[Debian-med-packaging] Bug#1075208: libstatgen: ftbfs with GCC-14

Wed Jul 3 13:34:27 BST 2024

Package: src:libstatgen
Version: 1.0.15-7
Severity: important
Tags: sid trixie
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-14

[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-14/g++-14, but succeeds to build with gcc-13/g++-13. 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/2024/07/01/libstatgen_1.0.15-7_unstable_gccexp.log
The last lines of the build log are at the end of this report.

To build with GCC 14, either set CC=gcc-14 CXX=g++-14 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-14/porting_to.html

[...]
+#MISSING: 1.0.15-7# _ZNSt6vectorIhSaIhEE17_M_realloc_insertIJRKhEEEvN9__gnu_cxx17__normal_iteratorIPhS1_EEDpOT_ at Base 1.0.14
+#MISSING: 1.0.15-7# _ZNSt6vectorIhSaIhEE17_M_realloc_insertIJhEEEvN9__gnu_cxx17__normal_iteratorIPhS1_EEDpOT_ at Base 1.0.14
+ _ZNSt6vectorIiSaIiEE17_M_realloc_appendIJRKiEEEvDpOT_ at Base 1.0.15-7
+ _ZNSt6vectorIiSaIiEE17_M_realloc_appendIJiEEEvDpOT_ at Base 1.0.15-7
+#MISSING: 1.0.15-7# _ZNSt6vectorIiSaIiEE17_M_realloc_insertIJiEEEvN9__gnu_cxx17__normal_iteratorIPiS1_EEDpOT_ at Base 1.0.14
+#MISSING: 1.0.15-7# (optional)_ZNSt6vectorIiSaIiEED1Ev at Base 1.0.15
+#MISSING: 1.0.15-7# (optional)_ZNSt6vectorIiSaIiEED2Ev at Base 1.0.15
  _ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC1IS3_EEPKcRKS3_ at Base 1.0.15
  _ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC2IS3_EEPKcRKS3_ at Base 1.0.15
  _ZNSt7__cxx119to_stringEx at Base 1.0.15
  _ZNSt8_Rb_treeImSt4pairIKm5ChunkESt10_Select1stIS3_ESt4lessImESaIS3_EE22_M_emplace_hint_uniqueIJS0_ImS2_EEEESt17_Rb_tree_iteratorIS3_ESt23_Rb_tree_const_iteratorIS3_EDpOT_ at Base 1.0.15
- (optional)_ZNSt8_Rb_treeImSt4pairIKm5ChunkESt10_Select1stIS3_ESt4lessImESaIS3_EE24_M_get_insert_unique_posERS1_ at Base 1.0.15
- (optional)_ZNSt8_Rb_treeImSt4pairIKm5ChunkESt10_Select1stIS3_ESt4lessImESaIS3_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS3_ERS1_ at Base 1.0.15
+#MISSING: 1.0.15-7# (optional)_ZNSt8_Rb_treeImSt4pairIKm5ChunkESt10_Select1stIS3_ESt4lessImESaIS3_EE24_M_get_insert_unique_posERS1_ at Base 1.0.15
+#MISSING: 1.0.15-7# (optional)_ZNSt8_Rb_treeImSt4pairIKm5ChunkESt10_Select1stIS3_ESt4lessImESaIS3_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS3_ERS1_ at Base 1.0.15
  _ZSt16__do_uninit_copyIPK6StringPS0_ET0_T_S5_S4_ at Base 1.0.15
  _ZSt18__do_uninit_fill_nIPSt6vectorIbSaIbEEmS2_ET_S4_T0_RKT1_ at Base 1.0.15
- _ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EEOS8_S9_ at Base 1.0.15
- (optional)_ZZNSt8__detail18__to_chars_10_implIyEEvPcjT_E8__digits at Base 1.0.15
+#MISSING: 1.0.15-7# _ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EEOS8_S9_ at Base 1.0.15
+#MISSING: 1.0.15-7# (optional)_ZZNSt8__detail18__to_chars_10_implIyEEvPcjT_E8__digits at Base 1.0.15
  bQualityConvertor at Base 1.0.14
  (c++)"baseQualityConvertor::baseQualityConvertor()@Base" 1.0.14
  (c++)"baseQualityConvertor::toDouble(unsigned char)@Base" 1.0.14
@@ -1758,12 +1775,12 @@
  (c++)"std::_Bvector_base<std::allocator<bool> >::_M_deallocate()@Base" 1.0.14
  (c++)"std::_Deque_base<SamRecord*, std::allocator<SamRecord*> >::_M_initialize_map(unsigned long)@Base" 1.0.14
  (c++)"std::_Hashtable<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::__detail::_Identity, std::equal_to<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::hash<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::__detail::_Mod_range_hashing, std::__detail::_Default_ranged_hash, std::__detail::_Prime_rehash_policy, std::__detail::_Hashtable_traits<true, true, true> >::clear()@Base" 1.0.14
- (c++)"std::_Rb_tree<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::_Identity<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::less<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >::_M_get_insert_unique_pos(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)@Base" 1.0.14
- (c++)"std::_Rb_tree<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, NonOverlapRegionPos>, std::_Select1st<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, NonOverlapRegionPos> >, std::less<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, NonOverlapRegionPos> > >::_M_get_insert_hint_unique_pos(std::_Rb_tree_const_iterator<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, NonOverlapRegionPos> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)@Base" 1.0.14
