[Debian-med-packaging] Bug#1002217: gatb-core: FTBFS: dpkg-gensymbols: error: some symbols or patterns disappeared in the symbols file: see diff output below

[Lucas Nussbaum]

Source: gatb-core
Version: 1.4.2+dfsg-7
Severity: serious
Justification: FTBFS
Tags: bookworm sid ftbfs
User: lucas at debian.org
Usertags: ftbfs-20211220 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>>'
> # test data are installed manually from main source to enable Architecture all builds
> rm -rf debian/tmp/usr/test/db
> dh_missing
> make[1]: Leaving directory '/<<PKGBUILDDIR>>'
>    dh_dwz -a -O--sourcedirectory=gatb-core
>    dh_strip -a -O--sourcedirectory=gatb-core
>    dh_makeshlibs -a -O--sourcedirectory=gatb-core
> 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/libgatbcore3/DEBIAN/symbols doesn't match completely debian/libgatbcore3.symbols.amd64
> --- debian/libgatbcore3.symbols.amd64 (libgatbcore3_1.4.2+dfsg-7_amd64)
> +++ dpkg-gensymbolsRm0XCf	2021-12-20 18:43:02.722758120 +0000
> @@ -428,6 +428,7 @@
>   _ZN4gatb4core4kmer4impl12BloomBuilderILm32EE5buildEPNS0_5tools2dp8IteratorINS2_4KmerILm32EE5CountEEEPNS5_4misc11IPropertiesE at Base 1.4.2
>   _ZN4gatb4core4kmer4impl12BloomBuilderILm64EE5buildEPNS0_5tools2dp8IteratorINS2_4KmerILm64EE5CountEEEPNS5_4misc11IPropertiesE at Base 1.4.2
>   _ZN4gatb4core4kmer4impl12BloomBuilderILm96EE5buildEPNS0_5tools2dp8IteratorINS2_4KmerILm96EE5CountEEEPNS5_4misc11IPropertiesE at Base 1.4.2
> + _ZN4gatb4core4kmer4impl12KxmerPointerILm128EE4nextEv at Base 1.4.2+dfsg-7
>   _ZN4gatb4core4kmer4impl12KxmerPointerILm128EEC1EPPNS0_5tools4math8LargeIntILi4EEEiiiiiPmPPt at Base 1.4.2
>   _ZN4gatb4core4kmer4impl12KxmerPointerILm128EEC2EPPNS0_5tools4math8LargeIntILi4EEEiiiiiPmPPt at Base 1.4.2
>   _ZN4gatb4core4kmer4impl12KxmerPointerILm32EEC1EPPNS0_5tools4math8LargeIntILi1EEEiiiiiPmPPt at Base 1.4.2
> @@ -5328,9 +5329,9 @@
>   _ZN4gatb4core8debruijn4impl11GraphVectorINS2_15BranchingEdge_tINS2_6Node_tINS0_5tools4math15IntegerTemplateIN5boost3mpl7vector4IN4mpl_4int_ILi32EEENSD_ILi64EEENSD_ILi96EEENSD_ILi128EEEEEEEEENS2_6Edge_tISK_EEEELi16EED1Ev at Base 1.4.2
>   _ZN4gatb4core8debruijn4impl11GraphVectorINS2_15BranchingEdge_tINS2_6Node_tINS0_5tools4math15IntegerTemplateIN5boost3mpl7vector4IN4mpl_4int_ILi32EEENSD_ILi64EEENSD_ILi96EEENSD_ILi128EEEEEEEEENS2_6Edge_tISK_EEEELi16EED2Ev at Base 1.4.2
