Bug#1016297: marked as done (libstatgen: FTBFS: dpkg-gensymbols: error: some symbols or patterns disappeared in the symbols file: see diff output below)

[Debian Bug Tracking System]

Your message dated Thu, 04 Aug 2022 13:34:06 +0000
with message-id <e1ojazg-00597d...@fasolo.debian.org>
and subject line Bug#1016297: fixed in libstatgen 1.0.15-6
has caused the Debian Bug report #1016297,
regarding libstatgen: FTBFS: dpkg-gensymbols: error: some symbols or patterns 
disappeared in the symbols file: see diff output below
to be marked as done.

This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.

(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)


-- 
1016297: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1016297
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems

--- Begin Message ---

Source: libstatgen
Version: 1.0.15-5
Severity: serious
Justification: FTBFS
Tags: bookworm sid ftbfs
User: lu...@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@Base 1.0.15
>   _ZNK13VcfRecordInfo11getInfoPairB5cxx11Ei@Base 1.0.15
>   
> _ZNKSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES5_St9_IdentityIS5_ESt4lessIS5_ESaIS5_EE4findERKS5_@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_@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@Base
>  1.0.15
>   _ZNSt12_Destroy_auxILb0EE9__destroyIP6StringEEvT_S4_@Base 1.0.14
>   _ZNSt12_Destroy_auxILb0EE9__destroyIPN9IndexBase9ReferenceEEEvT_S5_@Base 
> 1.0.14
> @@ -1649,7 +1650,7 @@
>   _ZNSt12_Vector_baseIfSaIfEED2Ev@Base 1.0.14
>   _ZNSt12_Vector_baseIiSaIiEED1Ev@Base 1.0.14
>   _ZNSt12_Vector_baseIiSaIiEED2Ev@Base 1.0.14
> - 
> _ZNSt22__uninitialized_fill_nILb0EE15__uninit_fill_nIPSt6vectorIbSaIbEEmS4_EET_S6_T0_RKT1_@Base
>  1.0.14
> +#MISSING: 1.0.15-5# 
> _ZNSt22__uninitialized_fill_nILb0EE15__uninit_fill_nIPSt6vectorIbSaIbEEmS4_EET_S6_T0_RKT1_@Base
>  1.0.14
>   
> _ZNSt6vectorIP12SamHeaderTagSaIS1_EE17_M_realloc_insertIJS1_EEEvN9__gnu_cxx17__normal_iteratorIPS1_S3_EEDpOT_@Base
>  1.0.14
>   
> _ZNSt6vectorIcSaIcEE17_M_realloc_insertIJcEEEvN9__gnu_cxx17__normal_iteratorIPcS1_EEDpOT_@Base
>  1.0.14
>   
> _ZNSt6vectorIfSaIfEE17_M_realloc_insertIJRKfEEEvN9__gnu_cxx17__normal_iteratorIPfS1_EEDpOT_@Base
>  1.0.14
> @@ -1660,6 +1661,12 @@
>   _ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC1IS3_EEPKcRKS3_@Base 
> 1.0.15
>   _ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC2IS3_EEPKcRKS3_@Base 
> 1.0.15
>   _ZNSt7__cxx119to_stringEx@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_@Base
>  1.0.15-5
> + 
> _ZNSt8_Rb_treeImSt4pairIKm5ChunkESt10_Select1stIS3_ESt4lessImESaIS3_EE24_M_get_insert_unique_posERS1_@Base
>  1.0.15-5
> + 
> _ZNSt8_Rb_treeImSt4pairIKm5ChunkESt10_Select1stIS3_ESt4lessImESaIS3_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS3_ERS1_@Base
>  1.0.15-5
> + _ZSt16__do_uninit_copyIPK6StringPS0_ET0_T_S5_S4_@Base 1.0.15-5
> + _ZSt18__do_uninit_fill_nIPSt6vectorIbSaIbEEmS2_ET_S4_T0_RKT1_@Base 1.0.15-5
> + 
> _ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EEOS8_S9_@Base
>  1.0.15-5
>   _ZZNSt8__detail18__to_chars_10_implIyEEvPcjT_E8__digits@Base 1.0.15
>   bQualityConvertor@Base 1.0.14
>   (c++)"baseQualityConvertor::baseQualityConvertor()@Base" 1.0.14
> @@ -1709,7 +1716,7 @@
>   globalRandom@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@Base 1.0.14
>   kftp_connect_file@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@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@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@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=lu...@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20220728&fusertaguser=lu...@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.

--- End Message ---

--- Begin Message ---

Source: libstatgen
Source-Version: 1.0.15-6
Done: Andreas Tille <ti...@debian.org>

We believe that the bug you reported is fixed in the latest version of
libstatgen, which is due to be installed in the Debian FTP archive.

A summary of the changes between this version and the previous one is
attached.

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to 1016...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Andreas Tille <ti...@debian.org> (supplier of updated libstatgen package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)


-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256

Format: 1.8
Date: Thu, 04 Aug 2022 14:59:25 +0200
Source: libstatgen
Architecture: source
Version: 1.0.15-6
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Andreas Tille <ti...@debian.org>
Closes: 1016297
Changes:
 libstatgen (1.0.15-6) unstable; urgency=medium
 .
   * Team upload.
   * Packaging update
   * Standards-Version: 4.6.1 (routine-update)
   * Fix symbols file to match gcc-12 build
     Closes: #1016297
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 d2e835598c0860509e3e2d569ea69e084c5acc73 20752 
libstatgen_1.0.15-6.debian.tar.xz
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libstatgen_1.0.15-6_amd64.buildinfo
Checksums-Sha256:
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libstatgen_1.0.15-6.dsc
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Files:
 a57b9189f82545c84081720fa9d784ec 2176 science optional libstatgen_1.0.15-6.dsc
 072e95764fa4461bf2d142ffe426e545 20752 science optional 
libstatgen_1.0.15-6.debian.tar.xz
 fefbf297e67ba31de47c31436e50d9e5 7551 science optional 
libstatgen_1.0.15-6_amd64.buildinfo

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