[Debian-med-packaging] Bug#957442: libgenome: ftbfs with GCC-10

Fri Apr 17 12:04:20 BST 2020

Package: src:libgenome
Version: 1.3.11+svn20110227.4616-2
Severity: normal
Tags: sid bullseye
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-10

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-10/g++-10, but succeeds to build with gcc-9/g++-9. 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/gcc10-20200225/libgenome_1.3.11+svn20110227.4616-2_unstable_gcc10.log
The last lines of the build log are at the end of this report.

To build with GCC 10, either set CC=gcc-10 CXX=g++-10 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-10/porting_to.html

[...]
+ _ZNSt12_Vector_baseIPN6genome12gnFileContigESaIS2_EED2Ev at Base 1.3.11+svn20110227.4616-2
+ _ZNSt12_Vector_baseIPN6genome13gnBaseFeatureESaIS2_EED1Ev at Base 1.3.11+svn20110227.4616-2
+ _ZNSt12_Vector_baseIPN6genome13gnBaseFeatureESaIS2_EED2Ev at Base 1.3.11+svn20110227.4616-2
+ _ZNSt12_Vector_baseIPN6genome15gnBaseQualifierESaIS2_EED1Ev at Base 1.3.11+svn20110227.4616-2
+ _ZNSt12_Vector_baseIPN6genome15gnBaseQualifierESaIS2_EED2Ev at Base 1.3.11+svn20110227.4616-2
  _ZNSt6vectorIN6genome10gnLocationESaIS1_EE17_M_realloc_insertIJRKS1_EEEvN9__gnu_cxx17__normal_iteratorIPS1_S3_EEDpOT_ at Base 1.3.11+svn20110227.4616
+ _ZNSt6vectorIN6genome10gnLocationESaIS1_EE6insertEN9__gnu_cxx17__normal_iteratorIPKS1_S3_EERS6_ at Base 1.3.11+svn20110227.4616-2
  _ZNSt6vectorIN6genome10gnLocationESaIS1_EED1Ev at Base 1.3.11+svn20110227.4616
  _ZNSt6vectorIN6genome10gnLocationESaIS1_EED2Ev at Base 1.3.11+svn20110227.4616
  _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE12emplace_backIJS5_EEEvDpOT_ at Base 1.3.11+svn20110227.4616
@@ -630,20 +637,22 @@
  _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE8_M_eraseEN9__gnu_cxx17__normal_iteratorIPS5_S7_EE at Base 1.3.11+svn20110227.4616
  _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED1Ev at Base 1.3.11+svn20110227.4616
  _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED2Ev at Base 1.3.11+svn20110227.4616
- _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EEaSERKS7_ at Base 1.3.11+svn20110227.4616
+#MISSING: 1.3.11+svn20110227.4616-2# _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EEaSERKS7_ at Base 1.3.11+svn20110227.4616
  (optional)_ZNSt6vectorIPN6genome12gnBaseHeaderESaIS2_EE17_M_realloc_insertIJRKS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ at Base 1.3.11+svn20110227.4616
  (optional)_ZNSt6vectorIPN6genome12gnBaseHeaderESaIS2_EE17_M_realloc_insertIJS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ at Base 1.3.11+svn20110227.4616
+ _ZNSt6vectorIPN6genome12gnBaseHeaderESaIS2_EE6insertEN9__gnu_cxx17__normal_iteratorIPKS2_S4_EERS7_ at Base 1.3.11+svn20110227.4616-2
  _ZNSt6vectorIPN6genome12gnBaseSourceESaIS2_EE17_M_realloc_insertIJRKS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ at Base 1.3.11+svn20110227.4616
  _ZNSt6vectorIPN6genome12gnBaseSourceESaIS2_EE8_M_eraseEN9__gnu_cxx17__normal_iteratorIPS2_S4_EE at Base 1.3.11+svn20110227.4616
- (optional)_ZNSt6vectorIPN6genome12gnContigSpecESaIS2_EE13_M_insert_auxIS2_EEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEOT_ at Base 1.3.11+svn20110227.4616
+#MISSING: 1.3.11+svn20110227.4616-2# (optional)_ZNSt6vectorIPN6genome12gnContigSpecESaIS2_EE13_M_insert_auxIS2_EEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEOT_ at Base 1.3.11+svn20110227.4616
  _ZNSt6vectorIPN6genome12gnContigSpecESaIS2_EE17_M_realloc_insertIJRKS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ at Base 1.3.11+svn20110227.4616
