[Debian-med-packaging] Bug#1037722: libbpp-seq-omics: ftbfs with GCC-13

[Matthias Klose]

Package: src:libbpp-seq-omics
Version: 2.4.1-9
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/libbpp-seq-omics_2.4.1-9_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

[...]
  _ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC2IS3_EEPKcRKS3_ at Base 2.4.1
  _ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED0Ev at Base 2.4.1
@@ -568,33 +585,33 @@
  _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_jESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE24_M_get_insert_unique_posERS7_ at Base 2.4.1
  _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_jESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS8_ERS7_ at Base 2.4.1
  _ZNSt8_Rb_treeIPN3bpp5RangeImEES3_St9_IdentityIS3_ENS0_10rangeComp_ImEESaIS3_EE16_M_insert_uniqueIS3_EESt4pairISt17_Rb_tree_iteratorIS3_EbEOT_ at Base 2.4.1
- _ZNSt8_Rb_treeIPN3bpp5RangeImEES3_St9_IdentityIS3_ENS0_10rangeComp_ImEESaIS3_EE24_M_get_insert_unique_posERKS3_ at Base 2.4.1
- _ZNSt8_Rb_treeIPN3bpp5RangeImEES3_St9_IdentityIS3_ENS0_10rangeComp_ImEESaIS3_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS3_ERKS3_ at Base 2.4.1
- _ZNSt8_Rb_treeIcSt4pairIKcSt3mapImS2_ImmSt4lessImESaIS0_IKmmEEES4_SaIS0_IS5_S8_EEEESt10_Select1stISC_ES3_IcESaISC_EE24_M_get_insert_unique_posERS1_ at Base 2.4.1
- _ZNSt8_Rb_treeIcSt4pairIKcSt3mapImS2_ImmSt4lessImESaIS0_IKmmEEES4_SaIS0_IS5_S8_EEEESt10_Select1stISC_ES3_IcESaISC_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorISC_ERS1_ at Base 2.4.1
- _ZNSt8_Rb_treeIiSt4pairIKiNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEESt10_Select1stIS8_ESt4lessIiESaIS8_EE24_M_get_insert_unique_posERS1_ at Base 2.4.1
- _ZNSt8_Rb_treeIiSt4pairIKiNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEESt10_Select1stIS8_ESt4lessIiESaIS8_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS8_ERS1_ at Base 2.4.1
- _ZNSt8_Rb_treeIiSt4pairIKidESt10_Select1stIS2_ESt4lessIiESaIS2_EE24_M_get_insert_unique_posERS1_ at Base 2.4.1
- _ZNSt8_Rb_treeIiSt4pairIKidESt10_Select1stIS2_ESt4lessIiESaIS2_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS2_ERS1_ at Base 2.4.1
- _ZNSt8_Rb_treeIiSt4pairIKiiESt10_Select1stIS2_ESt4lessIiESaIS2_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJRS1_EESD_IJEEEEESt17_Rb_tree_iteratorIS2_ESt23_Rb_tree_const_iteratorIS2_EDpOT_ at Base 2.4.1
- _ZNSt8_Rb_treeIiSt4pairIKiiESt10_Select1stIS2_ESt4lessIiESaIS2_EE24_M_get_insert_unique_posERS1_ at Base 2.4.1
- _ZNSt8_Rb_treeIiSt4pairIKiiESt10_Select1stIS2_ESt4lessIiESaIS2_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS2_ERS1_ at Base 2.4.1
- _ZNSt8_Rb_treeIiSt4pairIKijESt10_Select1stIS2_ESt4lessIiESaIS2_EE24_M_get_insert_unique_posERS1_ at Base 2.4.1
- _ZNSt8_Rb_treeIiSt4pairIKijESt10_Select1stIS2_ESt4lessIiESaIS2_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS2_ERS1_ at Base 2.4.1
