[Debian-med-packaging] Bug#897797: libsmithwaterman: ftbfs with GCC-8

[Matthias Klose]

Package: src:libsmithwaterman
Version: 0.0+git20160702.2610e25-3
Severity: normal
Tags: sid buster
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-8

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-8/g++-8, but succeeds to build with gcc-7/g++-7. The
severity of this report will be raised before the buster release.

The full build log can be found at:
http://aws-logs.debian.net/2018/05/01/gcc8/libsmithwaterman_0.0+git20160702.2610e25-3_unstable_gcc8.log.gz
The last lines of the build log are at the end of this report.

To build with GCC 8, either set CC=gcc-8 CXX=g++-8 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-8/porting_to.html

[...]
   dh_installdocs -a -O--no-parallel
   dh_installchangelogs -a -O--no-parallel
   dh_installman -a -O--no-parallel
   dh_perl -a -O--no-parallel
   dh_link -a -O--no-parallel
   dh_strip_nondeterminism -a -O--no-parallel
   dh_compress -a -O--no-parallel
   dh_fixperms -a -O--no-parallel
   dh_missing -a -O--no-parallel
   dh_strip -a -O--no-parallel
   dh_makeshlibs -a -O--no-parallel
dpkg-gensymbols: warning: some new symbols appeared in the symbols file: see diff output below
dpkg-gensymbols: warning: 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+git20160702.2610e25-3_amd64)
+++ dpkg-gensymbolsZYza9J	2018-05-02 13:29:00.735154786 +0000
@@ -50,7 +50,7 @@
  (arch=!mips !mipsel)_ZNKSt5ctypeIcE8do_widenEc at Base 0.0+git20160702.2610e25
  _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
- _ZNSt6vectorI11IndelAlleleSaIS0_EE17_M_realloc_insertIJS0_EEEvN9__gnu_cxx17__normal_iteratorIPS0_S2_EEDpOT_ at Base 0.0+git20160702.2610e25
+#MISSING: 0.0+git20160702.2610e25-3# _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
  _ZNSt6vectorISt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiSt4lessIS6_ESaISt4pairIKS6_iEEESaISD_EE12emplace_backIJSD_EEEvDpOT_ at Base 0.0+git20160702.2610e25
@@ -59,16 +59,19 @@
  _ZNSt6vectorISt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiSt4lessIS6_ESaISt4pairIKS6_iEEESaISD_EED2Ev at Base 0.0+git20160702.2610e25
  _ZNSt6vectorISt4pairIiNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEESaIS7_EE12emplace_backIJS7_EEEvDpOT_ at Base 0.0+git20160702.2610e25
  _ZNSt6vectorISt4pairIiNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEESaIS7_EE17_M_realloc_insertIJRKS7_EEEvN9__gnu_cxx17__normal_iteratorIPS7_S9_EEDpOT_ at Base 0.0+git20160702.2610e25
- _ZNSt6vectorISt4pairIiNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEESaIS7_EE17_M_realloc_insertIJS7_EEEvN9__gnu_cxx17__normal_iteratorIPS7_S9_EEDpOT_ at Base 0.0+git20160702.2610e25
+#MISSING: 0.0+git20160702.2610e25-3# _ZNSt6vectorISt4pairIiNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEESaIS7_EE17_M_realloc_insertIJS7_EEEvN9__gnu_cxx17__normal_iteratorIPS7_S9_EEDpOT_ at Base 0.0+git20160702.2610e25
  _ZNSt6vectorISt4pairIiNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEESaIS7_EED1Ev at Base 0.0+git20160702.2610e25
  _ZNSt6vectorISt4pairIiNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEESaIS7_EED2Ev at Base 0.0+git20160702.2610e25
  _ZNSt6vectorIfSaIfEE12emplace_backIJfEEEvDpOT_ at Base 0.0+git20160702.2610e25
  _ZNSt6vectorIfSaIfEE17_M_realloc_insertIJfEEEvN9__gnu_cxx17__normal_iteratorIPfS1_EEDpOT_ at Base 0.0+git20160702.2610e25
+ _ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE12_M_constructIPKcEEvT_S8_St20forward_iterator_tag at Base 0.0+git20160702.2610e25-3
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  _ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED0Ev at Base 0.0+git20160702.2610e25
  _ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED1Ev at Base 0.0+git20160702.2610e25
  _ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED2Ev at Base 0.0+git20160702.2610e25
  _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_iESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE12_M_erase_auxESt23_Rb_tree_const_iteratorIS8_E at Base 0.0+git20160702.2610e25
- (arch=alpha armel armhf any-i386 mips mipsel s390x powerpc powerpcspe ppc64)_ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_iESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE24_M_get_insert_unique_posERS7_ at Base 0.0+git20160702.2610e25
+ _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_iESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJRS7_EESJ_IJEEEEESt17_Rb_tree_iteratorIS8_ESt23_Rb_tree_const_iteratorIS8_EDpOT_ at Base 0.0+git20160702.2610e25-3
+ _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_iESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE24_M_get_insert_unique_posERS7_ at Base 0.0+git20160702.2610e25
  (arch=any-amd64 arm64 mips64el ppc64el hppa ia64 riscv64 sh4 sparc64 x32)_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
  _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_iESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE8_M_eraseEPSt13_Rb_tree_nodeIS8_E at Base 0.0+git20160702.2610e25
  (arch=mips mipsel)_ZSteqIcEN9__gnu_cxx11__enable_ifIXsrSt9__is_charIT_E7__valueEbE6__typeERKNSt7__cxx1112basic_stringIS3_St11char_traitsIS3_ESaIS3_EEESE_ at Base 0.0+git20160702.2610e25
dh_makeshlibs: failing due to earlier errors
make: *** [debian/rules:8: binary-arch] Error 2
dpkg-buildpackage: error: fakeroot debian/rules binary-arch subprocess returned exit status 2