[Debian-med-packaging] Bug#984092: libbpp-seq-omics: ftbfs with GCC-11

[Matthias Klose]

Package: src:libbpp-seq-omics
Version: 2.4.1-5
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/libbpp-seq-omics_2.4.1-5_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.

[...]
+++ dpkg-gensymbolsTekV7w	2021-03-01 21:02:24.325500245 +0000
@@ -38,6 +38,7 @@
  _ZN3bpp12EdSymbolList25beforeSequenceSubstitutedERKNS_27SymbolListSubstitutionEventE at Base 2.4.1
  _ZN3bpp12EdSymbolList7shuffleEv at Base 2.4.1
  _ZN3bpp12EdSymbolListixEm at Base 2.4.1
+ _ZN3bpp12SequenceMaskC1ERKSt6vectorIbSaIbEEb at Base 2.4.1-5
  _ZN3bpp12SequenceMaskD0Ev at Base 2.4.1
  _ZN3bpp13AlphabetStateD0Ev at Base 2.4.1
  _ZN3bpp13AlphabetStateD1Ev at Base 2.4.1
@@ -126,8 +127,8 @@
  _ZN3bpp19OutOfRangeExceptionD2Ev at Base 2.4.1
  _ZN3bpp19VectorSiteContainerD0Ev at Base 2.4.1
  _ZN3bpp19VectorSiteContainerD1Ev at Base 2.4.1
- _ZN3bpp20AbstractCoreSequence11setCommentsERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS7_EE at Base 2.4.1
- _ZN3bpp20AbstractCoreSequence7setNameERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 2.4.1
+#MISSING: 2.4.1-5# _ZN3bpp20AbstractCoreSequence11setCommentsERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS7_EE at Base 2.4.1
+#MISSING: 2.4.1-5# _ZN3bpp20AbstractCoreSequence7setNameERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 2.4.1
  _ZN3bpp20BasicSequenceFeature12getAttributeERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 2.4.1
  _ZN3bpp20BasicSequenceFeature12setAttributeERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_ at Base 2.4.1
  _ZN3bpp20BasicSequenceFeature13setSequenceIdERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 2.4.1
@@ -516,13 +517,17 @@
  _ZNSt15_Sp_counted_ptrIDnLN9__gnu_cxx12_Lock_policyE2EE10_M_disposeEv at Base 2.4.1
  _ZNSt16_Sp_counted_baseILN9__gnu_cxx12_Lock_policyE2EE10_M_destroyEv at Base 2.4.1
  _ZNSt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEPN3bpp10BppNumberIESt4lessIS5_ESaISt4pairIKS5_S8_EEEixERSC_ at Base 2.4.1
+ _ZNSt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES5_St4lessIS5_ESaISt4pairIKS5_S5_EEEixEOS5_ at Base 2.4.1-5
+ _ZNSt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEjSt4lessIS5_ESaISt4pairIKS5_jEEEixERS9_ at Base 2.4.1-5
  _ZNSt5dequeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED1Ev at Base 2.4.1
  _ZNSt5dequeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED2Ev at Base 2.4.1
  _ZNSt5dequeIPN3bpp8MafBlockESaIS2_EE16_M_push_back_auxIJRKS2_EEEvDpOT_ at Base 2.4.1
  _ZNSt5dequeISt6vectorIbSaIbEESaIS2_EE16_M_push_back_auxIJRKS2_EEEvDpOT_ at Base 2.4.1
  _ZNSt5dequeISt6vectorIiSaIiEESaIS2_EE16_M_push_back_auxIJRKS2_EEEvDpOT_ at Base 2.4.1
- _ZNSt5dequeIjSaIjEE16_M_push_back_auxIJjEEEvDpOT_ at Base 2.4.1
- _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE12emplace_backIJS5_EEEvDpOT_ at Base 2.4.1
+ _ZNSt5dequeIjSaIjEE12emplace_backIJjEEERjDpOT_ at Base 2.4.1-5
+#MISSING: 2.4.1-5# _ZNSt5dequeIjSaIjEE16_M_push_back_auxIJjEEEvDpOT_ at Base 2.4.1
+ _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE12emplace_backIJS5_EEERS5_DpOT_ at Base 2.4.1-5
