[Debian-med-packaging] Bug#1016297: libstatgen: FTBFS: dpkg-gensymbols: error: some symbols or patterns disappeared in the symbols file: see diff output below
Lucas Nussbaum
lucas at debian.org
Fri Jul 29 19:09:21 BST 2022
Source: libstatgen
Version: 1.0.15-5
Severity: serious
Justification: FTBFS
Tags: bookworm sid ftbfs
User: lucas at debian.org
Usertags: ftbfs-20220728 ftbfs-bookworm
Hi,
During a rebuild of all packages in sid, your package failed to build
on amd64.
Relevant part (hopefully):
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> mkdir -p debian/libstatgen-dev/usr/include/libStatGen/
> cp -L include/* debian/libstatgen-dev/usr/include/libStatGen/
> ln -s libStatGen.so.1 libStatGen.so
> d-shlibmove --commit \
> --multiarch \
> --devunversioned \
> --exclude-a \
> libStatGen.so
> Library package automatic movement utility
> set -e
> install -d -m 755 debian/libstatgen-dev/usr/lib/x86_64-linux-gnu
> install -d -m 755 debian/libstatgen1/usr/lib/x86_64-linux-gnu
> mv ./libStatGen.la debian/libstatgen-dev/usr/lib/x86_64-linux-gnu || true
> mv ./libStatGen.so debian/libstatgen-dev/usr/lib/x86_64-linux-gnu
> mv /<<PKGBUILDDIR>>/libStatGen.so.1 debian/libstatgen1/usr/lib/x86_64-linux-gnu
> PKGDEV=libstatgen-dev
> PKGSHL=libstatgen1
> mv: cannot stat './libStatGen.la': No such file or directory
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
> dh_installdocs -O--no-parallel
> dh_installchangelogs -O--no-parallel
> dh_installsystemduser -O--no-parallel
> dh_perl -O--no-parallel
> dh_link -O--no-parallel
> dh_strip_nondeterminism -O--no-parallel
> dh_compress -O--no-parallel
> dh_fixperms -O--no-parallel
> dh_missing -O--no-parallel
> dh_dwz -a -O--no-parallel
> dh_strip -a -O--no-parallel
> dh_makeshlibs -a -O--no-parallel
> 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/libstatgen1/DEBIAN/symbols doesn't match completely debian/libstatgen1.symbols
> --- debian/libstatgen1.symbols (libstatgen1_1.0.15-5_amd64)
> +++ dpkg-gensymbolsh3JD9Q 2022-07-29 09:31:11.378115176 +0000
> @@ -1636,6 +1636,7 @@
> _ZN9FastQFile11interleavedEv at Base 1.0.15
> _ZNK13VcfRecordInfo11getInfoPairB5cxx11Ei at Base 1.0.15
> _ZNKSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES5_St9_IdentityIS5_ESt4lessIS5_ESaIS5_EE4findERKS5_ at Base 1.0.14
> + _ZNSt10_HashtableINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES5_SaIS5_ENSt8__detail9_IdentityESt8equal_toIS5_ESt4hashIS5_ENS7_18_Mod_range_hashingENS7_20_Default_ranged_hashENS7_20_Prime_rehash_policyENS7_17_Hashtable_traitsILb1ELb1ELb1EEEE4findERKS5_ at Base 1.0.15-5
> _ZNSt10_HashtableINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES5_SaIS5_ENSt8__detail9_IdentityESt8equal_toIS5_ESt4hashIS5_ENS7_18_Mod_range_hashingENS7_20_Default_ranged_hashENS7_20_Prime_rehash_policyENS7_17_Hashtable_traitsILb1ELb1ELb1EEEE9_M_rehashEmRKm at Base 1.0.15
> _ZNSt12_Destroy_auxILb0EE9__destroyIP6StringEEvT_S4_ at Base 1.0.14
> _ZNSt12_Destroy_auxILb0EE9__destroyIPN9IndexBase9ReferenceEEEvT_S5_ at Base 1.0.14
> @@ -1649,7 +1650,7 @@
> _ZNSt12_Vector_baseIfSaIfEED2Ev at Base 1.0.14
> _ZNSt12_Vector_baseIiSaIiEED1Ev at Base 1.0.14
> _ZNSt12_Vector_baseIiSaIiEED2Ev at Base 1.0.14
> - _ZNSt22__uninitialized_fill_nILb0EE15__uninit_fill_nIPSt6vectorIbSaIbEEmS4_EET_S6_T0_RKT1_ at Base 1.0.14
> +#MISSING: 1.0.15-5# _ZNSt22__uninitialized_fill_nILb0EE15__uninit_fill_nIPSt6vectorIbSaIbEEmS4_EET_S6_T0_RKT1_ at Base 1.0.14
> _ZNSt6vectorIP12SamHeaderTagSaIS1_EE17_M_realloc_insertIJS1_EEEvN9__gnu_cxx17__normal_iteratorIPS1_S3_EEDpOT_ at Base 1.0.14
> _ZNSt6vectorIcSaIcEE17_M_realloc_insertIJcEEEvN9__gnu_cxx17__normal_iteratorIPcS1_EEDpOT_ at Base 1.0.14
> _ZNSt6vectorIfSaIfEE17_M_realloc_insertIJRKfEEEvN9__gnu_cxx17__normal_iteratorIPfS1_EEDpOT_ at Base 1.0.14
> @@ -1660,6 +1661,12 @@
> _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 1.0.15-5
> + _ZNSt8_Rb_treeImSt4pairIKm5ChunkESt10_Select1stIS3_ESt4lessImESaIS3_EE24_M_get_insert_unique_posERS1_ at Base 1.0.15-5
> + _ZNSt8_Rb_treeImSt4pairIKm5ChunkESt10_Select1stIS3_ESt4lessImESaIS3_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS3_ERS1_ at Base 1.0.15-5
> + _ZSt16__do_uninit_copyIPK6StringPS0_ET0_T_S5_S4_ at Base 1.0.15-5
> + _ZSt18__do_uninit_fill_nIPSt6vectorIbSaIbEEmS2_ET_S4_T0_RKT1_ at Base 1.0.15-5
