[Debian-med-packaging] Bug#957438: libfastahack: ftbfs with GCC-10

Fri Apr 17 12:04:15 BST 2020

Package: src:libfastahack
Version: 1.0.0+dfsg-5
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/libfastahack_1.0.0+dfsg-5_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

[...]
	 * dh_install: fastahack (1), libfastahack-dev (0), libfastahack0 (0)
	 * dh_installdocs: fastahack (1), libfastahack-dev (0), libfastahack0 (0)
	 * dh_installman: fastahack (1), libfastahack-dev (0), libfastahack0 (0)
	If the missing files are installed by another tool, please file a bug against it.
	When filing the report, if the tool is not part of debhelper itself, please reference the
	"Logging helpers and dh_missing" section from the "PROGRAMMING" guide for debhelper (10.6.3+).
	  (in the debhelper package: /usr/share/doc/debhelper/PROGRAMMING.gz)
	Be sure to test with dpkg-buildpackage -A/-B as the results may vary when only a subset is built
	For a short-term work-around: Add the files to debian/not-installed
   dh_dwz
   dh_strip
   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: 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/libfastahack0/DEBIAN/symbols doesn't match completely debian/libfastahack0.symbols

--- debian/libfastahack0.symbols (libfastahack0_1.0.0+dfsg-5_amd64)
+++ dpkg-gensymbolsbTXQub	2020-02-26 12:52:21.200502437 +0000
@@ -32,29 +32,33 @@
  _ZN15FastaIndexEntryD1Ev at Base 0.0+git20160702.bbc645f
  _ZN15FastaIndexEntryD2Ev at Base 0.0+git20160702.bbc645f
  _ZNKSt5ctypeIcE8do_widenEc at Base 0.0+git20160702.bbc645f
- _ZNSt4pairINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE15FastaIndexEntryED1Ev at Base 0.0+git20160702.bbc645f
- _ZNSt4pairINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE15FastaIndexEntryED2Ev at Base 0.0+git20160702.bbc645f
+#MISSING: 1.0.0+dfsg-5# _ZNSt4pairINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE15FastaIndexEntryED1Ev at Base 0.0+git20160702.bbc645f
+#MISSING: 1.0.0+dfsg-5# _ZNSt4pairINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE15FastaIndexEntryED2Ev at Base 0.0+git20160702.bbc645f
  _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
+ _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EEC1ERKS7_ at Base 1.0.0+dfsg-5
+ _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EEC2ERKS7_ at Base 1.0.0+dfsg-5
  _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED1Ev at Base 0.0+git20160702.bbc645f
  _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED2Ev at Base 0.0+git20160702.bbc645f
- (optional)_ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE12_M_constructIPKcEEvT_S8_St20forward_iterator_tag at Base 0.0+git20160702.bbc645f
- (optional)_ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE12_M_constructIPcEEvT_S7_St20forward_iterator_tag at Base 0.0+git20160702.bbc645f
- (optional)_ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_15FastaIndexEntryESt10_Select1stIS9_ESt4lessIS5_ESaIS9_EE10_M_insert_IS6_IS5_S8_ENSF_11_Alloc_nodeEEESt17_Rb_tree_iteratorIS9_EPSt18_Rb_tree_node_baseSM_OT_RT0_ at Base 0.0+git20160702.bbc645f
- (optional)_ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_15FastaIndexEntryESt10_Select1stIS9_ESt4lessIS5_ESaIS9_EE14_M_insert_nodeEPSt18_Rb_tree_node_baseSH_PSt13_Rb_tree_nodeIS9_E at Base 0.0+git20160702.bbc645f
- (optional)_ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_15FastaIndexEntryESt10_Select1stIS9_ESt4lessIS5_ESaIS9_EE16_M_insert_uniqueIS6_IS5_S8_EEES6_ISt17_Rb_tree_iteratorIS9_EbEOT_ at Base 0.0+git20160702.bbc645f
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+#MISSING: 1.0.0+dfsg-5# (optional)_ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEE12_M_constructIPcEEvT_S7_St20forward_iterator_tag at Base 0.0+git20160702.bbc645f
+#MISSING: 1.0.0+dfsg-5# (optional)_ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_15FastaIndexEntryESt10_Select1stIS9_ESt4lessIS5_ESaIS9_EE10_M_insert_IS6_IS5_S8_ENSF_11_Alloc_nodeEEESt17_Rb_tree_iteratorIS9_EPSt18_Rb_tree_node_baseSM_OT_RT0_ at Base 0.0+git20160702.bbc645f
+#MISSING: 1.0.0+dfsg-5# (optional)_ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_15FastaIndexEntryESt10_Select1stIS9_ESt4lessIS5_ESaIS9_EE14_M_insert_nodeEPSt18_Rb_tree_node_baseSH_PSt13_Rb_tree_nodeIS9_E at Base 0.0+git20160702.bbc645f
+#MISSING: 1.0.0+dfsg-5# (optional)_ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_15FastaIndexEntryESt10_Select1stIS9_ESt4lessIS5_ESaIS9_EE16_M_insert_uniqueIS6_IS5_S8_EEES6_ISt17_Rb_tree_iteratorIS9_EbEOT_ at Base 0.0+git20160702.bbc645f
  _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_EE22_M_emplace_hint_uniqueIJRKSt21piecewise_construct_tSt5tupleIJRS7_EESK_IJEEEEESt17_Rb_tree_iteratorIS9_ESt23_Rb_tree_const_iteratorIS9_EDpOT_ at Base 0.0+git20160702.bbc645f
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  _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
- _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_15FastaIndexEntryESt10_Select1stIS9_ESt4lessIS5_ESaIS9_EE8_M_eraseEPSt13_Rb_tree_nodeIS9_E at Base 0.0+git20160702.bbc645f
- _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_jESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE8_M_eraseEPSt13_Rb_tree_nodeIS8_E at Base 0.0+git20160702.bbc645f
+#MISSING: 1.0.0+dfsg-5# _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_15FastaIndexEntryESt10_Select1stIS9_ESt4lessIS5_ESaIS9_EE8_M_eraseEPSt13_Rb_tree_nodeIS9_E at Base 0.0+git20160702.bbc645f
+#MISSING: 1.0.0+dfsg-5# _ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_jESt10_Select1stIS8_ESt4lessIS5_ESaIS8_EE8_M_eraseEPSt13_Rb_tree_nodeIS8_E 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
  _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
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  _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
+ _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-5
  _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:40: override_dh_makeshlibs] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:9: binary] Error 2
dpkg-buildpackage: error: fakeroot debian/rules binary subprocess returned exit status 2

