[Debian-med-packaging] Bug#1012978: libgenome: ftbfs with GCC-12

Matthias Klose doko at debian.org
Thu Jun 16 13:10:57 BST 2022 

Package: src:libgenome
Version: 1.3.11+svn20110227.4616-4
Severity: normal
Tags: sid bookworm
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-12

[This bug is targeted to the upcoming bookworm 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-12/g++-12, but succeeds to build with gcc-11/g++-11. The
severity of this report will be raised before the bookworm release.

The full build log can be found at:
http://qa-logs.debian.net/2022/06/09/gcc12/libgenome_1.3.11+svn20110227.4616-4_unstable_gcc12.log
The last lines of the build log are at the end of this report.

To build with GCC 11, either set CC=gcc-11 CXX=g++-11 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-11/porting_to.html

GCC 11 defaults to the GNU++17 standard.  If your package installs
header files in /usr/include, please don't work around C++17 issues
by choosing a lower C++ standard for the package build, but fix these
issues to build with the C++17 standard.

[...]
   dh_compress
   dh_fixperms
   dh_missing
   dh_dwz -a
   dh_strip -a
   dh_makeshlibs -a
dpkg-gensymbols: warning: some new symbols appeared in the symbols file: see diff output below
dpkg-gensymbols: error: some symbols or patterns disappeared in the symbols file: see diff output below
dpkg-gensymbols: warning: debian/libgenome0/DEBIAN/symbols doesn't match completely debian/libgenome0.symbols.amd64
--- debian/libgenome0.symbols.amd64 (libgenome0_1.3.11+svn20110227.4616-4_amd64)
+++ dpkg-gensymbolsX2tVHu	2022-06-10 09:07:50.462671163 +0000
@@ -627,23 +627,23 @@
  _ZNSt12_Vector_baseIPN6genome15gnBaseQualifierESaIS2_EED1Ev at Base 1.3.11+svn20110227.4616
  _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
- _ZNSt6vectorIN6genome10gnLocationESaIS1_EE6insertEN9__gnu_cxx17__normal_iteratorIPKS1_S3_EERS6_ at Base 1.3.11+svn20110227.4616
+#MISSING: 1.3.11+svn20110227.4616-4# _ZNSt6vectorIN6genome10gnLocationESaIS1_EE6insertEN9__gnu_cxx17__normal_iteratorIPKS1_S3_EERS6_ at Base 1.3.11+svn20110227.4616
  _ZNSt6vectorIN6genome10gnLocationESaIS1_EED1Ev at Base 1.3.11+svn20110227.4616
  _ZNSt6vectorIN6genome10gnLocationESaIS1_EED2Ev at Base 1.3.11+svn20110227.4616
  _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE17_M_realloc_insertIJRKS5_EEEvN9__gnu_cxx17__normal_iteratorIPS5_S7_EEDpOT_ at Base 1.3.11+svn20110227.4616
  _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE17_M_realloc_insertIJS5_EEEvN9__gnu_cxx17__normal_iteratorIPS5_S7_EEDpOT_ at Base 1.3.11+svn20110227.4616
- _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE6insertEN9__gnu_cxx17__normal_iteratorIPKS5_S7_EERSA_ at Base 1.3.11+svn20110227.4616
- _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE8_M_eraseEN9__gnu_cxx17__normal_iteratorIPS5_S7_EE at Base 1.3.11+svn20110227.4616
+#MISSING: 1.3.11+svn20110227.4616-4# _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE6insertEN9__gnu_cxx17__normal_iteratorIPKS5_S7_EERSA_ at Base 1.3.11+svn20110227.4616
+#MISSING: 1.3.11+svn20110227.4616-4# _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
  (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
+#MISSING: 1.3.11+svn20110227.4616-4# _ZNSt6vectorIPN6genome12gnBaseHeaderESaIS2_EE6insertEN9__gnu_cxx17__normal_iteratorIPKS2_S4_EERS7_ at Base 1.3.11+svn20110227.4616
  _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
+#MISSING: 1.3.11+svn20110227.4616-4# _ZNSt6vectorIPN6genome12gnBaseSourceESaIS2_EE8_M_eraseEN9__gnu_cxx17__normal_iteratorIPS2_S4_EE 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
+#MISSING: 1.3.11+svn20110227.4616-4# _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
  _ZNSt6vectorIPN6genome12gnFileContigESaIS2_EE17_M_realloc_insertIJS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ 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
@@ -651,21 +651,22 @@
  _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
- _ZNSt6vectorIPN6genome14gnFragmentSpecESaIS2_EEaSERKS4_ at Base 1.3.11+svn20110227.4616
+#MISSING: 1.3.11+svn20110227.4616-4# _ZNSt6vectorIPN6genome14gnFragmentSpecESaIS2_EEaSERKS4_ at Base 1.3.11+svn20110227.4616
  _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
  _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
- (optional)_ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE12_M_constructIPKcEEvT_S8_St20forward_iterator_tag at Base 1.3.11+svn20110227.4616
+#MISSING: 1.3.11+svn20110227.4616-4# (optional)_ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE12_M_constructIPKcEEvT_S8_St20forward_iterator_tag at Base 1.3.11+svn20110227.4616
  _ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC1IS3_EEPKcRKS3_ at Base 1.3.11+svn20110227.4616
  _ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC2IS3_EEPKcRKS3_ 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_S5_ESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE20_Reuse_or_alloc_nodeclIRKS8_EEPSt13_Rb_tree_nodeIS8_EOT_ at Base 1.3.11+svn20110227.4616
+#MISSING: 1.3.11+svn20110227.4616-4# _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
  _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
+ _ZSt16__do_uninit_copyIPKN6genome10gnLocationEPS1_ET0_T_S6_S5_ at Base 1.3.11+svn20110227.4616-4
  _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: debian/rules binary subprocess returned exit status 2

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