> + _ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EEOS8_S9_ at Base 1.0.15-5
> _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
> @@ -1709,7 +1716,7 @@
> globalRandom at Base 1.0.14
> (c++)"hash(unsigned char const*, unsigned int, unsigned int)@Base" 1.0.14
> (c++)"hash_no_case(unsigned char const*, unsigned int, unsigned int)@Base" 1.0.14
> - (c++)"ifclose(InputFile*&)@Base" 1.0.14
> +#MISSING: 1.0.15-5# (c++)"ifclose(InputFile*&)@Base" 1.0.14
> (c++)"ifprintf(InputFile*, char const*, ...)@Base" 1.0.14
> kftp_connect at Base 1.0.14
> kftp_connect_file at Base 1.0.14
> @@ -1740,23 +1747,23 @@
> (c++)"operator<<(std::basic_ostream<char, std::char_traits<char> >&, genomeSequenceMmapHeader&)@Base" 1.0.14
> (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> >::_M_find_before_node(unsigned long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long) const at Base" 1.0.14
> +#MISSING: 1.0.15-5# (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> >::_M_find_before_node(unsigned long, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long) const at 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
> - (c++)"std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > std::operator+<char, std::char_traits<char>, std::allocator<char> >(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&&, char const*)@Base" 1.0.14
> +#MISSING: 1.0.15-5# (c++)"std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > std::operator+<char, std::char_traits<char>, std::allocator<char> >(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&&, 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
> (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::pair<std::_Rb_tree_iterator<std::pair<unsigned long const, Chunk> >, bool> std::_Rb_tree<unsigned long, std::pair<unsigned long const, Chunk>, std::_Select1st<std::pair<unsigned long const, Chunk> >, std::less<unsigned long>, std::allocator<std::pair<unsigned long const, Chunk> > >::_M_emplace_unique<std::pair<unsigned long, Chunk> >(std::pair<unsigned long, Chunk>&&)@Base" 1.0.14
> +#MISSING: 1.0.15-5# (c++)"std::pair<std::_Rb_tree_iterator<std::pair<unsigned long const, Chunk> >, bool> std::_Rb_tree<unsigned long, std::pair<unsigned long const, Chunk>, std::_Select1st<std::pair<unsigned long const, Chunk> >, std::less<unsigned long>, std::allocator<std::pair<unsigned long const, Chunk> > >::_M_emplace_unique<std::pair<unsigned long, Chunk> >(std::pair<unsigned long, Chunk>&&)@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
> (c++)"std::vector<IndexBase::Reference, std::allocator<IndexBase::Reference> >::_M_default_append(unsigned long)@Base" 1.0.14
> (c++)"std::vector<IndexBase::Reference, std::allocator<IndexBase::Reference> >::~vector()@Base" 1.0.14
> (c++)"std::vector<String, std::allocator<String> >::_M_default_append(unsigned long)@Base" 1.0.14
> - (c++)"std::vector<String, std::allocator<String> >::operator=(std::vector<String, std::allocator<String> > const&)@Base" 1.0.14
> +#MISSING: 1.0.15-5# (c++)"std::vector<String, std::allocator<String> >::operator=(std::vector<String, std::allocator<String> > const&)@Base" 1.0.14
> (c++)"std::vector<VcfGenotypeSample*, std::allocator<VcfGenotypeSample*> >::_M_default_append(unsigned long)@Base" 1.0.14
> (c++)"std::vector<VcfRecordInfo::InfoElement*, std::allocator<VcfRecordInfo::InfoElement*> >::_M_default_append(unsigned long)@Base" 1.0.14
> (c++)"std::vector<bool, std::allocator<bool> >::_M_fill_insert(std::_Bit_iterator, unsigned long, bool)@Base" 1.0.14
> dh_makeshlibs: error: failing due to earlier errors
> make: *** [debian/rules:12: binary] Error 25
The full build log is available from:
http://qa-logs.debian.net/2022/07/28/libstatgen_1.0.15-5_unstable.log
All bugs filed during this archive rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20220728;users=lucas@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20220728&fusertaguser=lucas@debian.org&allbugs=1&cseverity=1&ctags=1&caffected=1#results
A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
If you reassign this bug to another package, please marking it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects
If you fail to reproduce this, please provide a build log and diff it with mine
so that we can identify if something relevant changed in the meantime.
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