- _ZNSt8_Rb_treeIiSt4pairIKimESt10_Select1stIS2_ESt4lessIiESaIS2_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJRS1_EESD_IJEEEEESt17_Rb_tree_iteratorIS2_ESt23_Rb_tree_const_iteratorIS2_EDpOT_ at Base 2.4.1
- _ZNSt8_Rb_treeIiSt4pairIKimESt10_Select1stIS2_ESt4lessIiESaIS2_EE24_M_get_insert_unique_posERS1_ at Base 2.4.1
- _ZNSt8_Rb_treeIiSt4pairIKimESt10_Select1stIS2_ESt4lessIiESaIS2_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS2_ERS1_ at Base 2.4.1
- _ZNSt8_Rb_treeImSt4pairIKmSt3mapImmSt4lessImESaIS0_IS1_mEEEESt10_Select1stIS8_ES4_SaIS8_EE24_M_get_insert_unique_posERS1_ at Base 2.4.1
- _ZNSt8_Rb_treeImSt4pairIKmSt3mapImmSt4lessImESaIS0_IS1_mEEEESt10_Select1stIS8_ES4_SaIS8_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS8_ERS1_ at Base 2.4.1
- _ZNSt8_Rb_treeImSt4pairIKmmESt10_Select1stIS2_ESt4lessImESaIS2_EE24_M_get_insert_unique_posERS1_ at Base 2.4.1
- _ZNSt8_Rb_treeImSt4pairIKmmESt10_Select1stIS2_ESt4lessImESaIS2_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS2_ERS1_ at Base 2.4.1
+#MISSING: 2.4.1-9# _ZNSt8_Rb_treeIPN3bpp5RangeImEES3_St9_IdentityIS3_ENS0_10rangeComp_ImEESaIS3_EE24_M_get_insert_unique_posERKS3_ at Base 2.4.1
+#MISSING: 2.4.1-9# _ZNSt8_Rb_treeIPN3bpp5RangeImEES3_St9_IdentityIS3_ENS0_10rangeComp_ImEESaIS3_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS3_ERKS3_ at Base 2.4.1
+#MISSING: 2.4.1-9# _ZNSt8_Rb_treeIcSt4pairIKcSt3mapImS2_ImmSt4lessImESaIS0_IKmmEEES4_SaIS0_IS5_S8_EEEESt10_Select1stISC_ES3_IcESaISC_EE24_M_get_insert_unique_posERS1_ at Base 2.4.1
+#MISSING: 2.4.1-9# _ZNSt8_Rb_treeIcSt4pairIKcSt3mapImS2_ImmSt4lessImESaIS0_IKmmEEES4_SaIS0_IS5_S8_EEEESt10_Select1stISC_ES3_IcESaISC_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorISC_ERS1_ at Base 2.4.1
+#MISSING: 2.4.1-9# _ZNSt8_Rb_treeIiSt4pairIKiNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEESt10_Select1stIS8_ESt4lessIiESaIS8_EE24_M_get_insert_unique_posERS1_ at Base 2.4.1
+#MISSING: 2.4.1-9# _ZNSt8_Rb_treeIiSt4pairIKiNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEESt10_Select1stIS8_ESt4lessIiESaIS8_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS8_ERS1_ at Base 2.4.1
+#MISSING: 2.4.1-9# _ZNSt8_Rb_treeIiSt4pairIKidESt10_Select1stIS2_ESt4lessIiESaIS2_EE24_M_get_insert_unique_posERS1_ at Base 2.4.1
+#MISSING: 2.4.1-9# _ZNSt8_Rb_treeIiSt4pairIKidESt10_Select1stIS2_ESt4lessIiESaIS2_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS2_ERS1_ at Base 2.4.1
+#MISSING: 2.4.1-9# _ZNSt8_Rb_treeIiSt4pairIKiiESt10_Select1stIS2_ESt4lessIiESaIS2_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJRS1_EESD_IJEEEEESt17_Rb_tree_iteratorIS2_ESt23_Rb_tree_const_iteratorIS2_EDpOT_ at Base 2.4.1
+#MISSING: 2.4.1-9# _ZNSt8_Rb_treeIiSt4pairIKiiESt10_Select1stIS2_ESt4lessIiESaIS2_EE24_M_get_insert_unique_posERS1_ at Base 2.4.1
+#MISSING: 2.4.1-9# _ZNSt8_Rb_treeIiSt4pairIKiiESt10_Select1stIS2_ESt4lessIiESaIS2_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS2_ERS1_ at Base 2.4.1
+#MISSING: 2.4.1-9# _ZNSt8_Rb_treeIiSt4pairIKijESt10_Select1stIS2_ESt4lessIiESaIS2_EE24_M_get_insert_unique_posERS1_ at Base 2.4.1
