[Debian-med-packaging] Bug#1012992: libseqlib: ftbfs with GCC-12

Thu Jun 16 13:11:24 BST 2022

Package: src:libseqlib
Version: 1.2.0+dfsg-8
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/libseqlib_1.2.0+dfsg-8_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.

[...]
  _ZNSt8__detail9_CompilerINSt7__cxx1112regex_traitsIcEEE25_M_insert_bracket_matcherILb0ELb0EEEvb at Base 1.2.0
  _ZNSt8__detail9_CompilerINSt7__cxx1112regex_traitsIcEEE25_M_insert_bracket_matcherILb0ELb1EEEvb at Base 1.2.0
@@ -504,6 +524,7 @@
  _ZNSt8__detail9_CompilerINSt7__cxx1112regex_traitsIcEEEC2EPKcS6_RKSt6localeNSt15regex_constants18syntax_option_typeE at Base 1.2.0
  _ZNSt8__detail9_ExecutorIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS5_9sub_matchISB_EEENS5_12regex_traitsIcEELb0EE12_M_lookaheadEl at Base 1.2.0
  _ZNSt8__detail9_ExecutorIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS5_9sub_matchISB_EEENS5_12regex_traitsIcEELb0EE16_M_rep_once_moreENSH_11_Match_modeEl at Base 1.2.0
+ _ZNSt8__detail9_ExecutorIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS5_9sub_matchISB_EEENS5_12regex_traitsIcEELb0EE17_M_handle_backrefENSH_11_Match_modeEl at Base 1.2.0+dfsg-8
  _ZNSt8__detail9_ExecutorIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS5_9sub_matchISB_EEENS5_12regex_traitsIcEELb0EE6_M_dfsENSH_11_Match_modeEl at Base 1.2.0
  _ZNSt8__detail9_ExecutorIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS5_9sub_matchISB_EEENS5_12regex_traitsIcEELb0EEC1ESB_SB_RSt6vectorISD_SE_ERKNS5_11basic_regexIcSG_EENSt15regex_constants15match_flag_typeE at Base 1.2.0
  _ZNSt8__detail9_ExecutorIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS5_9sub_matchISB_EEENS5_12regex_traitsIcEELb0EEC2ESB_SB_RSt6vectorISD_SE_ERKNS5_11basic_regexIcSG_EENSt15regex_constants15match_flag_typeE at Base 1.2.0
@@ -523,6 +544,10 @@
  (optional)_ZSt13__adjust_heapIN9__gnu_cxx17__normal_iteratorIPN12aho_corasick7ahoemitIcEESt6vectorIS4_SaIS4_EEEElS4_NS0_5__ops15_Iter_comp_iterIZNS2_13interval_treeIS4_E15remove_overlapsERKS8_EUlRKS4_SH_E_EEEvT_T0_SL_T1_T2_ at Base 1.2.0
  (optional)_ZSt13__heap_selectIN9__gnu_cxx17__normal_iteratorIPN6SeqLib13GenomicRegionESt6vectorIS3_SaIS3_EEEENS0_5__ops15_Iter_less_iterEEvT_SB_SB_T0_ at Base 1.2.0
  (optional)_ZSt13binary_searchIN9__gnu_cxx17__normal_iteratorIPKcSt6vectorIcSaIcEEEEcEbT_S8_RKT0_ at Base 1.2.0
+ _ZSt16__do_uninit_copyIN9__gnu_cxx17__normal_iteratorIPKN12aho_corasick7ahoemitIcEESt6vectorIS4_SaIS4_EEEEPS4_ET0_T_SD_SC_ at Base 1.2.0+dfsg-8
+ _ZSt16__do_uninit_copyIPKN6SeqLib13GenomicRegionEPS1_ET0_T_S6_S5_ at Base 1.2.0+dfsg-8
+ _ZSt16__do_uninit_copyIPKN6SeqLib6Filter10ReadFilterEPS2_ET0_T_S7_S6_ at Base 1.2.0+dfsg-8
+ _ZSt16__do_uninit_copyIPKN6SeqLib6Filter12AbstractRuleEPS2_ET0_T_S7_S6_ at Base 1.2.0+dfsg-8
  (optional)_ZSt16__insertion_sortIN9__gnu_cxx17__normal_iteratorIP9mem_aln_tSt6vectorIS2_SaIS2_EEEENS0_5__ops15_Iter_comp_iterIPFbRKS2_SB_EEEEvT_SF_T0_ at Base 1.2.0
