[Debian-med-packaging] Bug#1015474: libbpp-popgen: ftbfs with LTO (link time optimization) enabled

[Matthias Klose]

Package: src:libbpp-popgen
Version: 2.4.1-6
Severity: minor
Tags: sid bookworm
User: debian-gcc at lists.debian.org
Usertags: ftbfs-lto

This package currently fails to build (at least on the amd64
architecture) with link time optimizations enabled.  For a background
for LTO please see

https://wiki.debian.org/ToolChain/LTO

The goal is to enable this optimization by default in an upcoming
Debian release in dpkg-buildflags for 64bit architectures.  The goal
is to get this package to build with link time optimizations, or to
explicitly disable link time optimizations for this package build.

To reproduce the build failure, enable the lto optimization in
testing/unstable by adding "optimize=+lto" to DEB_BUILD_MAINT_OPTIONS
in the debian/rules file, or if this macro is unset, just set it:

export DEB_BUILD_MAINT_OPTIONS = optimize=+lto

Please try to fix the build with lto enabled, fixing the packaging or
forwarding the issue upstream. If the issue cannot be fixed,
explicitly disallow building the package with lto by adding to your
rules file:

export DEB_BUILD_MAINT_OPTIONS = optimize=-lto

or adding that string to your existing setting of DEB_BUILD_MAINT_OPTIONS.

The full build log can be found at:
http://qa-logs.debian.net/2022/06/09/dpkglto/libbpp-popgen_2.4.1-6_unstable_dpkglto.log
The last lines of the build log are at the end of this report.

