[Debian-med-packaging] Bug#984104: libfastahack: ftbfs with GCC-11

[Matthias Klose]

Package: src:libfastahack
Version: 1.0.0+dfsg-7
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/libfastahack_1.0.0+dfsg-7_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.

[...]
mv /<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu/libfastahack.so.0 debian/libfastahack0/usr/lib/x86_64-linux-gnu
mv /<<PKGBUILDDIR>>/debian/tmp/usr/lib/x86_64-linux-gnu/libfastahack.so.0.0.0 debian/libfastahack0/usr/lib/x86_64-linux-gnu
PKGDEV=libfastahack-dev
PKGSHL=libfastahack0
install -d -m 755 debian/libfastahack-dev/usr/include
mv debian/tmp/usr/include/fastahack debian/libfastahack-dev/usr/include
install -d -m 755 debian/libfastahack-dev/usr/lib/x86_64-linux-gnu/pkgconfig
mv debian/tmp/usr/lib/*/pkgconfig/*.pc debian/libfastahack-dev/usr/lib/x86_64-linux-gnu/pkgconfig
find debian -name libfastahack.la -delete
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_installdocs
   dh_installchangelogs
   debian/rules override_dh_installman
make[1]: Entering directory '/<<PKGBUILDDIR>>'
help2man --no-discard-stderr --no-info --version-string=1.0.0+dfsg-7 \
	--name="fastahack - indexing and extracting sequences and subsequences from FASTA files" \
	./fastahack > debian/fastahack.1
dh_installman
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   dh_perl
   dh_link
   dh_strip_nondeterminism
   dh_compress
   dh_fixperms
   dh_missing
   dh_dwz -a
   dh_strip -a
   debian/rules override_dh_makeshlibs
make[1]: Entering directory '/<<PKGBUILDDIR>>'
echo "On architecture amd64 symbols file is provided"
On architecture amd64 symbols file is provided
dh_makeshlibs
dpkg-gensymbols: error: some symbols or patterns disappeared in the symbols file: see diff output below
dpkg-gensymbols: warning: debian/libfastahack0/DEBIAN/symbols doesn't match completely debian/libfastahack0.symbols
--- debian/libfastahack0.symbols (libfastahack0_1.0.0+dfsg-7_amd64)
+++ dpkg-gensymbolsKCtwDB	2021-03-01 21:09:58.987468905 +0000
@@ -32,9 +32,9 @@
  _ZN15FastaIndexEntryD1Ev at Base 0.0+git20160702.bbc645f
  _ZN15FastaIndexEntryD2Ev at Base 0.0+git20160702.bbc645f
  _ZNKSt5ctypeIcE8do_widenEc at Base 0.0+git20160702.bbc645f
- (optional)_ZNSt12_Destroy_auxILb0EE9__destroyIPNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEvT_S9_ at Base 1.0.0+dfsg
- (optional)_ZNSt4pairINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE15FastaIndexEntryED1Ev at Base 1.0.0+dfsg
- (optional)_ZNSt4pairINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE15FastaIndexEntryED2Ev at Base 1.0.0+dfsg
+#MISSING: 1.0.0+dfsg-7# (optional)_ZNSt12_Destroy_auxILb0EE9__destroyIPNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEvT_S9_ at Base 1.0.0+dfsg
+#MISSING: 1.0.0+dfsg-7# (optional)_ZNSt4pairINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE15FastaIndexEntryED1Ev at Base 1.0.0+dfsg
+#MISSING: 1.0.0+dfsg-7# (optional)_ZNSt4pairINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE15FastaIndexEntryED2Ev at Base 1.0.0+dfsg
  _ZNSt6vectorI15FastaIndexEntrySaIS0_EE17_M_realloc_insertIJRKS0_EEEvN9__gnu_cxx17__normal_iteratorIPS0_S2_EEDpOT_ at Base 0.0+git20160702.bbc645f
