[Debian-med-packaging] Bug#1037728: libgenome: ftbfs with GCC-13

Matthias Klose doko at debian.org
Wed Jun 14 10:26:49 BST 2023 

Package: src:libgenome
Version: 1.3.11+svn20110227.4616-5
Severity: normal
Tags: sid trixie
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-13

[This bug is targeted to the upcoming trixie release]

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-13/g++-13, but succeeds to build with gcc-12/g++-12. The
severity of this report will be raised before the trixie release.

The full build log can be found at:
http://qa-logs.debian.net/2023/05/22/logs/libgenome_1.3.11+svn20110227.4616-5_unstable_gccexp.log
The last lines of the build log are at the end of this report.

To build with GCC 13, either set CC=gcc-13 CXX=g++-13 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-13/porting_to.html

[...]
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+#MISSING: 1.3.11+svn20110227.4616-5# _ZNSt12_Vector_baseIPN6genome15gnBaseQualifierESaIS2_EED1Ev at Base 1.3.11+svn20110227.4616
+#MISSING: 1.3.11+svn20110227.4616-5# _ZNSt12_Vector_baseIPN6genome15gnBaseQualifierESaIS2_EED2Ev at Base 1.3.11+svn20110227.4616
  _ZNSt6vectorIN6genome10gnLocationESaIS1_EE17_M_realloc_insertIJRKS1_EEEvN9__gnu_cxx17__normal_iteratorIPS1_S3_EEDpOT_ at Base 1.3.11+svn20110227.4616
- (optional)_ZNSt6vectorIN6genome10gnLocationESaIS1_EE6insertEN9__gnu_cxx17__normal_iteratorIPKS1_S3_EERS6_ at Base 1.3.11+svn20110227.4616
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  _ZNSt6vectorIN6genome10gnLocationESaIS1_EED1Ev at Base 1.3.11+svn20110227.4616
  _ZNSt6vectorIN6genome10gnLocationESaIS1_EED2Ev at Base 1.3.11+svn20110227.4616
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  _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE17_M_realloc_insertIJS5_EEEvN9__gnu_cxx17__normal_iteratorIPS5_S7_EEDpOT_ at Base 1.3.11+svn20110227.4616
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- (optional)_ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE8_M_eraseEN9__gnu_cxx17__normal_iteratorIPS5_S7_EE at Base 1.3.11+svn20110227.4616
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  (optional)_ZNSt6vectorIPN6genome12gnBaseHeaderESaIS2_EE17_M_realloc_insertIJS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ at Base 1.3.11+svn20110227.4616
- (optional)_ZNSt6vectorIPN6genome12gnBaseHeaderESaIS2_EE6insertEN9__gnu_cxx17__normal_iteratorIPKS2_S4_EERS7_ at Base 1.3.11+svn20110227.4616
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  _ZNSt6vectorIPN6genome12gnBaseSourceESaIS2_EE17_M_realloc_insertIJRKS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ at Base 1.3.11+svn20110227.4616
- (optional)_ZNSt6vectorIPN6genome12gnBaseSourceESaIS2_EE8_M_eraseEN9__gnu_cxx17__normal_iteratorIPS2_S4_EE at Base 1.3.11+svn20110227.4616
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  _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
- (optional)_ZNSt6vectorIPN6genome12gnContigSpecESaIS2_EEaSERKS4_ at Base 1.3.11+svn20110227.4616
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  _ZNSt6vectorIPN6genome12gnFileContigESaIS2_EE17_M_realloc_insertIJRKS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ 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
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  _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
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  _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
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  _ZNSt6vectorIPN6genome15gnBaseQualifierESaIS2_EE17_M_realloc_insertIJRKS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ at Base 1.3.11+svn20110227.4616
  _ZNSt6vectorIPN6genome15gnBaseQualifierESaIS2_EE17_M_realloc_insertIJS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ at Base 1.3.11+svn20110227.4616
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  _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
  (optional)_ZSt16__do_uninit_copyIPKN6genome10gnLocationEPS1_ET0_T_S6_S5_ at Base 1.3.11+svn20110227.4616
- _ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EES5_RKS8_ at Base 1.3.11+svn20110227.4616
+#MISSING: 1.3.11+svn20110227.4616-5# _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
  _ZTIN6genome10gnSequenceE 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: debian/rules binary subprocess returned exit status 2

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