  _ZNSt6vectorIPN6genome12gnContigSpecESaIS2_EE17_M_realloc_insertIJS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ at Base 1.3.11+svn20110227.4616
  _ZNSt6vectorIPN6genome12gnContigSpecESaIS2_EEaSERKS4_ at Base 1.3.11+svn20110227.4616
  _ZNSt6vectorIPN6genome12gnFileContigESaIS2_EE17_M_realloc_insertIJRKS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ at Base 1.3.11+svn20110227.4616
- _ZNSt6vectorIPN6genome13gnBaseFeatureESaIS2_EE12emplace_backIJS2_EEEvDpOT_ at Base 1.3.11+svn20110227.4616
+ _ZNSt6vectorIPN6genome12gnFileContigESaIS2_EE17_M_realloc_insertIJS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ at Base 1.3.11+svn20110227.4616-2
+#MISSING: 1.3.11+svn20110227.4616-2# _ZNSt6vectorIPN6genome13gnBaseFeatureESaIS2_EE12emplace_backIJS2_EEEvDpOT_ at Base 1.3.11+svn20110227.4616
  _ZNSt6vectorIPN6genome13gnBaseFeatureESaIS2_EE17_M_realloc_insertIJRKS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ at Base 1.3.11+svn20110227.4616
  (optional)_ZNSt6vectorIPN6genome13gnBaseFeatureESaIS2_EE17_M_realloc_insertIJS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ at Base 1.3.11+svn20110227.4616
- (optional)_ZNSt6vectorIPN6genome14gnFragmentSpecESaIS2_EE13_M_insert_auxIS2_EEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEOT_ at Base 1.3.11+svn20110227.4616
+#MISSING: 1.3.11+svn20110227.4616-2# (optional)_ZNSt6vectorIPN6genome14gnFragmentSpecESaIS2_EE13_M_insert_auxIS2_EEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEOT_ at Base 1.3.11+svn20110227.4616
  _ZNSt6vectorIPN6genome14gnFragmentSpecESaIS2_EE17_M_realloc_insertIJRKS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ at Base 1.3.11+svn20110227.4616
  _ZNSt6vectorIPN6genome14gnFragmentSpecESaIS2_EE17_M_realloc_insertIJS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ at Base 1.3.11+svn20110227.4616
  _ZNSt6vectorIPN6genome14gnFragmentSpecESaIS2_EE8_M_eraseEN9__gnu_cxx17__normal_iteratorIPS2_S4_EE at Base 1.3.11+svn20110227.4616
@@ -653,19 +662,21 @@
  _ZNSt6vectorIjSaIjEE17_M_realloc_insertIJRKjEEEvN9__gnu_cxx17__normal_iteratorIPjS1_EEDpOT_ at Base 1.3.11+svn20110227.4616
  _ZNSt6vectorIySaIyEE17_M_realloc_insertIJyEEEvN9__gnu_cxx17__normal_iteratorIPyS1_EEDpOT_ at Base 1.3.11+svn20110227.4616
  _ZNSt7__cxx1110_List_baseINS_12basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE8_M_clearEv at Base 1.3.11+svn20110227.4616
+ _ZNSt7__cxx1110_List_baseIPKN6genome12gnBaseFilterESaIS4_EE8_M_clearEv at Base 1.3.11+svn20110227.4616-2
  (optional)_ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE12_M_constructIPKcEEvT_S8_St20forward_iterator_tag at Base 1.3.11+svn20110227.4616
- (optional)_ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE12_M_constructIPcEEvT_S7_St20forward_iterator_tag at Base 1.3.11+svn20110227.4616
- _ZNSt7__cxx114listIPKN6genome12gnBaseFilterESaIS4_EE18_M_assign_dispatchISt20_List_const_iteratorIS4_EEEvT_SA_St12__false_type at Base 1.3.11+svn20110227.4616
+#MISSING: 1.3.11+svn20110227.4616-2# (optional)_ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE12_M_constructIPcEEvT_S7_St20forward_iterator_tag at Base 1.3.11+svn20110227.4616
+#MISSING: 1.3.11+svn20110227.4616-2# _ZNSt7__cxx114listIPKN6genome12gnBaseFilterESaIS4_EE18_M_assign_dispatchISt20_List_const_iteratorIS4_EEEvT_SA_St12__false_type at Base 1.3.11+svn20110227.4616
  _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_PN6genome12gnBaseSourceEESt10_Select1stISB_ESt4lessIS5_ESaISB_EE16_M_insert_uniqueISB_EES6_ISt17_Rb_tree_iteratorISB_EbEOT_ at Base 1.3.11+svn20110227.4616