  _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE17_M_realloc_insertIJRKS5_EEEvN9__gnu_cxx17__normal_iteratorIPS5_S7_EEDpOT_ at Base 0.0+git20160702.bbc645f
  (optional)_ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE17_M_realloc_insertIJS5_EEEvN9__gnu_cxx17__normal_iteratorIPS5_S7_EEDpOT_ at Base 0.0+git20160702.bbc645f
@@ -45,13 +45,13 @@
  _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_15FastaIndexEntryESt10_Select1stIS9_ESt4lessIS5_ESaIS9_EE17_M_emplace_uniqueIJS6_IS5_S8_EEEES6_ISt17_Rb_tree_iteratorIS9_EbEDpOT_ at Base 0.0+git20160702.bbc645f
  _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_15FastaIndexEntryESt10_Select1stIS9_ESt4lessIS5_ESaIS9_EE24_M_get_insert_unique_posERS7_ at Base 0.0+git20160702.bbc645f
  _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_15FastaIndexEntryESt10_Select1stIS9_ESt4lessIS5_ESaIS9_EE29_M_get_insert_hint_unique_posESt23_Rb_tree_const_iteratorIS9_ERS7_ at Base 0.0+git20160702.bbc645f
- _ZSt11__push_heapIN9__gnu_cxx17__normal_iteratorIP15FastaIndexEntrySt6vectorIS2_SaIS2_EEEElS2_NS0_5__ops14_Iter_comp_valIPFbS2_S2_EEEEvT_T0_SE_T1_RT2_ at Base 0.0+git20160702.bbc645f
+#MISSING: 1.0.0+dfsg-7# _ZSt11__push_heapIN9__gnu_cxx17__normal_iteratorIP15FastaIndexEntrySt6vectorIS2_SaIS2_EEEElS2_NS0_5__ops14_Iter_comp_valIPFbS2_S2_EEEEvT_T0_SE_T1_RT2_ at Base 0.0+git20160702.bbc645f
  _ZSt11__remove_ifIPcN9__gnu_cxx5__ops16_Iter_equals_valIKcEEET_S6_S6_T0_ at Base 0.0+git20160702.bbc645f
  _ZSt13__adjust_heapIN9__gnu_cxx17__normal_iteratorIP15FastaIndexEntrySt6vectorIS2_SaIS2_EEEElS2_NS0_5__ops15_Iter_comp_iterIPFbS2_S2_EEEEvT_T0_SE_T1_T2_ at Base 0.0+git20160702.bbc645f
  _ZSt13__heap_selectIN9__gnu_cxx17__normal_iteratorIP15FastaIndexEntrySt6vectorIS2_SaIS2_EEEENS0_5__ops15_Iter_comp_iterIPFbS2_S2_EEEEvT_SD_SD_T0_ at Base 1.0.0+dfsg
  _ZSt16__insertion_sortIN9__gnu_cxx17__normal_iteratorIP15FastaIndexEntrySt6vectorIS2_SaIS2_EEEENS0_5__ops15_Iter_comp_iterIPFbS2_S2_EEEEvT_SD_T0_ at Base 0.0+git20160702.bbc645f
  _ZSt16__introsort_loopIN9__gnu_cxx17__normal_iteratorIP15FastaIndexEntrySt6vectorIS2_SaIS2_EEEElNS0_5__ops15_Iter_comp_iterIPFbS2_S2_EEEEvT_SD_T0_T1_ at Base 0.0+git20160702.bbc645f
- (optional)_ZSt22__move_median_to_firstIN9__gnu_cxx17__normal_iteratorIP15FastaIndexEntrySt6vectorIS2_SaIS2_EEEENS0_5__ops15_Iter_comp_iterIPFbS2_S2_EEEEvT_SD_SD_SD_T0_ at Base 1.0.0+dfsg
+#MISSING: 1.0.0+dfsg-7# (optional)_ZSt22__move_median_to_firstIN9__gnu_cxx17__normal_iteratorIP15FastaIndexEntrySt6vectorIS2_SaIS2_EEEENS0_5__ops15_Iter_comp_iterIPFbS2_S2_EEEEvT_SD_SD_SD_T0_ at Base 1.0.0+dfsg
  _ZSt25__unguarded_linear_insertIN9__gnu_cxx17__normal_iteratorIP15FastaIndexEntrySt6vectorIS2_SaIS2_EEEENS0_5__ops14_Val_comp_iterIPFbS2_S2_EEEEvT_T0_ at Base 0.0+git20160702.bbc645f
  _ZlsRSoR10FastaIndex at Base 0.0+git20160702.bbc645f
  _ZlsRSoRK15FastaIndexEntry at Base 0.0+git20160702.bbc645f
dh_makeshlibs: error: failing due to earlier errors
make[1]: *** [debian/rules:41: override_dh_makeshlibs] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:9: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2