[Debian-med-packaging] Bug#957476: libsmithwaterman: ftbfs with GCC-10

[Matthias Klose]

Package: src:libsmithwaterman
Version: 0.0+git20160702.2610e25-7
Severity: normal
Tags: sid bullseye
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-10

Please keep this issue open in the bug tracker for the package it
was filed for.  If a fix in another package is required, please
file a bug for the other package (or clone), and add a block in this
package. Please keep the issue open until the package can be built in
a follow-up test rebuild.

The package fails to build in a test rebuild on at least amd64 with
gcc-10/g++-10, but succeeds to build with gcc-9/g++-9. The
severity of this report will be raised before the bullseye release,
so nothing has to be done for the buster release.

The full build log can be found at:
http://people.debian.org/~doko/logs/gcc10-20200225/libsmithwaterman_0.0+git20160702.2610e25-7_unstable_gcc10.log
The last lines of the build log are at the end of this report.

To build with GCC 10, either set CC=gcc-10 CXX=g++-10 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.

  apt-get -t=experimental install g++ 

Common build failures are new warnings resulting in build failures with
-Werror turned on, or new/dropped symbols in Debian symbols files.
For other C/C++ related build failures see the porting guide at
http://gcc.gnu.org/gcc-10/porting_to.html

[...]
install -d -m 755 debian/libsmithwaterman-dev/usr/include
mv debian/tmp/usr/include/smithwaterman debian/libsmithwaterman-dev/usr/include
install -d -m 755 debian/libsmithwaterman-dev/usr/lib/x86_64-linux-gnu/pkgconfig
mv debian/tmp/usr/lib/*/pkgconfig/*.pc debian/libsmithwaterman-dev/usr/lib/x86_64-linux-gnu/pkgconfig
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_installdocs -O--no-parallel
   dh_installchangelogs -O--no-parallel
   dh_installman -O--no-parallel
   dh_installinit -O--no-parallel
   dh_perl -O--no-parallel
   dh_link -O--no-parallel
   dh_strip_nondeterminism -O--no-parallel
   dh_compress -O--no-parallel
   dh_fixperms -O--no-parallel
   dh_missing -O--no-parallel
   dh_strip -O--no-parallel
   dh_makeshlibs -O--no-parallel
dpkg-gensymbols: warning: some new symbols appeared in the symbols file: see diff output below
dpkg-gensymbols: error: some symbols or patterns disappeared in the symbols file: see diff output below
dpkg-gensymbols: warning: debian/libsmithwaterman0/DEBIAN/symbols doesn't match completely debian/libsmithwaterman0.symbols
--- debian/libsmithwaterman0.symbols (libsmithwaterman0_0.0+git20160702.2610e25-7_amd64)
+++ dpkg-gensymbolsv6JZfx	2020-02-26 12:53:02.790519615 +0000
@@ -48,12 +48,16 @@
  _ZN20CBandedSmithWatermanD1Ev at Base 0.0+git20160702.2610e25
  _ZN20CBandedSmithWatermanD2Ev at Base 0.0+git20160702.2610e25
  (optional)_ZNKSt5ctypeIcE8do_widenEc at Base 0.0+git20160702.2610e25
+ _ZNSt12_Vector_baseIfSaIfEED1Ev at Base 0.0+git20160702.2610e25-7
+ _ZNSt12_Vector_baseIfSaIfEED2Ev at Base 0.0+git20160702.2610e25-7
+ _ZNSt15_Rb_tree_headerC1EOS_ at Base 0.0+git20160702.2610e25-7
+ _ZNSt15_Rb_tree_headerC2EOS_ at Base 0.0+git20160702.2610e25-7
  (optional)_ZNSt6vectorI11IndelAlleleSaIS0_EE12emplace_backIJS0_EEEvDpOT_ at Base 0.0+git20160702.2610e25
