[Debian-med-packaging] Bug#984207: libsmithwaterman: ftbfs with GCC-11

Wed Mar 3 16:15:00 GMT 2021

Package: src:libsmithwaterman
Version: 0.0+git20160702.2610e25-11
Severity: normal
Tags: sid bookworm
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-11

[This bug is not targeted to the upcoming bullseye release]

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-11/g++-11, but succeeds to build with gcc-10/g++-10. The
severity of this report will be raised before the bookworm release,
so nothing has to be done for the bullseye release.

The full build log can be found at:
http://people.debian.org/~doko/logs/20210228/filtered/gcc11/libsmithwaterman_0.0+git20160702.2610e25-11_unstable_gcc11.log
The last lines of the build log are at the end of this report.

To build with GCC 11, either set CC=gcc-11 CXX=g++-11 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-11/porting_to.html

GCC 11 defaults to the GNU++17 standard.  If your package installs
header files in /usr/include, please don't work around C++17 issues
by choosing a lower C++ standard for the package build, but fix these
issues to build with the C++17 standard.

[...]
   dh_fixperms -O--no-parallel
   dh_missing -O--no-parallel
   dh_dwz -a -O--no-parallel
   dh_strip -a -O--no-parallel
   dh_makeshlibs -a -O--no-parallel
Use of uninitialized value $rest in pattern match (m//) at /usr/share/perl5/Dpkg/Shlibs/Symbol.pm line 129, <$filehandle> line 51.
dpkg-gensymbols: warning: failed to parse line in debian/libsmithwaterman0.symbols:  (arch=!ppc64el) _ZNSt12_Vector_baseIfSaIfEED1Ev at Base 0.0+git20160702.2610e25
Use of uninitialized value $rest in pattern match (m//) at /usr/share/perl5/Dpkg/Shlibs/Symbol.pm line 129, <$filehandle> line 52.
dpkg-gensymbols: warning: failed to parse line in debian/libsmithwaterman0.symbols:  (arch=!ppc64el) _ZNSt12_Vector_baseIfSaIfEED2Ev at Base 0.0+git20160702.2610e25
Use of uninitialized value $rest in pattern match (m//) at /usr/share/perl5/Dpkg/Shlibs/Symbol.pm line 129, <$filehandle> line 53.
dpkg-gensymbols: warning: failed to parse line in debian/libsmithwaterman0.symbols:  (arch=!ppc64el) _ZNSt15_Rb_tree_headerC1EOS_ at Base 0.0+git20160702.2610e25
Use of uninitialized value $rest in pattern match (m//) at /usr/share/perl5/Dpkg/Shlibs/Symbol.pm line 129, <$filehandle> line 54.
dpkg-gensymbols: warning: failed to parse line in debian/libsmithwaterman0.symbols:  (arch=!ppc64el) _ZNSt15_Rb_tree_headerC2EOS_ at Base 0.0+git20160702.2610e25
Use of uninitialized value $rest in pattern match (m//) at /usr/share/perl5/Dpkg/Shlibs/Symbol.pm line 129, <$filehandle> line 64.
dpkg-gensymbols: warning: failed to parse line in debian/libsmithwaterman0.symbols:  (arch=!s390x) _ZNSt6vectorISt4pairIiNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEESaIS7_EE17_M_realloc_insertIJRKS7_EEEvN9__gnu_cxx17__normal_iteratorIPS7_S9_EEDpOT_ at Base 0.0+git20160702.2610e25
Use of uninitialized value $rest in pattern match (m//) at /usr/share/perl5/Dpkg/Shlibs/Symbol.pm line 129, <$filehandle> line 73.
dpkg-gensymbols: warning: failed to parse line in debian/libsmithwaterman0.symbols:  (arch=!s390x) _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_iESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE24_M_get_insert_unique_posERS7_ at Base 0.0+git20160702.2610e25
Use of uninitialized value $rest in pattern match (m//) at /usr/share/perl5/Dpkg/Shlibs/Symbol.pm line 129, <$filehandle> line 51.
dpkg-gensymbols: warning: failed to parse line in debian/libsmithwaterman0.symbols:  (arch=!ppc64el) _ZNSt12_Vector_baseIfSaIfEED1Ev at Base 0.0+git20160702.2610e25
Use of uninitialized value $rest in pattern match (m//) at /usr/share/perl5/Dpkg/Shlibs/Symbol.pm line 129, <$filehandle> line 52.