+#MISSING: 2.4.1-5# _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE12emplace_backIJS5_EEEvDpOT_ at Base 2.4.1
  _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE17_M_realloc_insertIJRKS5_EEEvN9__gnu_cxx17__normal_iteratorIPS5_S7_EEDpOT_ at Base 2.4.1
  _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE17_M_realloc_insertIJS5_EEEvN9__gnu_cxx17__normal_iteratorIPS5_S7_EEDpOT_ at Base 2.4.1
  _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EEC1ERKS7_ at Base 2.4.1
@@ -557,6 +562,8 @@
  _ZNSt6vectorIjSaIjEE17_M_realloc_insertIJjEEEvN9__gnu_cxx17__normal_iteratorIPjS1_EEDpOT_ at Base 2.4.1
  _ZNSt6vectorImSaImEE17_M_realloc_insertIJRKmEEEvN9__gnu_cxx17__normal_iteratorIPmS1_EEDpOT_ at Base 2.4.1
  _ZNSt6vectorImSaImEE17_M_realloc_insertIJmEEEvN9__gnu_cxx17__normal_iteratorIPmS1_EEDpOT_ at Base 2.4.1
+ _ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC1IS3_EEPKcRKS3_ at Base 2.4.1-5
+ _ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC2IS3_EEPKcRKS3_ at Base 2.4.1-5
  _ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED0Ev at Base 2.4.1
  _ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED1Ev at Base 2.4.1
  _ZNSt7__cxx1115basic_stringbufIcSt11char_traitsIcESaIcEED2Ev at Base 2.4.1
@@ -1150,7 +1157,7 @@
  _ZTv0_n56_N3bpp16GtfFeatureReader17getFeaturesOfTypeERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERNS_18SequenceFeatureSetE at Base 2.4.1
  _ZTv0_n56_N3bpp17SiteMafStatistics7computeERKNS_8MafBlockE at Base 2.4.1
  _ZTv0_n56_N3bpp19AbstractMafIterator20addIterationListenerEPNS_17IterationListenerE at Base 2.4.1
- _ZTv0_n56_N3bpp20AbstractCoreSequence7setNameERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 2.4.1
+#MISSING: 2.4.1-5# _ZTv0_n56_N3bpp20AbstractCoreSequence7setNameERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 2.4.1
  _ZTv0_n56_N3bpp21BedGraphFeatureReader17getFeaturesOfTypeERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERNS_18SequenceFeatureSetE at Base 2.4.1
  _ZTv0_n56_N3bpp22SequenceWithAnnotation7setNameERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 2.4.1
  _ZTv0_n56_N3bpp25PolymorphismMafStatistics7computeERKNS_8MafBlockE at Base 2.4.1
@@ -1175,7 +1182,7 @@
  _ZTv0_n64_NK3bpp30SequenceDiversityMafStatistics16getSupportedTagsB5cxx11Ev at Base 2.4.1
  _ZTv0_n64_NK3bpp34SiteFrequencySpectrumMafStatistics16getSupportedTagsB5cxx11Ev at Base 2.4.1
  _ZTv0_n64_NK3bpp37FourSpeciesPatternCountsMafStatistics16getSupportedTagsB5cxx11Ev at Base 2.4.1
- _ZTv0_n72_N3bpp20AbstractCoreSequence11setCommentsERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS7_EE at Base 2.4.1
+#MISSING: 2.4.1-5# _ZTv0_n72_N3bpp20AbstractCoreSequence11setCommentsERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS7_EE at Base 2.4.1
  _ZTv0_n72_N3bpp22SequenceWithAnnotation10setContentERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS7_EE at Base 2.4.1
  _ZTv0_n72_N3bpp22SequenceWithAnnotation11setCommentsERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS7_EE at Base 2.4.1
  _ZTv0_n72_NK3bpp5Fastq12nextSequenceERSiRNS_8SequenceE at Base 2.4.1
dh_makeshlibs: error: failing due to earlier errors
make: *** [debian/rules:10: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2