[Debian-med-packaging] Bug#1015478: libbpp-seq: ftbfs with LTO (link time optimization) enabled

[Matthias Klose]

Package: src:libbpp-seq
Version: 2.4.1-7
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-seq_2.4.1-7_unstable_dpkglto.log
The last lines of the build log are at the end of this report.

[...]
+#MISSING: 2.4.1-7# _ZTv0_n80_NK3bpp15NexusIOSequence13readSequencesERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEPKNS_8AlphabetE at Base 2.4.1
+#MISSING: 2.4.1-7# _ZTv0_n80_NK3bpp17AbstractOSequence14writeAlignmentERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKNS_13SiteContainerEb at Base 2.4.1
+#MISSING: 2.4.1-7# _ZTv0_n80_NK3bpp17AbstractOSequence14writeSequencesERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKNS_17SequenceContainerEb at Base 2.4.1
+#MISSING: 2.4.1-7# _ZTv0_n80_NK3bpp18AbstractOAlignment14writeAlignmentERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKNS_13SiteContainerEb at Base 2.4.1
+#MISSING: 2.4.1-7# _ZTv0_n80_NK3bpp4DCSE13readSequencesERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEPKNS_8AlphabetE at Base 2.4.1
+#MISSING: 2.4.1-7# _ZTv0_n80_NK3bpp4Mase14writeSequencesERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKNS_17SequenceContainerEb at Base 2.4.1
+#MISSING: 2.4.1-7# _ZTv0_n80_NK3bpp5Fasta14writeSequencesERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKNS_17SequenceContainerEb at Base 2.4.1
+#MISSING: 2.4.1-7# _ZTv0_n80_NK3bpp6Phylip13readSequencesERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEPKNS_8AlphabetE at Base 2.4.1
+#MISSING: 2.4.1-7# _ZTv0_n80_NK3bpp6Phylip14writeAlignmentERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKNS_13SiteContainerEb at Base 2.4.1
+#MISSING: 2.4.1-7# _ZTv0_n80_NK3bpp7Clustal13readSequencesERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEPKNS_8AlphabetE at Base 2.4.1
+#MISSING: 2.4.1-7# _ZTv0_n80_NK3bpp7Clustal14writeAlignmentERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKNS_13SiteContainerEb at Base 2.4.1
+#MISSING: 2.4.1-7# _ZTv0_n80_NK3bpp9Stockholm14writeAlignmentERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKNS_13SiteContainerEb at Base 2.4.1
  _ZTv0_n88_N3bpp12EdSymbolList10addElementERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 2.4.1
  _ZTv0_n88_N3bpp12SequenceMask21afterSequenceInsertedERKNS_24SymbolListInsertionEventE at Base 2.4.1
  _ZTv0_n88_N3bpp13BasicSequence10setToSizeLEm at Base 2.4.1
  _ZTv0_n88_N3bpp15BasicSymbolList10addElementERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 2.4.1
  _ZTv0_n88_N3bpp15SequenceQuality21afterSequenceInsertedERKNS_24SymbolListInsertionEventE at Base 2.4.1
- _ZTv0_n88_N3bpp19SequenceWithQuality10addElementERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 2.4.1
+#MISSING: 2.4.1-7# _ZTv0_n88_N3bpp19SequenceWithQuality10addElementERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 2.4.1
  _ZTv0_n88_N3bpp19VectorSiteContainer11setSequenceERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKNS_8SequenceEb at Base 2.4.1
  _ZTv0_n88_N3bpp20MapSequenceContainer11setSequenceERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKNS_8SequenceEb at Base 2.4.1
  _ZTv0_n88_N3bpp22SequenceWithAnnotation10setToSizeLEm at Base 2.4.1
- _ZTv0_n88_N3bpp23VectorSequenceContainer11setSequenceERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKNS_8SequenceEb at Base 2.4.1
+#MISSING: 2.4.1-7# _ZTv0_n88_N3bpp23VectorSequenceContainer11setSequenceERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKNS_8SequenceEb at Base 2.4.1
  _ZTv0_n88_N3bpp24AlignedSequenceContainer11setSequenceERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKNS_8SequenceEb at Base 2.4.1
- _ZTv0_n88_N3bpp29CompressedVectorSiteContainer11setSequenceERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKNS_8SequenceEb at Base 2.4.1
- _ZTv0_n88_NK3bpp12WordAlphabet12getNPositionEim at Base 2.4.1
- _ZTv0_n88_NK3bpp13CodonAlphabet12getNPositionEim at Base 2.4.1