- (c++)"std::_Rb_tree<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, NonOverlapRegionPos>, std::_Select1st<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, NonOverlapRegionPos> >, std::less<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, NonOverlapRegionPos> > >::_M_get_insert_unique_pos(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)@Base" 1.0.14
+#MISSING: 1.0.15-7# (c++)"std::_Rb_tree<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::_Identity<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::less<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >::_M_get_insert_unique_pos(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)@Base" 1.0.14
+#MISSING: 1.0.15-7# (c++)"std::_Rb_tree<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, NonOverlapRegionPos>, std::_Select1st<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, NonOverlapRegionPos> >, std::less<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, NonOverlapRegionPos> > >::_M_get_insert_hint_unique_pos(std::_Rb_tree_const_iterator<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, NonOverlapRegionPos> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)@Base" 1.0.14
+#MISSING: 1.0.15-7# (c++)"std::_Rb_tree<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, NonOverlapRegionPos>, std::_Select1st<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, NonOverlapRegionPos> >, std::less<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, NonOverlapRegionPos> > >::_M_get_insert_unique_pos(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)@Base" 1.0.14
  (c++)"std::__cxx11::basic_stringbuf<char, std::char_traits<char>, std::allocator<char> >::~basic_stringbuf()@Base" 1.0.14
  (c++)"std::ctype<char>::do_widen(char) const at Base" 1.0.14
- (c++)"std::pair<std::_Rb_tree_iterator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, bool> std::_Rb_tree<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::_Identity<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::less<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >::_M_insert_unique<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&&)@Base" 1.0.14
+#MISSING: 1.0.15-7# (c++)"std::pair<std::_Rb_tree_iterator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, bool> std::_Rb_tree<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::_Identity<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::less<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >::_M_insert_unique<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&&)@Base" 1.0.14
  (c++)"std::pair<std::_Rb_tree_iterator<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, unsigned int> >, bool> std::_Rb_tree<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, unsigned int>, std::_Select1st<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, unsigned int> >, std::less<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, unsigned int> > >::_M_emplace_unique<std::pair<char const*, unsigned int> >(std::pair<char const*, unsigned int>&&)@Base" 1.0.14
  (c++)"std::set<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::less<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >::~set()@Base" 1.0.14
  (c++)"std::vector<IndexBase::Bin, std::allocator<IndexBase::Bin> >::_M_default_append(unsigned long)@Base" 1.0.14
@@ -1919,16 +1936,16 @@
  (c++)"typeinfo name for VectorFunc at Base" 1.0.14
  (c++)"typeinfo name for std::_Vector_base<unsigned char, std::allocator<unsigned char> >@Base" 1.0.14
  (c++)"typeinfo name for std::vector<unsigned char, std::allocator<unsigned char> >@Base" 1.0.14
- (c++)"void std::vector<BaseCount, std::allocator<BaseCount> >::_M_realloc_insert<BaseCount const&>(__gnu_cxx::__normal_iterator<BaseCount*, std::vector<BaseCount, std::allocator<BaseCount> > >, BaseCount const&)@Base" 1.0.14
- (c++)"void std::vector<Cigar::CigarOperator, std::allocator<Cigar::CigarOperator> >::_M_realloc_insert<Cigar::CigarOperator const&>(__gnu_cxx::__normal_iterator<Cigar::CigarOperator*, std::vector<Cigar::CigarOperator, std::allocator<Cigar::CigarOperator> > >, Cigar::CigarOperator const&)@Base" 1.0.14