>   _ZN4gatb4core8debruijn4impl11GraphVectorINS2_6Edge_tINS2_6Node_tINS0_5tools4math15IntegerTemplateIN5boost3mpl7vector4IN4mpl_4int_ILi32EEENSD_ILi64EEENSD_ILi96EEENSD_ILi128EEEEEEEEEEELi16EEC1EOSM_ at Base 1.4.2
> - _ZN4gatb4core8debruijn4impl11GraphVectorINS2_6Edge_tINS2_6Node_tINS0_5tools4math15IntegerTemplateIN5boost3mpl7vector4IN4mpl_4int_ILi32EEENSD_ILi64EEENSD_ILi96EEENSD_ILi128EEEEEEEEEEELi16EEC1Ev at Base 1.4.2
> +#MISSING: 1.4.2+dfsg-7# _ZN4gatb4core8debruijn4impl11GraphVectorINS2_6Edge_tINS2_6Node_tINS0_5tools4math15IntegerTemplateIN5boost3mpl7vector4IN4mpl_4int_ILi32EEENSD_ILi64EEENSD_ILi96EEENSD_ILi128EEEEEEEEEEELi16EEC1Ev at Base 1.4.2
>   _ZN4gatb4core8debruijn4impl11GraphVectorINS2_6Edge_tINS2_6Node_tINS0_5tools4math15IntegerTemplateIN5boost3mpl7vector4IN4mpl_4int_ILi32EEENSD_ILi64EEENSD_ILi96EEENSD_ILi128EEEEEEEEEEELi16EEC2EOSM_ at Base 1.4.2
> - _ZN4gatb4core8debruijn4impl11GraphVectorINS2_6Edge_tINS2_6Node_tINS0_5tools4math15IntegerTemplateIN5boost3mpl7vector4IN4mpl_4int_ILi32EEENSD_ILi64EEENSD_ILi96EEENSD_ILi128EEEEEEEEEEELi16EEC2Ev at Base 1.4.2
> +#MISSING: 1.4.2+dfsg-7# _ZN4gatb4core8debruijn4impl11GraphVectorINS2_6Edge_tINS2_6Node_tINS0_5tools4math15IntegerTemplateIN5boost3mpl7vector4IN4mpl_4int_ILi32EEENSD_ILi64EEENSD_ILi96EEENSD_ILi128EEEEEEEEEEELi16EEC2Ev at Base 1.4.2
>   _ZN4gatb4core8debruijn4impl11GraphVectorINS2_6Edge_tINS2_6Node_tINS0_5tools4math15IntegerTemplateIN5boost3mpl7vector4IN4mpl_4int_ILi32EEENSD_ILi64EEENSD_ILi96EEENSD_ILi128EEEEEEEEEEELi16EED1Ev at Base 1.4.2
>   _ZN4gatb4core8debruijn4impl11GraphVectorINS2_6Edge_tINS2_6Node_tINS0_5tools4math15IntegerTemplateIN5boost3mpl7vector4IN4mpl_4int_ILi32EEENSD_ILi64EEENSD_ILi96EEENSD_ILi128EEEEEEEEEEELi16EED2Ev at Base 1.4.2
>   _ZN4gatb4core8debruijn4impl11GraphVectorINS2_6Node_tINS0_5tools4math15IntegerTemplateIN5boost3mpl7vector4IN4mpl_4int_ILi32EEENSC_ILi64EEENSC_ILi96EEENSC_ILi128EEEEEEEEELi16EEC1EOSK_ at Base 1.4.2
> @@ -5716,19 +5717,19 @@
>   _ZN4gatb4core8debruijn4impl13GraphTemplateINS2_6Node_tINS0_5tools4math8LargeIntILi4EEEEENS2_6Edge_tIS9_EEN5boost7variantINS2_9GraphDataILm128EEEJEEEED2Ev at Base 1.4.2
>   _ZN4gatb4core8debruijn4impl13GraphTemplateINS2_6Node_tINS0_5tools4math8LargeIntILi4EEEEENS2_6Edge_tIS9_EEN5boost7variantINS2_9GraphDataILm128EEEJEEEEaSERKSH_ at Base 1.4.2
>   _ZN4gatb4core8debruijn4impl13bcalm_loggingE at Base 1.4.2
> - _ZN4gatb4core8debruijn4impl14CustomListenerINS0_4kmer4impl4KmerILm128EE5CountEE15finishPostponedEv at Base 1.4.2
