[Debian-med-packaging] Bug#984210: libseqlib: ftbfs with GCC-11

Wed Mar 3 16:14:59 GMT 2021

Package: src:libseqlib
Version: 1.2.0+dfsg-4
Severity: normal
Tags: sid bookworm
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-11

[This bug is not targeted to the upcoming bullseye 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-11/g++-11, but succeeds to build with gcc-10/g++-10. The
severity of this report will be raised before the bookworm release,
so nothing has to be done for the bullseye release.

The full build log can be found at:
http://people.debian.org/~doko/logs/20210228/filtered/gcc11/libseqlib_1.2.0+dfsg-4_unstable_gcc11.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.

[...]
- (optional)_ZTI10idx_delete at Base 1.2.0
- (optional)_ZTI14bam_hdr_delete at Base 1.2.0
- (optional)_ZTI14htsFile_delete at Base 1.2.0
- (optional)_ZTI14hts_itr_delete at Base 1.2.0
- (optional)_ZTIN6SeqLib11free_deleteE at Base 1.2.0
+#MISSING: 1.2.0+dfsg-4# (optional)_ZTI10idx_delete at Base 1.2.0
+#MISSING: 1.2.0+dfsg-4# (optional)_ZTI14bam_hdr_delete at Base 1.2.0
+#MISSING: 1.2.0+dfsg-4# (optional)_ZTI14htsFile_delete at Base 1.2.0
+#MISSING: 1.2.0+dfsg-4# (optional)_ZTI14hts_itr_delete at Base 1.2.0
+#MISSING: 1.2.0+dfsg-4# (optional)_ZTIN6SeqLib11free_deleteE at Base 1.2.0
  _ZTINSt8__detail11_AnyMatcherINSt7__cxx1112regex_traitsIcEELb0ELb0ELb0EEE at Base 1.2.0
  _ZTINSt8__detail11_AnyMatcherINSt7__cxx1112regex_traitsIcEELb0ELb0ELb1EEE at Base 1.2.0
  _ZTINSt8__detail11_AnyMatcherINSt7__cxx1112regex_traitsIcEELb0ELb1ELb0EEE at Base 1.2.0
@@ -666,7 +669,7 @@
  (optional)_ZTISt11_Mutex_baseILN9__gnu_cxx12_Lock_policyE2EE at Base 1.2.0
  (optional)_ZTISt15_Sp_counted_ptrIPN12aho_corasick10basic_trieIcEELN9__gnu_cxx12_Lock_policyE2EE at Base 1.2.0
  (optional)_ZTISt15_Sp_counted_ptrIPSt13unordered_mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiSt4hashIS6_ESt8equal_toIS6_ESaISt4pairIKS6_iEEELN9__gnu_cxx12_Lock_policyE2EE at Base 1.2.0
- (optional)_ZTISt15_Sp_counted_ptrIPSt13unordered_mapIiN6SeqLib13TIntervalTreeIijEESt4hashIiESt8equal_toIiESaISt4pairIKiS3_EEELN9__gnu_cxx12_Lock_policyE2EE at Base 1.2.0
+#MISSING: 1.2.0+dfsg-4# (optional)_ZTISt15_Sp_counted_ptrIPSt13unordered_mapIiN6SeqLib13TIntervalTreeIijEESt4hashIiESt8equal_toIiESaISt4pairIKiS3_EEELN9__gnu_cxx12_Lock_policyE2EE at Base 1.2.0
  (optional)_ZTISt15_Sp_counted_ptrIPSt13unordered_mapIiN6SeqLib13TIntervalTreeIimEESt4hashIiESt8equal_toIiESaISt4pairIKiS3_EEELN9__gnu_cxx12_Lock_policyE2EE at Base 1.2.0
  (optional)_ZTISt15_Sp_counted_ptrIPSt6vectorIN6SeqLib13GenomicRegionESaIS2_EELN9__gnu_cxx12_Lock_policyE2EE at Base 1.2.0
