omics: ftbfs with GCC-8

Fri May 4 13:22:09 BST 2018

Package: src:libbpp-phyl-omics
Version: 2.4.0-2
Severity: normal
Tags: sid buster
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-8

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-8/g++-8, but succeeds to build with gcc-7/g++-7. The
severity of this report will be raised before the buster release.

The full build log can be found at:
http://aws-logs.debian.net/2018/05/01/gcc8/libbpp-phyl-omics_2.4.0-2_unstable_gcc8.log.gz
The last lines of the build log are at the end of this report.

To build with GCC 8, either set CC=gcc-8 CXX=g++-8 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-8/porting_to.html

[...]
  _ZNK3bpp9RowMatrixIdEclEmm at Base 2.4.0
  _ZNKSt5ctypeIcE8do_widenEc at Base 2.4.0
- _ZNKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE12_M_check_lenEmPKc at Base 2.4.0
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  _ZNKSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_PN3bpp8ClonableEESt10_Select1stISB_ESt4lessIS5_ESaISB_EE4findERS7_ at Base 2.4.0
  _ZNSt15_Sp_counted_ptrIDnLN9__gnu_cxx12_Lock_policyE2EE10_M_disposeEv at Base 2.4.0
  _ZNSt16_Sp_counted_baseILN9__gnu_cxx12_Lock_policyE2EE10_M_destroyEv at Base 2.4.0
  _ZNSt20__uninitialized_copyILb0EE13__uninit_copyIN9__gnu_cxx17__normal_iteratorIPKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt6vectorIS9_SaIS9_EEEEPS9_EET0_T_SI_SH_ at Base 2.4.0
- _ZNSt20__uninitialized_copyILb0EE13__uninit_copyISt13move_iteratorIPNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEES9_EET0_T_SC_SB_ at Base 2.4.0
+#MISSING: 2.4.0-2# _ZNSt20__uninitialized_copyILb0EE13__uninit_copyISt13move_iteratorIPNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEES9_EET0_T_SC_SB_ at Base 2.4.0
  _ZNSt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEPN3bpp10BppNumberIESt4lessIS5_ESaISt4pairIKS5_S8_EEEixERSC_ at Base 2.4.0
- _ZNSt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEPN3bpp8ClonableESt4lessIS5_ESaISt4pairIKS5_S8_EEEixERSC_ at Base 2.4.0
- _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE12emplace_backIJS5_EEEvDpOT_ at Base 2.4.0
+#MISSING: 2.4.0-2# _ZNSt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEPN3bpp8ClonableESt4lessIS5_ESaISt4pairIKS5_S8_EEEixERSC_ at Base 2.4.0
+ _ZNSt5dequeIPN3bpp8MafBlockESaIS2_EE16_M_push_back_auxIJRKS2_EEEvDpOT_ at Base 2.4.0-2
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  _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE15_M_range_insertIN9__gnu_cxx17__normal_iteratorIPKS5_S7_EEEEvNSA_IPS5_S7_EET_SG_St20forward_iterator_tag at Base 2.4.0
  _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE17_M_realloc_insertIJRKS5_EEEvN9__gnu_cxx17__normal_iteratorIPS5_S7_EEDpOT_ at Base 2.4.0
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+ _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE9push_backERKS5_ at Base 2.4.0-2
  _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED1Ev at Base 2.4.0
  _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED2Ev at Base 2.4.0
  _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EEaSERKS7_ at Base 2.4.0
  _ZNSt6vectorIPKN3bpp4NodeESaIS3_EE12emplace_backIJS3_EEEvDpOT_ at Base 2.4.0
- _ZNSt6vectorIPKN3bpp4NodeESaIS3_EE17_M_realloc_insertIJS3_EEEvN9__gnu_cxx17__normal_iteratorIPS3_S5_EEDpOT_ at Base 2.4.0
+#MISSING: 2.4.0-2# _ZNSt6vectorIPKN3bpp4NodeESaIS3_EE17_M_realloc_insertIJS3_EEEvN9__gnu_cxx17__normal_iteratorIPS3_S5_EEDpOT_ at Base 2.4.0
  _ZNSt6vectorIPN3bpp17IterationListenerESaIS2_EE17_M_realloc_insertIJRKS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ at Base 2.4.0
  _ZNSt6vectorIPN3bpp4NodeESaIS2_EE12emplace_backIJS2_EEEvDpOT_ at Base 2.4.0
- _ZNSt6vectorIPN3bpp4NodeESaIS2_EE17_M_realloc_insertIJS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ at Base 2.4.0
+#MISSING: 2.4.0-2# _ZNSt6vectorIPN3bpp4NodeESaIS2_EE17_M_realloc_insertIJS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ at Base 2.4.0
  _ZNSt6vectorIS_IdSaIdEESaIS1_EE17_M_default_appendEm at Base 2.4.0
  _ZNSt6vectorIS_IdSaIdEESaIS1_EED1Ev at Base 2.4.0
  _ZNSt6vectorIS_IdSaIdEESaIS1_EED2Ev at Base 2.4.0
  _ZNSt6vectorIiSaIiEE12emplace_backIJiEEEvDpOT_ at Base 2.4.0
+ _ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE12_M_constructIPKcEEvT_S8_St20forward_iterator_tag at Base 2.4.0-2
+ _ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE12_M_constructIPcEEvT_S7_St20forward_iterator_tag at Base 2.4.0-2
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  _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_PN3bpp10BppNumberIEESt10_Select1stISB_ESt4lessIS5_ESaISB_EE24_M_get_insert_unique_posERS7_ at Base 2.4.0
  _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_PN3bpp10BppNumberIEESt10_Select1stISB_ESt4lessIS5_ESaISB_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorISB_ERS7_ at Base 2.4.0
  _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_PN3bpp10BppNumberIEESt10_Select1stISB_ESt4lessIS5_ESaISB_EE4findERS7_ at Base 2.4.0
  _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_PN3bpp10BppNumberIEESt10_Select1stISB_ESt4lessIS5_ESaISB_EE8_M_eraseEPSt13_Rb_tree_nodeISB_E at Base 2.4.0
+ _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_PN3bpp8ClonableEESt10_Select1stISB_ESt4lessIS5_ESaISB_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJRS7_EESM_IJEEEEESt17_Rb_tree_iteratorISB_ESt23_Rb_tree_const_iteratorISB_EDpOT_ at Base 2.4.0-2
  _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_PN3bpp8ClonableEESt10_Select1stISB_ESt4lessIS5_ESaISB_EE24_M_get_insert_unique_posERS7_ at Base 2.4.0
  _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_PN3bpp8ClonableEESt10_Select1stISB_ESt4lessIS5_ESaISB_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorISB_ERS7_ at Base 2.4.0
  _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_PN3bpp8ClonableEESt10_Select1stISB_ESt4lessIS5_ESaISB_EE4findERS7_ 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