> +#MISSING: 1.4.2+dfsg-7# _ZN4gatb4core8debruijn4impl14CustomListenerINS0_4kmer4impl4KmerILm128EE5CountEE15finishPostponedEv at Base 1.4.2
>   _ZN4gatb4core8debruijn4impl14CustomListenerINS0_4kmer4impl4KmerILm128EE5CountEE6finishEv at Base 1.4.2
>   _ZN4gatb4core8debruijn4impl14CustomListenerINS0_4kmer4impl4KmerILm128EE5CountEED0Ev at Base 1.4.2
>   _ZN4gatb4core8debruijn4impl14CustomListenerINS0_4kmer4impl4KmerILm128EE5CountEED1Ev at Base 1.4.2
> - _ZN4gatb4core8debruijn4impl14CustomListenerINS0_4kmer4impl4KmerILm32EE5CountEE15finishPostponedEv at Base 1.4.2
> +#MISSING: 1.4.2+dfsg-7# _ZN4gatb4core8debruijn4impl14CustomListenerINS0_4kmer4impl4KmerILm32EE5CountEE15finishPostponedEv at Base 1.4.2
>   _ZN4gatb4core8debruijn4impl14CustomListenerINS0_4kmer4impl4KmerILm32EE5CountEE6finishEv at Base 1.4.2
>   _ZN4gatb4core8debruijn4impl14CustomListenerINS0_4kmer4impl4KmerILm32EE5CountEED0Ev at Base 1.4.2
>   _ZN4gatb4core8debruijn4impl14CustomListenerINS0_4kmer4impl4KmerILm32EE5CountEED1Ev at Base 1.4.2
> - _ZN4gatb4core8debruijn4impl14CustomListenerINS0_4kmer4impl4KmerILm64EE5CountEE15finishPostponedEv at Base 1.4.2
> +#MISSING: 1.4.2+dfsg-7# _ZN4gatb4core8debruijn4impl14CustomListenerINS0_4kmer4impl4KmerILm64EE5CountEE15finishPostponedEv at Base 1.4.2
>   _ZN4gatb4core8debruijn4impl14CustomListenerINS0_4kmer4impl4KmerILm64EE5CountEE6finishEv at Base 1.4.2
>   _ZN4gatb4core8debruijn4impl14CustomListenerINS0_4kmer4impl4KmerILm64EE5CountEED0Ev at Base 1.4.2
>   _ZN4gatb4core8debruijn4impl14CustomListenerINS0_4kmer4impl4KmerILm64EE5CountEED1Ev at Base 1.4.2
> - _ZN4gatb4core8debruijn4impl14CustomListenerINS0_4kmer4impl4KmerILm96EE5CountEE15finishPostponedEv at Base 1.4.2
> +#MISSING: 1.4.2+dfsg-7# _ZN4gatb4core8debruijn4impl14CustomListenerINS0_4kmer4impl4KmerILm96EE5CountEE15finishPostponedEv at Base 1.4.2
>   _ZN4gatb4core8debruijn4impl14CustomListenerINS0_4kmer4impl4KmerILm96EE5CountEE6finishEv at Base 1.4.2
>   _ZN4gatb4core8debruijn4impl14CustomListenerINS0_4kmer4impl4KmerILm96EE5CountEED0Ev at Base 1.4.2
>   _ZN4gatb4core8debruijn4impl14CustomListenerINS0_4kmer4impl4KmerILm96EE5CountEED1Ev at Base 1.4.2
> dh_makeshlibs: error: failing due to earlier errors
> make: *** [debian/rules:15: binary] Error 25


The full build log is available from:
http://qa-logs.debian.net/2021/12/20/gatb-core_1.4.2+dfsg-7_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.