  (optional)_ZTISt16_Sp_counted_baseILN9__gnu_cxx12_Lock_policyE2EE at Base 1.2.0
@@ -675,7 +678,7 @@
  (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)_ZTISt19_Sp_make_shared_tag at Base 1.2.0
+#MISSING: 1.2.0+dfsg-4# (optional)_ZTISt19_Sp_make_shared_tag 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
  _ZTS10idx_delete at Base 1.2.0
  _ZTS14bam_hdr_delete at Base 1.2.0
@@ -701,7 +704,7 @@
  (optional)_ZTSSt11_Mutex_baseILN9__gnu_cxx12_Lock_policyE2EE at Base 1.2.0
  (optional)_ZTSSt15_Sp_counted_ptrIPN12aho_corasick10basic_trieIcEELN9__gnu_cxx12_Lock_policyE2EE at Base 1.2.0
  (optional)_ZTSSt15_Sp_counted_ptrIPSt13unordered_mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiSt4hashIS6_ESt8equal_toIS6_ESaISt4pairIKS6_iEEELN9__gnu_cxx12_Lock_policyE2EE at Base 1.2.0
- (optional)_ZTSSt15_Sp_counted_ptrIPSt13unordered_mapIiN6SeqLib13TIntervalTreeIijEESt4hashIiESt8equal_toIiESaISt4pairIKiS3_EEELN9__gnu_cxx12_Lock_policyE2EE at Base 1.2.0
+#MISSING: 1.2.0+dfsg-4# (optional)_ZTSSt15_Sp_counted_ptrIPSt13unordered_mapIiN6SeqLib13TIntervalTreeIijEESt4hashIiESt8equal_toIiESaISt4pairIKiS3_EEELN9__gnu_cxx12_Lock_policyE2EE at Base 1.2.0
  (optional)_ZTSSt15_Sp_counted_ptrIPSt13unordered_mapIiN6SeqLib13TIntervalTreeIimEESt4hashIiESt8equal_toIiESaISt4pairIKiS3_EEELN9__gnu_cxx12_Lock_policyE2EE at Base 1.2.0
  (optional)_ZTSSt15_Sp_counted_ptrIPSt6vectorIN6SeqLib13GenomicRegionESaIS2_EELN9__gnu_cxx12_Lock_policyE2EE at Base 1.2.0
  (optional)_ZTSSt16_Sp_counted_baseILN9__gnu_cxx12_Lock_policyE2EE at Base 1.2.0
@@ -714,7 +717,7 @@
  (optional)_ZTSSt23_Sp_counted_ptr_inplaceINSt8__detail4_NFAINSt7__cxx1112regex_traitsIcEEEESaIS5_ELN9__gnu_cxx12_Lock_policyE2EE at Base 1.2.0
  (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_mapIiN6SeqLib13TIntervalTreeIijEESt4hashIiESt8equal_toIiESaISt4pairIKiS3_EEELN9__gnu_cxx12_Lock_policyE2EE at Base 1.2.0
+#MISSING: 1.2.0+dfsg-4# (optional)_ZTVSt15_Sp_counted_ptrIPSt13unordered_mapIiN6SeqLib13TIntervalTreeIijEESt4hashIiESt8equal_toIiESaISt4pairIKiS3_EEELN9__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
  (optional)_ZTVSt15_Sp_counted_ptrIPSt6vectorIN6SeqLib13GenomicRegionESaIS2_EELN9__gnu_cxx12_Lock_policyE2EE at Base 1.2.0
  (optional)_ZTVSt19_Sp_counted_deleterIP6bam1_tN6SeqLib11free_deleteESaIvELN9__gnu_cxx12_Lock_policyE2EE at Base 1.2.0
@@ -735,10 +738,10 @@
  _ZZNKSt8__detail9_ExecutorIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS5_9sub_matchISB_EEENS5_12regex_traitsIcEELb0EE10_M_is_wordEcE3__s at Base 1.2.0
  _ZZNKSt8__detail9_ExecutorIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS5_9sub_matchISB_EEENS5_12regex_traitsIcEELb1EE10_M_is_wordEcE3__s at Base 1.2.0
