[Debian-med-packaging] Bug#1015525: libssw: ftbfs with LTO (link time optimization) enabled

[Matthias Klose]

Package: src:libssw
Version: 1.1-13
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/libssw_1.1-13_unstable_dpkglto.log
The last lines of the build log are at the end of this report.

[...]
Target:     9707    TGTTGATTGTTTC-CTTT    9723
                    |**|*||| |||| ||||
Query:       958    TTCTAATT-TTTCACTTT    974

make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   create-stamp debian/debhelper-build-stamp
   dh_prep
   debian/rules override_dh_auto_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
sed 's/@DEB_HOST_MULTIARCH@/x86_64-linux-gnu/g' debian/libssw0.install.in > debian/libssw0.install
sed 's/@DEB_HOST_MULTIARCH@/x86_64-linux-gnu/g' debian/libssw-dev.install.in > debian/libssw-dev.install
sed -e 's/@DEB_HOST_MULTIARCH@/x86_64-linux-gnu/g' \
            -e 's/@DEB_JAVA_PKG_VERSION@/1.1/g' debian/libssw-dev.links.in > debian/libssw-dev.links
sed 's/@DEB_HOST_MULTIARCH@/x86_64-linux-gnu/g' debian/libssw-java.install.in > debian/libssw-java.install
sed -e 's/@DEB_HOST_MULTIARCH@/x86_64-linux-gnu/g' \
            -e 's/@DEB_JAVA_PKG_VERSION@/1.1/g' debian/libssw-java.links.in > debian/libssw-java.links
mv src/ssw.jar src/ssw-1.1.jar
dh_auto_install
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_install
   jh_installjavadoc
   dh_installdocs
   dh_installchangelogs
   debian/rules override_dh_installman
make[1]: Entering directory '/<<PKGBUILDDIR>>'
LD_LIBRARY_PATH=`pwd`/src help2man --version-string=' ' --help-option=' ' \
          -I debian/extra-man-info.txt \
          -N -n 'fast Smith-Waterman aligner' \
          --no-discard-stderr src/ssw-align \
            | fgrep -v ERROR > debian/ssw-align.1
dh_installman
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_perl
   dh_link
   jh_installlibs
   jh_classpath
   jh_manifest
   jh_exec
   jh_depends
   mh_installpoms
   mh_linkjars --skip-clean-poms
   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/libssw0/DEBIAN/symbols doesn't match completely debian/libssw0.symbols
--- debian/libssw0.symbols (libssw0_1.1-13_amd64)
+++ dpkg-gensymbolsVnLhzb	2022-06-10 09:01:36.513958266 +0000
@@ -21,10 +21,10 @@
  _ZNK20StripedSmithWaterman7Aligner13TranslateBaseEPKcRKiPa at Base 1.1
  _ZNK20StripedSmithWaterman7Aligner5AlignEPKcRKNS_6FilterEPNS_9AlignmentE at Base 1.1
  _ZNK20StripedSmithWaterman7Aligner5AlignEPKcS2_RKiRKNS_6FilterEPNS_9AlignmentE at Base 1.1
- (optional)_ZNSt6vectorIjSaIjEE17_M_realloc_insertIJRKjEEEvN9__gnu_cxx17__normal_iteratorIPjS1_EEDpOT_ at Base 1.1
- _ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED0Ev at Base 1.1
- _ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED1Ev at Base 1.1
- _ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED2Ev at Base 1.1
+#MISSING: 1.1-13# (optional)_ZNSt6vectorIjSaIjEE17_M_realloc_insertIJRKjEEEvN9__gnu_cxx17__normal_iteratorIPjS1_EEDpOT_ at Base 1.1
+#MISSING: 1.1-13# _ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED0Ev at Base 1.1
+#MISSING: 1.1-13# _ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED1Ev at Base 1.1
+#MISSING: 1.1-13# _ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED2Ev at Base 1.1
  align_destroy at Base 1.1
  init_destroy at Base 1.1
  mark_mismatch at Base 1.1
dh_makeshlibs: error: failing due to earlier errors
make: *** [debian/rules:20: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2