  (optional)_ZSt16__insertion_sortIN9__gnu_cxx17__normal_iteratorIPN12aho_corasick7ahoemitIcEESt6vectorIS4_SaIS4_EEEENS0_5__ops15_Iter_comp_iterIZNS2_13interval_treeIS4_E15remove_overlapsERKS8_EUlRKS4_SH_E_EEEvT_SK_T0_ at Base 1.2.0
  (optional)_ZSt16__introsort_loopIN9__gnu_cxx17__normal_iteratorIP9mem_aln_tSt6vectorIS2_SaIS2_EEEElNS0_5__ops15_Iter_comp_iterIPFbRKS2_SB_EEEEvT_SF_T0_T1_ at Base 1.2.0
@@ -534,7 +559,7 @@
  (optional)_ZSt4findIN9__gnu_cxx17__normal_iteratorIPKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt6vectorIS7_SaIS7_EEEES7_ET_SE_SE_RKT0_ at Base 1.2.0
  _ZSt4swapIN12aho_corasick7ahoemitIcEEENSt9enable_ifIXsrSt6__and_IJSt6__not_ISt15__is_tuple_likeIT_EESt21is_move_constructibleIS7_ESt18is_move_assignableIS7_EEE5valueEvE4typeERS7_SH_ at Base 1.2.0
  (optional)_ZSt4swapIN6SeqLib11PlottedReadEENSt9enable_ifIXsrSt6__and_IJSt6__not_ISt15__is_tuple_likeIT_EESt21is_move_constructibleIS6_ESt18is_move_assignableIS6_EEE5valueEvE4typeERS6_SG_ at Base 1.2.0
- (optional)_ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EEOS8_PKS5_ at Base 1.2.0
+#MISSING: 1.2.0+dfsg-8# (optional)_ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EEOS8_PKS5_ at Base 1.2.0
  _ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EEOS8_S9_ at Base 1.2.0
  _ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EEPKS5_RKS8_ at Base 1.2.0
  _ZTINSt8__detail11_AnyMatcherINSt7__cxx1112regex_traitsIcEELb0ELb0ELb0EEE at Base 1.2.0
@@ -564,7 +589,8 @@
  (optional)_ZTISt19_Sp_counted_deleterIP9hts_idx_t10idx_deleteSaIvELN9__gnu_cxx12_Lock_policyE2EE at Base 1.2.0
  (optional)_ZTISt19_Sp_counted_deleterIP9hts_itr_t14hts_itr_deleteSaIvELN9__gnu_cxx12_Lock_policyE2EE at Base 1.2.0
  (optional)_ZTISt19_Sp_counted_deleterIP9sam_hdr_t14bam_hdr_deleteSaIvELN9__gnu_cxx12_Lock_policyE2EE at Base 1.2.0
- (optional)_ZTISt23_Sp_counted_ptr_inplaceINSt8__detail4_NFAINSt7__cxx1112regex_traitsIcEEEESaIS5_ELN9__gnu_cxx12_Lock_policyE2EE at Base 1.2.0
+#MISSING: 1.2.0+dfsg-8# (optional)_ZTISt23_Sp_counted_ptr_inplaceINSt8__detail4_NFAINSt7__cxx1112regex_traitsIcEEEESaIS5_ELN9__gnu_cxx12_Lock_policyE2EE at Base 1.2.0
+ _ZTISt23_Sp_counted_ptr_inplaceINSt8__detail4_NFAINSt7__cxx1112regex_traitsIcEEEESaIvELN9__gnu_cxx12_Lock_policyE2EE at Base 1.2.0+dfsg-8
  _ZTS10idx_delete at Base 1.2.0
  _ZTS14bam_hdr_delete at Base 1.2.0
  _ZTS14htsFile_delete at Base 1.2.0
@@ -598,7 +624,8 @@
  (optional)_ZTSSt19_Sp_counted_deleterIP9hts_itr_t14hts_itr_deleteSaIvELN9__gnu_cxx12_Lock_policyE2EE at Base 1.2.0
  (optional)_ZTSSt19_Sp_counted_deleterIP9sam_hdr_t14bam_hdr_deleteSaIvELN9__gnu_cxx12_Lock_policyE2EE at Base 1.2.0
  _ZTSSt19_Sp_make_shared_tag at Base 1.2.0
- (optional)_ZTSSt23_Sp_counted_ptr_inplaceINSt8__detail4_NFAINSt7__cxx1112regex_traitsIcEEEESaIS5_ELN9__gnu_cxx12_Lock_policyE2EE at Base 1.2.0
