[Debian-med-packaging] Bug#1015477: libbpp-raa: ftbfs with LTO (link time optimization) enabled

[Matthias Klose]

Package: src:libbpp-raa
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-raa_2.4.1-6_unstable_dpkglto.log
The last lines of the build log are at the end of this report.

[...]
mv /<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu/libbpp-raa.so.4.0.0 debian/libbpp-raa4/usr/lib/x86_64-linux-gnu
PKGDEV=libbpp-raa-dev
PKGSHL=libbpp-raa4
install -d -m 755 debian/libbpp-raa-dev/usr/include
mv debian/tmp/usr/include/Bpp debian/libbpp-raa-dev/usr/include
install -d -m 755 debian/libbpp-raa-dev/usr/lib/x86_64-linux-gnu
mv debian/tmp/usr/lib/x86_64-linux-gnu/cmake debian/libbpp-raa-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: error: some symbols or patterns disappeared in the symbols file: see diff output below
dpkg-gensymbols: warning: debian/libbpp-raa4/DEBIAN/symbols doesn't match completely debian/libbpp-raa4.symbols.amd64
--- debian/libbpp-raa4.symbols.amd64 (libbpp-raa4_2.4.1-6_amd64)
+++ dpkg-gensymbolsovHrDi	2022-06-10 09:08:35.552287980 +0000
@@ -11,12 +11,12 @@
  _ZN3bpp14RaaSpeciesTree8findNodeEi at Base 2.4.1
  _ZN3bpp14RaaSpeciesTree8getMajorEi at Base 2.4.1
  _ZN3bpp14RaaSpeciesTree9nextChildEii at Base 2.4.1
- _ZN3bpp16BadCharExceptionD0Ev at Base 2.4.1
- _ZN3bpp16BadCharExceptionD1Ev at Base 2.4.1
- _ZN3bpp16BadCharExceptionD2Ev at Base 2.4.1
- _ZN3bpp17AlphabetExceptionD0Ev at Base 2.4.1
- _ZN3bpp17AlphabetExceptionD1Ev at Base 2.4.1
- _ZN3bpp17AlphabetExceptionD2Ev at Base 2.4.1
+#MISSING: 2.4.1-6# _ZN3bpp16BadCharExceptionD0Ev at Base 2.4.1
+#MISSING: 2.4.1-6# _ZN3bpp16BadCharExceptionD1Ev at Base 2.4.1
+#MISSING: 2.4.1-6# _ZN3bpp16BadCharExceptionD2Ev at Base 2.4.1
+#MISSING: 2.4.1-6# _ZN3bpp17AlphabetExceptionD0Ev at Base 2.4.1
+#MISSING: 2.4.1-6# _ZN3bpp17AlphabetExceptionD1Ev at Base 2.4.1
+#MISSING: 2.4.1-6# _ZN3bpp17AlphabetExceptionD2Ev at Base 2.4.1
  _ZN3bpp3RAA10deleteListEPNS_7RaaListE at Base 2.4.1
  _ZN3bpp3RAA10getSeqFragERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiiRS6_ at Base 2.4.1
  _ZN3bpp3RAA10getSeqFragEiiiRNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 2.4.1
@@ -70,15 +70,15 @@
  _ZN3bpp7RaaList8zeroListEv at Base 2.4.1
  _ZN3bpp7RaaListC1Ev at Base 2.4.1
  _ZN3bpp7RaaListC2Ev at Base 2.4.1
- _ZNK3bpp17AlphabetException11getAlphabetEv at Base 2.4.1
- _ZNSt12_Vector_baseINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED1Ev at Base 2.4.1
- _ZNSt12_Vector_baseINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED2Ev 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_insertIJS5_EEEvN9__gnu_cxx17__normal_iteratorIPS5_S7_EEDpOT_ at Base 2.4.1
- _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED1Ev at Base 2.4.1
- _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED2Ev at Base 2.4.1
- _ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC1IS3_EEPKcRKS3_ at Base 2.4.1
- _ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC2IS3_EEPKcRKS3_ at Base 2.4.1
+#MISSING: 2.4.1-6# _ZNK3bpp17AlphabetException11getAlphabetEv at Base 2.4.1
+#MISSING: 2.4.1-6# _ZNSt12_Vector_baseINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED1Ev at Base 2.4.1
+#MISSING: 2.4.1-6# _ZNSt12_Vector_baseINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED2Ev at Base 2.4.1
+#MISSING: 2.4.1-6# _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE17_M_default_appendEm at Base 2.4.1
+#MISSING: 2.4.1-6# _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE17_M_realloc_insertIJS5_EEEvN9__gnu_cxx17__normal_iteratorIPS5_S7_EEDpOT_ at Base 2.4.1
+#MISSING: 2.4.1-6# _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED1Ev at Base 2.4.1
+#MISSING: 2.4.1-6# _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED2Ev at Base 2.4.1
+#MISSING: 2.4.1-6# _ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC1IS3_EEPKcRKS3_ at Base 2.4.1
+#MISSING: 2.4.1-6# _ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC2IS3_EEPKcRKS3_ at Base 2.4.1
  _ZTINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 2.4.1
  _ZTSNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 2.4.1
  ajout_reponse 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