  _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_PN6genome12gnBaseSourceEESt10_Select1stISB_ESt4lessIS5_ESaISB_EE4findERS7_ at Base 1.3.11+svn20110227.4616
- _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_PN6genome12gnBaseSourceEESt10_Select1stISB_ESt4lessIS5_ESaISB_EE8_M_eraseEPSt13_Rb_tree_nodeISB_E at Base 1.3.11+svn20110227.4616
- (optional)_ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_S5_ESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJRS7_EESJ_IJEEEEESt17_Rb_tree_iteratorIS8_ESt23_Rb_tree_const_iteratorIS8_EDpOT_ at Base 1.3.11+svn20110227.4616
+#MISSING: 1.3.11+svn20110227.4616-2# _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_PN6genome12gnBaseSourceEESt10_Select1stISB_ESt4lessIS5_ESaISB_EE8_M_eraseEPSt13_Rb_tree_nodeISB_E at Base 1.3.11+svn20110227.4616
+ _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_S5_ESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE20_Reuse_or_alloc_nodeclIRKS8_EEPSt13_Rb_tree_nodeIS8_EOT_ at Base 1.3.11+svn20110227.4616-2
+#MISSING: 1.3.11+svn20110227.4616-2# (optional)_ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_S5_ESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJRS7_EESJ_IJEEEEESt17_Rb_tree_iteratorIS8_ESt23_Rb_tree_const_iteratorIS8_EDpOT_ at Base 1.3.11+svn20110227.4616
  _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_S5_ESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE24_M_get_insert_unique_posERS7_ at Base 1.3.11+svn20110227.4616
  _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_S5_ESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS8_ERS7_ at Base 1.3.11+svn20110227.4616
- _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_S5_ESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE7_M_copyINSE_20_Reuse_or_alloc_nodeEEEPSt13_Rb_tree_nodeIS8_EPKSI_PSt18_Rb_tree_node_baseRT_ at Base 1.3.11+svn20110227.4616
- _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_S5_ESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE8_M_eraseEPSt13_Rb_tree_nodeIS8_E at Base 1.3.11+svn20110227.4616
- _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_S5_ESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EEaSERKSE_ at Base 1.3.11+svn20110227.4616
- _ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EERKS8_SA_ at Base 1.3.11+svn20110227.4616
+#MISSING: 1.3.11+svn20110227.4616-2# _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_S5_ESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE7_M_copyINSE_20_Reuse_or_alloc_nodeEEEPSt13_Rb_tree_nodeIS8_EPKSI_PSt18_Rb_tree_node_baseRT_ at Base 1.3.11+svn20110227.4616
+#MISSING: 1.3.11+svn20110227.4616-2# _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_S5_ESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE8_M_eraseEPSt13_Rb_tree_nodeIS8_E at Base 1.3.11+svn20110227.4616
+#MISSING: 1.3.11+svn20110227.4616-2# _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_S5_ESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EEaSERKSE_ at Base 1.3.11+svn20110227.4616
+#MISSING: 1.3.11+svn20110227.4616-2# _ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EERKS8_SA_ at Base 1.3.11+svn20110227.4616
  _ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EES5_RKS8_ at Base 1.3.11+svn20110227.4616
  _ZTIN6genome10gnBaseSpecE at Base 1.3.11+svn20110227.4616
  _ZTIN6genome10gnLocationE at Base 1.3.11+svn20110227.4616
dh_makeshlibs: error: failing due to earlier errors
make: *** [debian/rules:6: binary] Error 25
dpkg-buildpackage: error: fakeroot debian/rules binary subprocess returned exit status 2