  _ZZNSt19_Sp_make_shared_tag5_S_tiEvE5__tag at Base 1.2.0
- (optional)_ZZNSt8__detail9_CompilerINSt7__cxx1112regex_traitsIcEEE13_M_quantifierEvENKUlvE_clEv at Base 1.2.0
- (optional)_ZZNSt8__detail9_CompilerINSt7__cxx1112regex_traitsIcEEE18_M_expression_termILb0ELb0EEEbRSt4pairIbcERNS_15_BracketMatcherIS3_XT_EXT0_EEEENKUlcE_clEc at Base 1.2.0
- (optional)_ZZNSt8__detail9_CompilerINSt7__cxx1112regex_traitsIcEEE18_M_expression_termILb0ELb1EEEbRSt4pairIbcERNS_15_BracketMatcherIS3_XT_EXT0_EEEENKUlcE_clEc at Base 1.2.0
- (optional)_ZZNSt8__detail9_CompilerINSt7__cxx1112regex_traitsIcEEE18_M_expression_termILb1ELb0EEEbRSt4pairIbcERNS_15_BracketMatcherIS3_XT_EXT0_EEEENKUlcE_clEc at Base 1.2.0
- (optional)_ZZNSt8__detail9_CompilerINSt7__cxx1112regex_traitsIcEEE18_M_expression_termILb1ELb0EEEbRSt4pairIbcERNS_15_BracketMatcherIS3_XT_EXT0_EEEENKUlvE0_clEv at Base 1.2.0
- (optional)_ZZNSt8__detail9_CompilerINSt7__cxx1112regex_traitsIcEEE18_M_expression_termILb1ELb1EEEbRSt4pairIbcERNS_15_BracketMatcherIS3_XT_EXT0_EEEENKUlcE_clEc at Base 1.2.0
- (optional)_ZZNSt8__detail9_CompilerINSt7__cxx1112regex_traitsIcEEE18_M_expression_termILb1ELb1EEEbRSt4pairIbcERNS_15_BracketMatcherIS3_XT_EXT0_EEEENKUlvE0_clEv at Base 1.2.0
+#MISSING: 1.2.0+dfsg-4# (optional)_ZZNSt8__detail9_CompilerINSt7__cxx1112regex_traitsIcEEE13_M_quantifierEvENKUlvE_clEv at Base 1.2.0
+#MISSING: 1.2.0+dfsg-4# (optional)_ZZNSt8__detail9_CompilerINSt7__cxx1112regex_traitsIcEEE18_M_expression_termILb0ELb0EEEbRSt4pairIbcERNS_15_BracketMatcherIS3_XT_EXT0_EEEENKUlcE_clEc at Base 1.2.0
+#MISSING: 1.2.0+dfsg-4# (optional)_ZZNSt8__detail9_CompilerINSt7__cxx1112regex_traitsIcEEE18_M_expression_termILb0ELb1EEEbRSt4pairIbcERNS_15_BracketMatcherIS3_XT_EXT0_EEEENKUlcE_clEc at Base 1.2.0
+#MISSING: 1.2.0+dfsg-4# (optional)_ZZNSt8__detail9_CompilerINSt7__cxx1112regex_traitsIcEEE18_M_expression_termILb1ELb0EEEbRSt4pairIbcERNS_15_BracketMatcherIS3_XT_EXT0_EEEENKUlcE_clEc at Base 1.2.0
+#MISSING: 1.2.0+dfsg-4# (optional)_ZZNSt8__detail9_CompilerINSt7__cxx1112regex_traitsIcEEE18_M_expression_termILb1ELb0EEEbRSt4pairIbcERNS_15_BracketMatcherIS3_XT_EXT0_EEEENKUlvE0_clEv at Base 1.2.0
+#MISSING: 1.2.0+dfsg-4# (optional)_ZZNSt8__detail9_CompilerINSt7__cxx1112regex_traitsIcEEE18_M_expression_termILb1ELb1EEEbRSt4pairIbcERNS_15_BracketMatcherIS3_XT_EXT0_EEEENKUlcE_clEc at Base 1.2.0
+#MISSING: 1.2.0+dfsg-4# (optional)_ZZNSt8__detail9_CompilerINSt7__cxx1112regex_traitsIcEEE18_M_expression_termILb1ELb1EEEbRSt4pairIbcERNS_15_BracketMatcherIS3_XT_EXT0_EEEENKUlvE0_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

