[Debian-med-packaging] Bug#997447: libbpp-popgen: FTBFS: dpkg-gensymbols: error: some symbols or patterns disappeared in the symbols file: see diff output below

Sat Oct 23 21:27:59 BST 2021

Source: libbpp-popgen
Version: 2.4.1-5
Severity: serious
Justification: FTBFS
Tags: bookworm sid ftbfs
User: lucas at debian.org
Usertags: ftbfs-20211023 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>>'
> dh_install
> d-shlibmove --commit \
> 	    --multiarch \
> 	    --devunversioned \
> 	    --exclude-la \
>                     --movedev debian/tmp/usr/include/* usr/include \
>                     --movedev debian/tmp/usr/lib/*/cmake usr/lib/x86_64-linux-gnu \
>                     debian/tmp/usr/lib/*/*.so
> Library package automatic movement utility
>  --> libbpp-core-dev package exists.
>  --> libbpp-seq-dev package exists.
> set -e
> install -d -m 755 debian/libbpp-popgen-dev/usr/lib/x86_64-linux-gnu
> install -d -m 755 debian/libbpp-popgen8/usr/lib/x86_64-linux-gnu
> mv debian/tmp/usr/lib/x86_64-linux-gnu/libbpp-popgen.a debian/libbpp-popgen-dev/usr/lib/x86_64-linux-gnu
> mv debian/tmp/usr/lib/x86_64-linux-gnu/libbpp-popgen.so debian/libbpp-popgen-dev/usr/lib/x86_64-linux-gnu
> mv /<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu/libbpp-popgen.so.8 debian/libbpp-popgen8/usr/lib/x86_64-linux-gnu
> mv /<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu/libbpp-popgen.so.8.0.0 debian/libbpp-popgen8/usr/lib/x86_64-linux-gnu
> PKGDEV=libbpp-popgen-dev
> PKGSHL=libbpp-popgen8
> install -d -m 755 debian/libbpp-popgen-dev/usr/include
> mv debian/tmp/usr/include/Bpp debian/libbpp-popgen-dev/usr/include
> install -d -m 755 debian/libbpp-popgen-dev/usr/lib/x86_64-linux-gnu
> mv debian/tmp/usr/lib/x86_64-linux-gnu/cmake debian/libbpp-popgen-dev/usr/lib/x86_64-linux-gnu
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
>    dh_installdocs
>    dh_installchangelogs
>    dh_perl
>    dh_link
>    dh_strip_nondeterminism
>    dh_compress
>    dh_fixperms
>    dh_missing
>    dh_dwz -a
>    dh_strip -a
>    dh_makeshlibs -a
> 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/libbpp-popgen8/DEBIAN/symbols doesn't match completely debian/libbpp-popgen8.symbols.amd64
> --- debian/libbpp-popgen8.symbols.amd64 (libbpp-popgen8_2.4.1-5_amd64)
> +++ dpkg-gensymbolseF3Nca	2021-10-23 07:34:38.348480986 +0000
> @@ -61,6 +61,7 @@
>   _ZN3bpp11PopgenlibIOD1Ev at Base 2.4.1
>   _ZN3bpp11PopgenlibIOD2Ev at Base 2.4.1
>   _ZN3bpp11RandomTools9getSampleImEEvRKSt6vectorIT_SaIS3_EERS5_b at Base 2.4.1
> + _ZN3bpp11VectorTools11countValuesINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESt3mapIT_mSt4lessIS9_ESaISt4pairIKS9_mEEERKSt6vectorIS9_SaIS9_EE at Base 2.4.1-5
>   _ZN3bpp11VectorTools3covIddEET0_RKSt6vectorIT_SaIS4_EES8_b at Base 2.4.1
>   _ZN3bpp11VectorTools6uniqueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESt6vectorIT_SaIS9_EERKSB_ at Base 2.4.1
>   _ZN3bpp11VectorTools6uniqueImEESt6vectorIT_SaIS3_EERKS5_ at Base 2.4.1
> @@ -662,7 +663,7 @@
>   _ZN3bpp9TextTools8toStringIcEENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEET_ at Base 2.4.1
>   _ZN3bpp9TextTools8toStringIiEENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEET_ at Base 2.4.1
>   _ZN3bpp9TextTools8toStringImEENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEET_ at Base 2.4.1
> - _ZN3bppdvIdEESt6vectorIT_SaIS2_EERKS4_S6_ at Base 2.4.1
> +#MISSING: 2.4.1-5# _ZN3bppdvIdEESt6vectorIT_SaIS2_EERKS4_S6_ at Base 2.4.1
>   _ZN3bppdvIdiEESt6vectorIT_SaIS2_EERKS4_RKT0_ at Base 2.4.1
>   _ZN3bppmiIdiEESt6vectorIT_SaIS2_EERKS4_RKT0_ at Base 2.4.1
>   _ZN3bppmlIdEESt6vectorIT_SaIS2_EERKS4_S6_ at Base 2.4.1
> @@ -759,6 +760,7 @@