[...]
- _ZTv0_n304_N3bpp19VectorSiteContainer7valueAtEmm at Base 2.4.1
- _ZTv0_n312_NK3bpp19VectorSiteContainer7valueAtEmm at Base 2.4.1
- _ZTv0_n320_N3bpp19VectorSiteContainerclEmm at Base 2.4.1
- _ZTv0_n328_NK3bpp19VectorSiteContainerclEmm at Base 2.4.1
- _ZTv0_n32_NK3bpp11GeneticCode17getSourceAlphabetEv at Base 2.4.1
- _ZTv0_n32_NK3bpp9IODataSet11getDataTypeB5cxx11Ev at Base 2.4.1
- _ZTv0_n40_NK3bpp11PopgenlibIO13getFormatNameB5cxx11Ev at Base 2.4.1
- _ZTv0_n40_NK3bpp15DarwinVarSingle13getFormatNameB5cxx11Ev at Base 2.4.1
- _ZTv0_n40_NK3bpp19GeneMapperCsvExport13getFormatNameB5cxx11Ev at Base 2.4.1
- _ZTv0_n40_NK3bpp7Genepop13getFormatNameB5cxx11Ev at Base 2.4.1
- _ZTv0_n40_NK3bpp7Genetix13getFormatNameB5cxx11Ev at Base 2.4.1
- _ZTv0_n40_NK3bpp9DarwinDon13getFormatNameB5cxx11Ev at Base 2.4.1
- _ZTv0_n48_NK3bpp11PopgenlibIO20getFormatDescriptionB5cxx11Ev at Base 2.4.1
- _ZTv0_n48_NK3bpp15BasicSymbolList11getAlphabetEv at Base 2.4.1
- _ZTv0_n48_NK3bpp15DarwinVarSingle20getFormatDescriptionB5cxx11Ev at Base 2.4.1
- _ZTv0_n48_NK3bpp16AbstractCoreSite11getPositionEv at Base 2.4.1
- _ZTv0_n48_NK3bpp19GeneMapperCsvExport20getFormatDescriptionB5cxx11Ev at Base 2.4.1
- _ZTv0_n48_NK3bpp20AbstractCoreSequence7getNameB5cxx11Ev at Base 2.4.1
- _ZTv0_n48_NK3bpp25AbstractSequenceContainer11getAlphabetEv at Base 2.4.1
- _ZTv0_n48_NK3bpp4Site11getPositionEv at Base 2.4.1
- _ZTv0_n48_NK3bpp7Genepop20getFormatDescriptionB5cxx11Ev at Base 2.4.1
- _ZTv0_n48_NK3bpp7Genetix20getFormatDescriptionB5cxx11Ev at Base 2.4.1
- _ZTv0_n48_NK3bpp9DarwinDon20getFormatDescriptionB5cxx11Ev at Base 2.4.1
- _ZTv0_n56_N3bpp16AbstractCoreSite11setPositionEi at Base 2.4.1
- _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
+#MISSING: 2.4.1-6# _ZTv0_n272_NK3bpp25AbstractSequenceContainer7getNameB5cxx11Em at Base 2.4.1
+#MISSING: 2.4.1-6# _ZTv0_n280_NK3bpp25AbstractSequenceContainer11getCommentsB5cxx11Em at Base 2.4.1
+#MISSING: 2.4.1-6# _ZTv0_n304_N3bpp19VectorSiteContainer7valueAtEmm at Base 2.4.1
+#MISSING: 2.4.1-6# _ZTv0_n312_NK3bpp19VectorSiteContainer7valueAtEmm at Base 2.4.1
+#MISSING: 2.4.1-6# _ZTv0_n320_N3bpp19VectorSiteContainerclEmm at Base 2.4.1
+#MISSING: 2.4.1-6# _ZTv0_n328_NK3bpp19VectorSiteContainerclEmm at Base 2.4.1
+#MISSING: 2.4.1-6# _ZTv0_n32_NK3bpp11GeneticCode17getSourceAlphabetEv at Base 2.4.1
+#MISSING: 2.4.1-6# _ZTv0_n32_NK3bpp9IODataSet11getDataTypeB5cxx11Ev at Base 2.4.1
+#MISSING: 2.4.1-6# _ZTv0_n40_NK3bpp11PopgenlibIO13getFormatNameB5cxx11Ev at Base 2.4.1
+#MISSING: 2.4.1-6# _ZTv0_n40_NK3bpp15DarwinVarSingle13getFormatNameB5cxx11Ev at Base 2.4.1
+#MISSING: 2.4.1-6# _ZTv0_n40_NK3bpp19GeneMapperCsvExport13getFormatNameB5cxx11Ev at Base 2.4.1
+#MISSING: 2.4.1-6# _ZTv0_n40_NK3bpp7Genepop13getFormatNameB5cxx11Ev at Base 2.4.1
+#MISSING: 2.4.1-6# _ZTv0_n40_NK3bpp7Genetix13getFormatNameB5cxx11Ev at Base 2.4.1
+#MISSING: 2.4.1-6# _ZTv0_n40_NK3bpp9DarwinDon13getFormatNameB5cxx11Ev at Base 2.4.1
+#MISSING: 2.4.1-6# _ZTv0_n48_NK3bpp11PopgenlibIO20getFormatDescriptionB5cxx11Ev at Base 2.4.1
+#MISSING: 2.4.1-6# _ZTv0_n48_NK3bpp15BasicSymbolList11getAlphabetEv at Base 2.4.1
+#MISSING: 2.4.1-6# _ZTv0_n48_NK3bpp15DarwinVarSingle20getFormatDescriptionB5cxx11Ev at Base 2.4.1
+#MISSING: 2.4.1-6# _ZTv0_n48_NK3bpp16AbstractCoreSite11getPositionEv at Base 2.4.1
+#MISSING: 2.4.1-6# _ZTv0_n48_NK3bpp19GeneMapperCsvExport20getFormatDescriptionB5cxx11Ev at Base 2.4.1
+#MISSING: 2.4.1-6# _ZTv0_n48_NK3bpp20AbstractCoreSequence7getNameB5cxx11Ev at Base 2.4.1
+#MISSING: 2.4.1-6# _ZTv0_n48_NK3bpp25AbstractSequenceContainer11getAlphabetEv at Base 2.4.1
+#MISSING: 2.4.1-6# _ZTv0_n48_NK3bpp4Site11getPositionEv at Base 2.4.1
+#MISSING: 2.4.1-6# _ZTv0_n48_NK3bpp7Genepop20getFormatDescriptionB5cxx11Ev at Base 2.4.1
+#MISSING: 2.4.1-6# _ZTv0_n48_NK3bpp7Genetix20getFormatDescriptionB5cxx11Ev at Base 2.4.1
+#MISSING: 2.4.1-6# _ZTv0_n48_NK3bpp9DarwinDon20getFormatDescriptionB5cxx11Ev at Base 2.4.1
+#MISSING: 2.4.1-6# _ZTv0_n56_N3bpp16AbstractCoreSite11setPositionEi at Base 2.4.1
+#MISSING: 2.4.1-6# _ZTv0_n56_N3bpp4Site11setPositionEi at Base 2.4.1
+#MISSING: 2.4.1-6# _ZTv0_n56_NK3bpp15BasicSymbolList4sizeEv at Base 2.4.1
+#MISSING: 2.4.1-6# _ZTv0_n56_NK3bpp25AbstractSequenceContainer8toStringERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 2.4.1
+#MISSING: 2.4.1-6# _ZTv0_n64_NK3bpp20AbstractCoreSequence11getCommentsB5cxx11Ev at Base 2.4.1
  _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
+#MISSING: 2.4.1-6# _ZTv0_n80_N3bpp29PolymorphismSequenceContainer11addSequenceERKNS_8SequenceEb at Base 2.4.1
  _ZTv0_n80_NK3bpp15DarwinVarSingle5writeERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKNS_7DataSetEb at Base 2.4.1
  _ZTv0_n80_NK3bpp9DarwinDon5writeERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKNS_7DataSetEb at Base 2.4.1
  _ZTv0_n96_N3bpp29PolymorphismSequenceContainer14removeSequenceERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 2.4.1
- _ZZNSt8__detail18__to_chars_10_implImEEvPcjT_E8__digits at Base 2.4.1
+#MISSING: 2.4.1-6# _ZZNSt8__detail18__to_chars_10_implImEEvPcjT_E8__digits at Base 2.4.1
dh_makeshlibs: error: failing due to earlier errors
make: *** [debian/rules:8: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2