[Debian-med-packaging] Bug#952232: libstatgen: FTBFS: dpkg-gensymbols: error: some symbols or patterns disappeared in the symbols file: see diff output below

[Lucas Nussbaum]

Source: libstatgen
Version: 1.0.14-5
Severity: serious
Justification: FTBFS on amd64
Tags: bullseye sid ftbfs
Usertags: ftbfs-20200222 ftbfs-bullseye

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.0 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/libstatgen0/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.0 debian/libstatgen0/usr/lib/x86_64-linux-gnu
> PKGDEV=libstatgen-dev
> PKGSHL=libstatgen0
> mv: cannot stat './libStatGen.la': No such file or directory
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
>    dh_installdocs
>    dh_installchangelogs
>    dh_perl
>    dh_link
>    dh_strip_nondeterminism
>    dh_compress
>    dh_fixperms
>    dh_missing
>    dh_strip
>    dh_makeshlibs
> 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/libstatgen0/DEBIAN/symbols doesn't match completely debian/libstatgen0.symbols
> --- debian/libstatgen0.symbols (libstatgen0_1.0.14-5_amd64)
> +++ dpkg-gensymbolsdde9Ud	2020-02-23 02:40:44.569405938 +0000
> @@ -1628,8 +1628,13 @@
>   (c++)"VectorFunc::VectorFunc()@Base" 1.0.14
>   (c++)"VectorFunc::VectorFunc(double (*)(Vector&))@Base" 1.0.14
>   (c++)"VectorFunc::~VectorFunc()@Base" 1.0.14
> + _ZN11MiniDeflate14OutputLiteralsERPhiS1_RiP8_IO_FILE at Base 1.0.14-5
> + _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 1.0.14-5
> + _ZNSt6vectorIcSaIcEE17_M_realloc_insertIJcEEEvN9__gnu_cxx17__normal_iteratorIPcS1_EEDpOT_ at Base 1.0.14-5
>   _ZNSt6vectorIfSaIfEE17_M_realloc_insertIJRKfEEEvN9__gnu_cxx17__normal_iteratorIPfS1_EEDpOT_ at Base 1.0.14
>   _ZNSt6vectorIfSaIfEE17_M_realloc_insertIJfEEEvN9__gnu_cxx17__normal_iteratorIPfS1_EEDpOT_ at Base 1.0.14
> + _ZNSt6vectorIhSaIhEE17_M_realloc_insertIJRKhEEEvN9__gnu_cxx17__normal_iteratorIPhS1_EEDpOT_ at Base 1.0.14-5
> + _ZNSt6vectorIhSaIhEE17_M_realloc_insertIJhEEEvN9__gnu_cxx17__normal_iteratorIPhS1_EEDpOT_ at Base 1.0.14-5
>   _ZNSt6vectorIiSaIiEE17_M_realloc_insertIJiEEEvN9__gnu_cxx17__normal_iteratorIPiS1_EEDpOT_ at Base 1.0.14
>   bQualityConvertor at Base 1.0.14
>   (c++)"baseQualityConvertor::baseQualityConvertor()@Base" 1.0.14
> @@ -1711,7 +1716,7 @@
>   (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
> - (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_insert_unique_node(unsigned long, unsigned long, std::__detail::_Hash_node<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, true>*, unsigned long)@Base" 1.0.14
> +#MISSING: 1.0.14-5# (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_insert_unique_node(unsigned long, unsigned long, std::__detail::_Hash_node<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, true>*, 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::_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> >::find(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > 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> >::~_Hashtable()@Base" 1.0.14
> dh_makeshlibs: error: failing due to earlier errors
> make: *** [debian/rules:11: binary] Error 25

The full build log is available from:
   http://qa-logs.debian.net/2020/02/22/libstatgen_1.0.14-5_unstable.log

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!

About the archive rebuild: The rebuild was done on EC2 VM instances from
Amazon Web Services, using a clean, minimal and up-to-date chroot. Every
failed build was retried once to eliminate random failures.