+#MISSING: 2.4.1-9# _ZNSt8_Rb_treeIiSt4pairIKijESt10_Select1stIS2_ESt4lessIiESaIS2_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS2_ERS1_ at Base 2.4.1
+#MISSING: 2.4.1-9# _ZNSt8_Rb_treeIiSt4pairIKimESt10_Select1stIS2_ESt4lessIiESaIS2_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJRS1_EESD_IJEEEEESt17_Rb_tree_iteratorIS2_ESt23_Rb_tree_const_iteratorIS2_EDpOT_ at Base 2.4.1
+#MISSING: 2.4.1-9# _ZNSt8_Rb_treeIiSt4pairIKimESt10_Select1stIS2_ESt4lessIiESaIS2_EE24_M_get_insert_unique_posERS1_ at Base 2.4.1
+#MISSING: 2.4.1-9# _ZNSt8_Rb_treeIiSt4pairIKimESt10_Select1stIS2_ESt4lessIiESaIS2_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS2_ERS1_ at Base 2.4.1
+#MISSING: 2.4.1-9# _ZNSt8_Rb_treeImSt4pairIKmSt3mapImmSt4lessImESaIS0_IS1_mEEEESt10_Select1stIS8_ES4_SaIS8_EE24_M_get_insert_unique_posERS1_ at Base 2.4.1
+#MISSING: 2.4.1-9# _ZNSt8_Rb_treeImSt4pairIKmSt3mapImmSt4lessImESaIS0_IS1_mEEEESt10_Select1stIS8_ES4_SaIS8_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS8_ERS1_ at Base 2.4.1
+#MISSING: 2.4.1-9# _ZNSt8_Rb_treeImSt4pairIKmmESt10_Select1stIS2_ESt4lessImESaIS2_EE24_M_get_insert_unique_posERS1_ at Base 2.4.1
+#MISSING: 2.4.1-9# _ZNSt8_Rb_treeImSt4pairIKmmESt10_Select1stIS2_ESt4lessImESaIS2_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS2_ERS1_ at Base 2.4.1
  _ZSt13__heap_selectIN9__gnu_cxx17__normal_iteratorIPNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt6vectorIS7_SaIS7_EEEENS0_5__ops15_Iter_less_iterEEvT_SF_SF_T0_ at Base 2.4.1
  _ZSt16__do_uninit_copyIN9__gnu_cxx17__normal_iteratorIPKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt6vectorIS7_SaIS7_EEEEPS7_ET0_T_SG_SF_ at Base 2.4.1
  _ZSt16__introsort_loopIN9__gnu_cxx17__normal_iteratorIPPN3bpp5RangeImEESt6vectorIS5_SaIS5_EEEElNS0_5__ops15_Iter_comp_iterINS2_10rangeComp_ImEEEEEvT_SG_T0_T1_ at Base 2.4.1
- _ZSt19piecewise_construct at Base 2.4.1
+#MISSING: 2.4.1-9# _ZSt19piecewise_construct at Base 2.4.1
  _ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EEOS8_S9_ at Base 2.4.1
  _ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EEPKS5_OS8_ at Base 2.4.1
- _ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EEPKS5_RKS8_ at Base 2.4.1
+#MISSING: 2.4.1-9# _ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EEPKS5_RKS8_ at Base 2.4.1
  _ZTIN3bpp10BppIntegerE at Base 2.4.1
  _ZTIN3bpp10BppNumberIE at Base 2.4.1
  _ZTIN3bpp10MultiRangeImEE at Base 2.4.1
@@ -984,7 +1001,7 @@
  _ZTv0_n24_N3bpp13AlphabetStateD0Ev at Base 2.4.1
  _ZTv0_n24_N3bpp13AlphabetStateD1Ev at Base 2.4.1
  _ZTv0_n24_N3bpp13BasicSequenceD0Ev at Base 2.4.1
- _ZTv0_n24_N3bpp13BasicSequenceD1Ev at Base 2.4.1
+#MISSING: 2.4.1-9# _ZTv0_n24_N3bpp13BasicSequenceD1Ev at Base 2.4.1
  _ZTv0_n24_N3bpp15SequenceQualityD0Ev at Base 2.4.1
  _ZTv0_n24_N3bpp16GffFeatureReaderD0Ev at Base 2.4.1
  _ZTv0_n24_N3bpp16GffFeatureReaderD1Ev at Base 2.4.1
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