dpkg-gensymbols: warning: failed to parse line in debian/libsmithwaterman0.symbols:  (arch=!ppc64el) _ZNSt12_Vector_baseIfSaIfEED2Ev at Base 0.0+git20160702.2610e25
Use of uninitialized value $rest in pattern match (m//) at /usr/share/perl5/Dpkg/Shlibs/Symbol.pm line 129, <$filehandle> line 53.
dpkg-gensymbols: warning: failed to parse line in debian/libsmithwaterman0.symbols:  (arch=!ppc64el) _ZNSt15_Rb_tree_headerC1EOS_ at Base 0.0+git20160702.2610e25
Use of uninitialized value $rest in pattern match (m//) at /usr/share/perl5/Dpkg/Shlibs/Symbol.pm line 129, <$filehandle> line 54.
dpkg-gensymbols: warning: failed to parse line in debian/libsmithwaterman0.symbols:  (arch=!ppc64el) _ZNSt15_Rb_tree_headerC2EOS_ at Base 0.0+git20160702.2610e25
Use of uninitialized value $rest in pattern match (m//) at /usr/share/perl5/Dpkg/Shlibs/Symbol.pm line 129, <$filehandle> line 64.
dpkg-gensymbols: warning: failed to parse line in debian/libsmithwaterman0.symbols:  (arch=!s390x) _ZNSt6vectorISt4pairIiNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEESaIS7_EE17_M_realloc_insertIJRKS7_EEEvN9__gnu_cxx17__normal_iteratorIPS7_S9_EEDpOT_ at Base 0.0+git20160702.2610e25
Use of uninitialized value $rest in pattern match (m//) at /usr/share/perl5/Dpkg/Shlibs/Symbol.pm line 129, <$filehandle> line 73.
dpkg-gensymbols: warning: failed to parse line in debian/libsmithwaterman0.symbols:  (arch=!s390x) _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_iESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE24_M_get_insert_unique_posERS7_ at Base 0.0+git20160702.2610e25
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+git20160702.2610e25-11_amd64)
+++ dpkg-gensymbolsMAYCWR	2021-03-01 21:09:07.449138917 +0000
@@ -48,7 +48,11 @@
  _ZN20CBandedSmithWatermanD1Ev at Base 0.0+git20160702.2610e25
  _ZN20CBandedSmithWatermanD2Ev at Base 0.0+git20160702.2610e25
  (optional)_ZNKSt5ctypeIcE8do_widenEc at Base 0.0+git20160702.2610e25
- (arch=!ppc64el optional)_ZNSt6vectorI11IndelAlleleSaIS0_EE12emplace_backIJS0_EEEvDpOT_ at Base 0.0+git20160702.2610e25
+ _ZNSt12_Vector_baseIfSaIfEED1Ev at Base 0.0+git20160702.2610e25-11
+ _ZNSt12_Vector_baseIfSaIfEED2Ev at Base 0.0+git20160702.2610e25-11
+ _ZNSt15_Rb_tree_headerC1EOS_ at Base 0.0+git20160702.2610e25-11
+ _ZNSt15_Rb_tree_headerC2EOS_ at Base 0.0+git20160702.2610e25-11
+#MISSING: 0.0+git20160702.2610e25-11# (arch=!ppc64el 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
  (arch=!s390x 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
@@ -56,14 +60,18 @@
  (arch=!s390x 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
- (optional)_ZNSt6vectorISt4pairIiNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEESaIS7_EE12emplace_backIJS7_EEEvDpOT_ at Base 0.0+git20160702.2610e25
+#MISSING: 0.0+git20160702.2610e25-11# (optional)_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+git20160702.2610e25-11
  (arch=!s390x optional)_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
  (arch=!s390x optional)_ZNSt6vectorIfSaIfEE17_M_realloc_insertIJfEEEvN9__gnu_cxx17__normal_iteratorIPfS1_EEDpOT_ at Base 0.0+git20160702.2610e25
+ _ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC1IS3_EEPKcRKS3_ at Base 0.0+git20160702.2610e25-11
+ _ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC2IS3_EEPKcRKS3_ at Base 0.0+git20160702.2610e25-11
  _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_EE24_M_get_insert_unique_posERS7_ at Base 0.0+git20160702.2610e25-11
  (arch=!s390x !ppc64el 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
  _ZeqRK11IndelAlleleS1_ at Base 0.0+git20160702.2610e25
  _ZlsRSoRK11IndelAllele at Base 0.0+git20160702.2610e25
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