+#MISSING: 2.4.1-7# _ZTv0_n88_N3bpp29CompressedVectorSiteContainer11setSequenceERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKNS_8SequenceEb at Base 2.4.1
+#MISSING: 2.4.1-7# _ZTv0_n88_NK3bpp12WordAlphabet12getNPositionEim at Base 2.4.1
+#MISSING: 2.4.1-7# _ZTv0_n88_NK3bpp13CodonAlphabet12getNPositionEim at Base 2.4.1
  _ZTv0_n96_N3bpp12EdSymbolList10addElementEmRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 2.4.1
- _ZTv0_n96_N3bpp12SequenceMask21beforeSequenceDeletedERKNS_23SymbolListDeletionEventE at Base 2.4.1
+#MISSING: 2.4.1-7# _ZTv0_n96_N3bpp12SequenceMask21beforeSequenceDeletedERKNS_23SymbolListDeletionEventE at Base 2.4.1
  _ZTv0_n96_N3bpp15BasicSymbolList10addElementEmRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 2.4.1
- _ZTv0_n96_N3bpp15SequenceQuality21beforeSequenceDeletedERKNS_23SymbolListDeletionEventE at Base 2.4.1
- _ZTv0_n96_N3bpp19SequenceWithQuality10addElementEmRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 2.4.1
+#MISSING: 2.4.1-7# _ZTv0_n96_N3bpp15SequenceQuality21beforeSequenceDeletedERKNS_23SymbolListDeletionEventE at Base 2.4.1
+#MISSING: 2.4.1-7# _ZTv0_n96_N3bpp19SequenceWithQuality10addElementEmRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 2.4.1
  _ZTv0_n96_N3bpp19VectorSiteContainer14removeSequenceERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 2.4.1
  _ZTv0_n96_N3bpp20MapSequenceContainer14removeSequenceERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 2.4.1
- _ZTv0_n96_N3bpp23VectorSequenceContainer14removeSequenceERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 2.4.1
- _ZTv0_n96_N3bpp29CompressedVectorSiteContainer14removeSequenceERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 2.4.1
- _ZTv0_n96_NK3bpp12WordAlphabet12getPositionsEi at Base 2.4.1
- _ZTv0_n96_NK3bpp13CodonAlphabet12getPositionsEi at Base 2.4.1
- _ZTv0_n96_NK3bpp19StandardGeneticCode21getNumberOfStopCodonsEv at Base 2.4.1
- _ZTv0_n96_NK3bpp28MoldMitochondrialGeneticCode21getNumberOfStopCodonsEv at Base 2.4.1
- _ZTv0_n96_NK3bpp29YeastMitochondrialGeneticCode21getNumberOfStopCodonsEv at Base 2.4.1
- _ZTv0_n96_NK3bpp32AscidianMitochondrialGeneticCode21getNumberOfStopCodonsEv at Base 2.4.1
- _ZTv0_n96_NK3bpp34EchinodermMitochondrialGeneticCode21getNumberOfStopCodonsEv at Base 2.4.1
- _ZTv0_n96_NK3bpp34VertebrateMitochondrialGeneticCode21getNumberOfStopCodonsEv at Base 2.4.1
- _ZTv0_n96_NK3bpp36InvertebrateMitochondrialGeneticCode21getNumberOfStopCodonsEv at Base 2.4.1
- _ZZNSt8__detail18__to_chars_10_implImEEvPcjT_E8__digits at Base 2.4.1
+#MISSING: 2.4.1-7# _ZTv0_n96_N3bpp23VectorSequenceContainer14removeSequenceERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 2.4.1
+#MISSING: 2.4.1-7# _ZTv0_n96_N3bpp29CompressedVectorSiteContainer14removeSequenceERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 2.4.1
+#MISSING: 2.4.1-7# _ZTv0_n96_NK3bpp12WordAlphabet12getPositionsEi at Base 2.4.1
+#MISSING: 2.4.1-7# _ZTv0_n96_NK3bpp13CodonAlphabet12getPositionsEi at Base 2.4.1
+#MISSING: 2.4.1-7# _ZTv0_n96_NK3bpp19StandardGeneticCode21getNumberOfStopCodonsEv at Base 2.4.1
+#MISSING: 2.4.1-7# _ZTv0_n96_NK3bpp28MoldMitochondrialGeneticCode21getNumberOfStopCodonsEv at Base 2.4.1
+#MISSING: 2.4.1-7# _ZTv0_n96_NK3bpp29YeastMitochondrialGeneticCode21getNumberOfStopCodonsEv at Base 2.4.1
+#MISSING: 2.4.1-7# _ZTv0_n96_NK3bpp32AscidianMitochondrialGeneticCode21getNumberOfStopCodonsEv at Base 2.4.1
+#MISSING: 2.4.1-7# _ZTv0_n96_NK3bpp34EchinodermMitochondrialGeneticCode21getNumberOfStopCodonsEv at Base 2.4.1
+#MISSING: 2.4.1-7# _ZTv0_n96_NK3bpp34VertebrateMitochondrialGeneticCode21getNumberOfStopCodonsEv at Base 2.4.1
+#MISSING: 2.4.1-7# _ZTv0_n96_NK3bpp36InvertebrateMitochondrialGeneticCode21getNumberOfStopCodonsEv at Base 2.4.1
+#MISSING: 2.4.1-7# _ZZNSt8__detail18__to_chars_10_implImEEvPcjT_E8__digits at Base 2.4.1
  _ZeqRKN3bpp4SiteES2_ at Base 2.4.1
  _ZltRKN3bpp4SiteES2_ at Base 2.4.1
dh_makeshlibs: error: failing due to earlier errors
make: *** [debian/rules:10: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2