- (c++)"void std::vector<SamHeaderRecord*, std::allocator<SamHeaderRecord*> >::_M_realloc_insert<SamHeaderRecord*>(__gnu_cxx::__normal_iterator<SamHeaderRecord**, std::vector<SamHeaderRecord*, std::allocator<SamHeaderRecord*> > >, SamHeaderRecord*&&)@Base" 1.0.14
- (c++)"void std::vector<SamHeaderTag*, std::allocator<SamHeaderTag*> >::_M_realloc_insert<SamHeaderTag* const&>(__gnu_cxx::__normal_iterator<SamHeaderTag**, std::vector<SamHeaderTag*, std::allocator<SamHeaderTag*> > >, SamHeaderTag* const&)@Base" 1.0.14
- (c++)"void std::vector<String, std::allocator<String> >::_M_realloc_insert<String const&>(__gnu_cxx::__normal_iterator<String*, std::vector<String, std::allocator<String> > >, String const&)@Base" 1.0.14
+#MISSING: 1.0.15-7# (c++)"void std::vector<BaseCount, std::allocator<BaseCount> >::_M_realloc_insert<BaseCount const&>(__gnu_cxx::__normal_iterator<BaseCount*, std::vector<BaseCount, std::allocator<BaseCount> > >, BaseCount const&)@Base" 1.0.14
+#MISSING: 1.0.15-7# (c++)"void std::vector<Cigar::CigarOperator, std::allocator<Cigar::CigarOperator> >::_M_realloc_insert<Cigar::CigarOperator const&>(__gnu_cxx::__normal_iterator<Cigar::CigarOperator*, std::vector<Cigar::CigarOperator, std::allocator<Cigar::CigarOperator> > >, Cigar::CigarOperator const&)@Base" 1.0.14
+#MISSING: 1.0.15-7# (c++)"void std::vector<SamHeaderRecord*, std::allocator<SamHeaderRecord*> >::_M_realloc_insert<SamHeaderRecord*>(__gnu_cxx::__normal_iterator<SamHeaderRecord**, std::vector<SamHeaderRecord*, std::allocator<SamHeaderRecord*> > >, SamHeaderRecord*&&)@Base" 1.0.14
+#MISSING: 1.0.15-7# (c++)"void std::vector<SamHeaderTag*, std::allocator<SamHeaderTag*> >::_M_realloc_insert<SamHeaderTag* const&>(__gnu_cxx::__normal_iterator<SamHeaderTag**, std::vector<SamHeaderTag*, std::allocator<SamHeaderTag*> > >, SamHeaderTag* const&)@Base" 1.0.14
+#MISSING: 1.0.15-7# (c++)"void std::vector<String, std::allocator<String> >::_M_realloc_insert<String const&>(__gnu_cxx::__normal_iterator<String*, std::vector<String, std::allocator<String> > >, String const&)@Base" 1.0.14
  (c++)"void std::vector<String, std::allocator<String> >::_M_realloc_insert<String>(__gnu_cxx::__normal_iterator<String*, std::vector<String, std::allocator<String> > >, String&&)@Base" 1.0.14
- (c++)"void std::vector<char, std::allocator<char> >::_M_realloc_insert<char const&>(__gnu_cxx::__normal_iterator<char*, std::vector<char, std::allocator<char> > >, char const&)@Base" 1.0.14
- (c++)"void std::vector<int, std::allocator<int> >::_M_realloc_insert<int const&>(__gnu_cxx::__normal_iterator<int*, std::vector<int, std::allocator<int> > >, int const&)@Base" 1.0.14
- (c++)"void std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >::_M_realloc_insert<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >(__gnu_cxx::__normal_iterator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&&)@Base" 1.0.14
- (c++)"void std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >::_M_realloc_insert<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&>(__gnu_cxx::__normal_iterator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)@Base" 1.0.14
+#MISSING: 1.0.15-7# (c++)"void std::vector<char, std::allocator<char> >::_M_realloc_insert<char const&>(__gnu_cxx::__normal_iterator<char*, std::vector<char, std::allocator<char> > >, char const&)@Base" 1.0.14
+#MISSING: 1.0.15-7# (c++)"void std::vector<int, std::allocator<int> >::_M_realloc_insert<int const&>(__gnu_cxx::__normal_iterator<int*, std::vector<int, std::allocator<int> > >, int const&)@Base" 1.0.14
+#MISSING: 1.0.15-7# (c++)"void std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >::_M_realloc_insert<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >(__gnu_cxx::__normal_iterator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&&)@Base" 1.0.14
+#MISSING: 1.0.15-7# (c++)"void std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >::_M_realloc_insert<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&>(__gnu_cxx::__normal_iterator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)@Base" 1.0.14
  (c++)"vtable for BGZFReader at Base" 1.0.14
  (c++)"vtable for BamIndex at Base" 1.0.14
  (c++)"vtable for BamInterface at Base" 1.0.14
dh_makeshlibs: error: failing due to earlier errors
make: *** [debian/rules:12: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2