  _ZNSt6vectorI11IndelAlleleSaIS0_EE17_M_realloc_insertIJRKS0_EEEvN9__gnu_cxx17__normal_iteratorIPS0_S2_EEDpOT_ at Base 0.0+git20160702.2610e25
  (optional)_ZNSt6vectorI11IndelAlleleSaIS0_EE17_M_realloc_insertIJS0_EEEvN9__gnu_cxx17__normal_iteratorIPS0_S2_EEDpOT_ at Base 0.0+git20160702.2610e25
  _ZNSt6vectorI11IndelAlleleSaIS0_EED1Ev at Base 0.0+git20160702.2610e25
  _ZNSt6vectorI11IndelAlleleSaIS0_EED2Ev at Base 0.0+git20160702.2610e25
- (optional)_ZNSt6vectorISt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiSt4lessIS6_ESaISt4pairIKS6_iEEESaISD_EE12emplace_backIJSD_EEEvDpOT_ at Base 0.0+git20160702.2610e25
+#MISSING: 0.0+git20160702.2610e25-7# (optional)_ZNSt6vectorISt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiSt4lessIS6_ESaISt4pairIKS6_iEEESaISD_EE12emplace_backIJSD_EEEvDpOT_ at Base 0.0+git20160702.2610e25
  (optional)_ZNSt6vectorISt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiSt4lessIS6_ESaISt4pairIKS6_iEEESaISD_EE17_M_realloc_insertIJSD_EEEvN9__gnu_cxx17__normal_iteratorIPSD_SF_EEDpOT_ at Base 0.0+git20160702.2610e25
  _ZNSt6vectorISt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiSt4lessIS6_ESaISt4pairIKS6_iEEESaISD_EED1Ev at Base 0.0+git20160702.2610e25
  _ZNSt6vectorISt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiSt4lessIS6_ESaISt4pairIKS6_iEEESaISD_EED2Ev at Base 0.0+git20160702.2610e25
@@ -62,19 +66,19 @@
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  _ZNSt6vectorISt4pairIiNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEESaIS7_EED1Ev at Base 0.0+git20160702.2610e25
  _ZNSt6vectorISt4pairIiNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEESaIS7_EED2Ev at Base 0.0+git20160702.2610e25
- (optional)_ZNSt6vectorIfSaIfEE12emplace_backIJfEEEvDpOT_ at Base 0.0+git20160702.2610e25
+#MISSING: 0.0+git20160702.2610e25-7# (optional)_ZNSt6vectorIfSaIfEE12emplace_backIJfEEEvDpOT_ at Base 0.0+git20160702.2610e25
  (optional)_ZNSt6vectorIfSaIfEE17_M_realloc_insertIJfEEEvN9__gnu_cxx17__normal_iteratorIPfS1_EEDpOT_ at Base 0.0+git20160702.2610e25
- (optional)_ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE12_M_constructIPKcEEvT_S8_St20forward_iterator_tag at Base 0.0+git20160702.2610e25
- (optional)_ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE12_M_constructIPcEEvT_S7_St20forward_iterator_tag at Base 0.0+git20160702.2610e25
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  _ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED1Ev at Base 0.0+git20160702.2610e25
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  (optional)_ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_iESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS8_ERS7_ at Base 0.0+git20160702.2610e25
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- (optional)_ZSteqIcEN9__gnu_cxx11__enable_ifIXsrSt9__is_charIT_E7__valueEbE6__typeERKNSt7__cxx1112basic_stringIS3_St11char_traitsIS3_ESaIS3_EEESE_ at Base 0.0+git20160702.2610e25
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  _ZeqRK11IndelAlleleS1_ at Base 0.0+git20160702.2610e25
  _ZlsRSoRK11IndelAllele at Base 0.0+git20160702.2610e25
  _ZltRK11IndelAlleleS1_ at Base 0.0+git20160702.2610e25
dh_makeshlibs: error: failing due to earlier errors
make: *** [debian/rules:8: binary] Error 25
dpkg-buildpackage: error: fakeroot debian/rules binary subprocess returned exit status 2