[Debian-med-packaging] Bug#984091: libbpp-popgen: ftbfs with GCC-11

Wed Mar 3 16:14:03 GMT 2021

Package: src:libbpp-popgen
Version: 2.4.1-4
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-popgen_2.4.1-4_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
   dh_missing
   dh_dwz -a
   dh_strip -a
   dh_makeshlibs -a
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/libbpp-popgen8/DEBIAN/symbols doesn't match completely debian/libbpp-popgen8.symbols.amd64

--- debian/libbpp-popgen8.symbols.amd64 (libbpp-popgen8_2.4.1-4_amd64)
+++ dpkg-gensymbolsR4xI3v	2021-03-01 21:05:28.480701152 +0000
@@ -61,6 +61,7 @@
  _ZN3bpp11PopgenlibIOD1Ev at Base 2.4.1
  _ZN3bpp11PopgenlibIOD2Ev at Base 2.4.1
  _ZN3bpp11RandomTools9getSampleImEEvRKSt6vectorIT_SaIS3_EERS5_b at Base 2.4.1
+ _ZN3bpp11VectorTools11countValuesINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESt3mapIT_mSt4lessIS9_ESaISt4pairIKS9_mEEERKSt6vectorIS9_SaIS9_EE at Base 2.4.1-4
  _ZN3bpp11VectorTools3covIddEET0_RKSt6vectorIT_SaIS4_EES8_b at Base 2.4.1
  _ZN3bpp11VectorTools6uniqueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESt6vectorIT_SaIS9_EERKSB_ at Base 2.4.1
  _ZN3bpp11VectorTools6uniqueImEESt6vectorIT_SaIS3_EERKS5_ at Base 2.4.1
@@ -662,7 +663,7 @@
  _ZN3bpp9TextTools8toStringIcEENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEET_ at Base 2.4.1
  _ZN3bpp9TextTools8toStringIiEENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEET_ at Base 2.4.1
  _ZN3bpp9TextTools8toStringImEENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEET_ at Base 2.4.1
- _ZN3bppdvIdEESt6vectorIT_SaIS2_EERKS4_S6_ at Base 2.4.1
+#MISSING: 2.4.1-4# _ZN3bppdvIdEESt6vectorIT_SaIS2_EERKS4_S6_ at Base 2.4.1
  _ZN3bppdvIdiEESt6vectorIT_SaIS2_EERKS4_RKT0_ at Base 2.4.1
  _ZN3bppmiIdiEESt6vectorIT_SaIS2_EERKS4_RKT0_ at Base 2.4.1
  _ZN3bppmlIdEESt6vectorIT_SaIS2_EERKS4_S6_ at Base 2.4.1
@@ -759,6 +760,7 @@
  _ZNK3bpp19VectorSiteContainer7valueAtEmm at Base 2.4.1
  _ZNK3bpp19VectorSiteContainerclERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEm at Base 2.4.1
  _ZNK3bpp19VectorSiteContainerclEmm at Base 2.4.1
+ _ZNK3bpp20AbstractCoreSequence11getCommentsB5cxx11Ev at Base 2.4.1-4
  _ZNK3bpp20AbstractCoreSequence7getNameB5cxx11Ev at Base 2.4.1
  _ZNK3bpp20AbstractOutputStream12getPrecisionEv at Base 2.4.1
  _ZNK3bpp20AbstractOutputStream27isScientificNotationEnabledEv at Base 2.4.1
@@ -937,11 +939,13 @@
  _ZNSt15_Rb_tree_headerC1EOS_ at Base 2.4.1
  _ZNSt15_Rb_tree_headerC2EOS_ at Base 2.4.1
  _ZNSt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEdSt4lessIS5_ESaISt4pairIKS5_dEEEixEOS5_ at Base 2.4.1
+ _ZNSt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEmSt4lessIS5_ESaISt4pairIKS5_mEEEixERS9_ at Base 2.4.1-4
  _ZNSt5dequeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED1Ev at Base 2.4.1
  _ZNSt5dequeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EED2Ev at Base 2.4.1
  _ZNSt6vectorIN3bpp19GeneMapperCsvExport6AlleleESaIS2_EE17_M_realloc_insertIJRKS2_EEEvN9__gnu_cxx17__normal_iteratorIPS2_S4_EEDpOT_ at Base 2.4.1
  _ZNSt6vectorIN3bpp9LocusInfoESaIS1_EE17_M_realloc_insertIJS1_EEEvN9__gnu_cxx17__normal_iteratorIPS1_S3_EEDpOT_ at Base 2.4.1
- _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE12emplace_backIJS5_EEEvDpOT_ at Base 2.4.1
+ _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE12emplace_backIJS5_EEERS5_DpOT_ at Base 2.4.1-4
+#MISSING: 2.4.1-4# _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE12emplace_backIJS5_EEEvDpOT_ at Base 2.4.1
  _ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE17_M_default_appendEm 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
@@ -984,6 +988,8 @@
  _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
  _ZNSt6vectorImSaImEE8_M_eraseEN9__gnu_cxx17__normal_iteratorIPmS1_EE at Base 2.4.1
+ _ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC1IS3_EEPKcRKS3_ at Base 2.4.1-4
+ _ZNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEC2IS3_EEPKcRKS3_ at Base 2.4.1-4
  _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
@@ -1345,6 +1351,7 @@
  _ZTv0_n56_N3bpp4Site11setPositionEi at Base 2.4.1
  _ZTv0_n56_NK3bpp15BasicSymbolList4sizeEv at Base 2.4.1
  _ZTv0_n56_NK3bpp25AbstractSequenceContainer8toStringERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE at Base 2.4.1
+ _ZTv0_n64_NK3bpp20AbstractCoreSequence11getCommentsB5cxx11Ev at Base 2.4.1-4
  _ZTv0_n72_NK3bpp15DarwinVarSingle5writeERSoRKNS_7DataSetE at Base 2.4.1
  _ZTv0_n72_NK3bpp9DarwinDon5writeERSoRKNS_7DataSetE at Base 2.4.1
  _ZTv0_n80_N3bpp29PolymorphismSequenceContainer11addSequenceERKNS_8SequenceEb at Base 2.4.1
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