>   _ZNK3bpp19VectorSiteContainer7valueAtEmm at Base 2.4.1
>   _ZNK3bpp19VectorSiteContainerclERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEm at Base 2.4.1
>   _ZNK3bpp19VectorSiteContainerclEmm at Base 2.4.1
> + _ZNK3bpp20AbstractCoreSequence11getCommentsB5cxx11Ev at Base 2.4.1-5
>   _ZNK3bpp20AbstractCoreSequence7getNameB5cxx11Ev at Base 2.4.1
>   _ZNK3bpp20AbstractOutputStream12getPrecisionEv at Base 2.4.1
>   _ZNK3bpp20AbstractOutputStream27isScientificNotationEnabledEv at Base 2.4.1
> @@ -935,11 +937,13 @@
>   _ZNSt12_Vector_baseImSaImEED2Ev at Base 2.4.1
>   _ZNSt13_Bvector_baseISaIbEE13_M_deallocateEv at Base 2.4.1
>   _ZNSt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEdSt4lessIS5_ESaISt4pairIKS5_dEEEixEOS5_ at Base 2.4.1
> + _ZNSt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEmSt4lessIS5_ESaISt4pairIKS5_mEEEixERS9_ at Base 2.4.1-5
>   _ZNSt5dequeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED1Ev at Base 2.4.1
>   _ZNSt5dequeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED2Ev at Base 2.4.1
>   _ZNSt6vectorIN3bpp19GeneMapperCsvExport6AlleleESaIS2_EE17_M_realloc_insertIJRKS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ at Base 2.4.1
>   _ZNSt6vectorIN3bpp9LocusInfoESaIS1_EE17_M_realloc_insertIJS1_EEEvN9__gnu_cxx17__normal_iteratorIPS1_S3_EEDpOT_ at Base 2.4.1
> - _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE12emplace_backIJS5_EEEvDpOT_ at Base 2.4.1
> + _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE12emplace_backIJS5_EEERS5_DpOT_ at Base 2.4.1-5
> +#MISSING: 2.4.1-5# _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE12emplace_backIJS5_EEEvDpOT_ at Base 2.4.1
>   _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE17_M_default_appendEm at Base 2.4.1
>   _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE17_M_realloc_insertIJRKS5_EEEvN9__gnu_cxx17__normal_iteratorIPS5_S7_EEDpOT_ at Base 2.4.1
>   _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE17_M_realloc_insertIJS5_EEEvN9__gnu_cxx17__normal_iteratorIPS5_S7_EEDpOT_ at Base 2.4.1
> @@ -982,6 +986,8 @@
>   _ZNSt6vectorImSaImEE17_M_realloc_insertIJRKmEEEvN9__gnu_cxx17__normal_iteratorIPmS1_EEDpOT_ at Base 2.4.1
>   _ZNSt6vectorImSaImEE17_M_realloc_insertIJmEEEvN9__gnu_cxx17__normal_iteratorIPmS1_EEDpOT_ at Base 2.4.1
>   _ZNSt6vectorImSaImEE8_M_eraseEN9__gnu_cxx17__normal_iteratorIPmS1_EE at Base 2.4.1
> + _ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC1IS3_EEPKcRKS3_ at Base 2.4.1-5
> + _ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC2IS3_EEPKcRKS3_ at Base 2.4.1-5
>   _ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED0Ev at Base 2.4.1
>   _ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED1Ev at Base 2.4.1
>   _ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED2Ev at Base 2.4.1
> @@ -1343,6 +1349,7 @@
>   _ZTv0_n56_N3bpp4Site11setPositionEi at Base 2.4.1
>   _ZTv0_n56_NK3bpp15BasicSymbolList4sizeEv at Base 2.4.1
>   _ZTv0_n56_NK3bpp25AbstractSequenceContainer8toStringERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 2.4.1
> + _ZTv0_n64_NK3bpp20AbstractCoreSequence11getCommentsB5cxx11Ev at Base 2.4.1-5
>   _ZTv0_n72_NK3bpp15DarwinVarSingle5writeERSoRKNS_7DataSetE at Base 2.4.1
>   _ZTv0_n72_NK3bpp9DarwinDon5writeERSoRKNS_7DataSetE at Base 2.4.1
>   _ZTv0_n80_N3bpp29PolymorphismSequenceContainer11addSequenceERKNS_8SequenceEb at Base 2.4.1
> dh_makeshlibs: error: failing due to earlier errors
> make: *** [debian/rules:8: binary] Error 25

The full build log is available from:
http://qa-logs.debian.net/2021/10/23/libbpp-popgen_2.4.1-5_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!

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.