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@Base 1.1
_ZNK20StripedSmithWaterman7Aligner5AlignEPKcRKNS_6FilterEPNS_9AlignmentE@Base 1.1
_ZNK20StripedSmithWaterman7Aligner5AlignEPKcS2_RKiRKNS_6FilterEPNS_9AlignmentE@Base 1.1
- (optional)_ZNSt6vectorIjSaIjEE17_M_realloc_insertIJRKjEEEvN9__gnu_cxx17__normal_iteratorIPjS1_EEDpOT_@Base 1.1
- _ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED0Ev@Base 1.1
- _ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED1Ev@Base 1.1
- _ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED2Ev@Base 1.1
+#MISSING: 1.1-13# (optional)_ZNSt6vectorIjSaIjEE17_M_realloc_insertIJRKjEEEvN9__gnu_cxx17__normal_iteratorIPjS1_EEDpOT_@Base 1.1
+#MISSING: 1.1-13# _ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED0Ev@Base 1.1
+#MISSING: 1.1-13# _ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED1Ev@Base 1.1
+#MISSING: 1.1-13# _ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED2Ev@Base 1.1
align_destroy@Base 1.1
init_destroy@Base 1.1
mark_mismatch@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