+#MISSING: 1.2.0+dfsg-8# (optional)_ZTSSt23_Sp_counted_ptr_inplaceINSt8__detail4_NFAINSt7__cxx1112regex_traitsIcEEEESaIS5_ELN9__gnu_cxx12_Lock_policyE2EE at Base 1.2.0
+ _ZTSSt23_Sp_counted_ptr_inplaceINSt8__detail4_NFAINSt7__cxx1112regex_traitsIcEEEESaIvELN9__gnu_cxx12_Lock_policyE2EE at Base 1.2.0+dfsg-8
  (optional)_ZTVSt15_Sp_counted_ptrIPN12aho_corasick10basic_trieIcEELN9__gnu_cxx12_Lock_policyE2EE at Base 1.2.0
  (optional)_ZTVSt15_Sp_counted_ptrIPSt13unordered_mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiSt4hashIS6_ESt8equal_toIS6_ESaISt4pairIKS6_iEEELN9__gnu_cxx12_Lock_policyE2EE at Base 1.2.0
  (optional)_ZTVSt15_Sp_counted_ptrIPSt13unordered_mapIiN6SeqLib13TIntervalTreeIimEESt4hashIiESt8equal_toIiESaISt4pairIKiS3_EEELN9__gnu_cxx12_Lock_policyE2EE at Base 1.2.0
@@ -608,13 +635,15 @@
  (optional)_ZTVSt19_Sp_counted_deleterIP9hts_idx_t10idx_deleteSaIvELN9__gnu_cxx12_Lock_policyE2EE at Base 1.2.0
  (optional)_ZTVSt19_Sp_counted_deleterIP9hts_itr_t14hts_itr_deleteSaIvELN9__gnu_cxx12_Lock_policyE2EE at Base 1.2.0
  (optional)_ZTVSt19_Sp_counted_deleterIP9sam_hdr_t14bam_hdr_deleteSaIvELN9__gnu_cxx12_Lock_policyE2EE at Base 1.2.0
- (optional)_ZTVSt23_Sp_counted_ptr_inplaceINSt8__detail4_NFAINSt7__cxx1112regex_traitsIcEEEESaIS5_ELN9__gnu_cxx12_Lock_policyE2EE at Base 1.2.0
+#MISSING: 1.2.0+dfsg-8# (optional)_ZTVSt23_Sp_counted_ptr_inplaceINSt8__detail4_NFAINSt7__cxx1112regex_traitsIcEEEESaIS5_ELN9__gnu_cxx12_Lock_policyE2EE at Base 1.2.0
+ _ZTVSt23_Sp_counted_ptr_inplaceINSt8__detail4_NFAINSt7__cxx1112regex_traitsIcEEEESaIvELN9__gnu_cxx12_Lock_policyE2EE at Base 1.2.0+dfsg-8
  _ZZNKSt7__cxx1112regex_traitsIcE16lookup_classnameIPKcEENS1_10_RegexMaskET_S6_bE12__classnames at Base 1.2.0
  _ZZNKSt7__cxx1112regex_traitsIcE18lookup_collatenameIPKcEENS_12basic_stringIcSt11char_traitsIcESaIcEEET_SA_E14__collatenames at Base 1.2.0
  _ZZNKSt8__detail11_AnyMatcherINSt7__cxx1112regex_traitsIcEELb0ELb0ELb0EEclEcE5__nul at Base 1.2.0
  _ZZNKSt8__detail11_AnyMatcherINSt7__cxx1112regex_traitsIcEELb0ELb0ELb1EEclEcE5__nul at Base 1.2.0
  _ZZNKSt8__detail11_AnyMatcherINSt7__cxx1112regex_traitsIcEELb0ELb1ELb0EEclEcE5__nul at Base 1.2.0
  _ZZNKSt8__detail11_AnyMatcherINSt7__cxx1112regex_traitsIcEELb0ELb1ELb1EEclEcE5__nul at Base 1.2.0
+ _ZZNKSt8__detail15_BracketMatcherINSt7__cxx1112regex_traitsIcEELb0ELb0EE8_M_applyEcSt17integral_constantIbLb0EEENKUlvE_clEv at Base 1.2.0+dfsg-8
  (optional)_ZZNKSt8__detail15_BracketMatcherINSt7__cxx1112regex_traitsIcEELb0ELb1EE8_M_applyEcSt17integral_constantIbLb0EEENKUlvE_clEv at Base 1.2.0
  (optional)_ZZNKSt8__detail15_BracketMatcherINSt7__cxx1112regex_traitsIcEELb1ELb0EE8_M_applyEcSt17integral_constantIbLb0EEENKUlvE_clEv at Base 1.2.0
  (optional)_ZZNKSt8__detail15_BracketMatcherINSt7__cxx1112regex_traitsIcEELb1ELb1EE8_M_applyEcSt17integral_constantIbLb0EEENKUlvE_clEv at Base 1.2.0
dh_makeshlibs: error: failing due to earlier errors
make: *** [debian/rules:10: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2

