[Debian-med-packaging] Bug#1012934: gatb-core: ftbfs with GCC-12

Thu Jun 16 13:08:59 BST 2022

Package: src:gatb-core
Version: 1.4.2+dfsg-8
Severity: normal
Tags: sid bookworm
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-12

[This bug is targeted to the upcoming bookworm 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-12/g++-12, but succeeds to build with gcc-11/g++-11. The
severity of this report will be raised before the bookworm release.

The full build log can be found at:
http://qa-logs.debian.net/2022/06/09/gcc12/gatb-core_1.4.2+dfsg-8_unstable_gcc12.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.

[...]
+#MISSING: 1.4.2+dfsg-8# _ZTSSt23_Sp_counted_ptr_inplaceIPKN4gatb4core5tools4math8LargeIntILi3EEESaIS7_ELN9__gnu_cxx12_Lock_policyE2EE at Base 1.4.2
+ _ZTSSt23_Sp_counted_ptr_inplaceIPKN4gatb4core5tools4math8LargeIntILi3EEESaIvELN9__gnu_cxx12_Lock_policyE2EE at Base 1.4.2+dfsg-8
+#MISSING: 1.4.2+dfsg-8# _ZTSSt23_Sp_counted_ptr_inplaceIPKN4gatb4core5tools4math8LargeIntILi4EEESaIS7_ELN9__gnu_cxx12_Lock_policyE2EE at Base 1.4.2
+ _ZTSSt23_Sp_counted_ptr_inplaceIPKN4gatb4core5tools4math8LargeIntILi4EEESaIvELN9__gnu_cxx12_Lock_policyE2EE at Base 1.4.2+dfsg-8
+#MISSING: 1.4.2+dfsg-8# _ZTSSt23_Sp_counted_ptr_inplaceIPKmSaIS1_ELN9__gnu_cxx12_Lock_policyE2EE at Base 1.4.2
+ _ZTSSt23_Sp_counted_ptr_inplaceIPKmSaIvELN9__gnu_cxx12_Lock_policyE2EE at Base 1.4.2+dfsg-8
+#MISSING: 1.4.2+dfsg-8# _ZTSSt23_Sp_counted_ptr_inplaceISt13packaged_taskIFviEESaIS2_ELN9__gnu_cxx12_Lock_policyE2EE at Base 1.4.2
+ _ZTSSt23_Sp_counted_ptr_inplaceISt13packaged_taskIFviEESaIvELN9__gnu_cxx12_Lock_policyE2EE at Base 1.4.2+dfsg-8
  _ZTSZN10ThreadPool7enqueueIRZN4gatb4core8debruijn4impl10prepare_ufILi128EEEvNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEPNS2_4bank5IBankEiRiiiRmmEUliE_JEEESt6futureINSt9result_ofIFT_iDpT0_EE4typeEEOSL_DpOSM_EUliE_ at Base 1.4.2
  _ZTSZN10ThreadPool7enqueueIRZN4gatb4core8debruijn4impl10prepare_ufILi32EEEvNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEPNS2_4bank5IBankEiRiiiRmmEUliE_JEEESt6futureINSt9result_ofIFT_iDpT0_EE4typeEEOSL_DpOSM_EUliE_ at Base 1.4.2
  _ZTSZN10ThreadPool7enqueueIRZN4gatb4core8debruijn4impl10prepare_ufILi64EEEvNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEPNS2_4bank5IBankEiRiiiRmmEUliE_JEEESt6futureINSt9result_ofIFT_iDpT0_EE4typeEEOSL_DpOSM_EUliE_ at Base 1.4.2
@@ -13345,11 +13484,16 @@
  _ZTVNSt13__future_base16_Task_state_baseIFviEEE at Base 1.4.2
  _ZTVNSt13__future_base7_ResultIvEE at Base 1.4.2
  _ZTVNSt6thread11_State_implINS_8_InvokerISt5tupleIJZN10ThreadPoolC4EmEUlvE_EEEEEE at Base 1.4.2
- _ZTVSt23_Sp_counted_ptr_inplaceIN4gatb4core5tools11collections4impl6BooPHFINS2_4math8LargeIntILi1EEENS4_16AdaptatorDefaultIS8_EENS2_4misc4impl12ProgressNoneEE18iterator_adaptatorESaISF_ELN9__gnu_cxx12_Lock_policyE2EE at Base 1.4.2
- _ZTVSt23_Sp_counted_ptr_inplaceIN4gatb4core5tools11collections4impl6BooPHFINS2_4math8LargeIntILi2EEENS4_16AdaptatorDefaultIS8_EENS2_4misc4impl12ProgressNoneEE18iterator_adaptatorESaISF_ELN9__gnu_cxx12_Lock_policyE2EE at Base 1.4.2
- _ZTVSt23_Sp_counted_ptr_inplaceIN4gatb4core5tools11collections4impl6BooPHFINS2_4math8LargeIntILi3EEENS4_16AdaptatorDefaultIS8_EENS2_4misc4impl12ProgressNoneEE18iterator_adaptatorESaISF_ELN9__gnu_cxx12_Lock_policyE2EE at Base 1.4.2
- _ZTVSt23_Sp_counted_ptr_inplaceIN4gatb4core5tools11collections4impl6BooPHFINS2_4math8LargeIntILi4EEENS4_16AdaptatorDefaultIS8_EENS2_4misc4impl12ProgressNoneEE18iterator_adaptatorESaISF_ELN9__gnu_cxx12_Lock_policyE2EE at Base 1.4.2
- _ZTVSt23_Sp_counted_ptr_inplaceIN9__gnu_cxx17__normal_iteratorIPKmSt6vectorImSaImEEEESaIS7_ELNS0_12_Lock_policyE2EE at Base 1.4.2
+#MISSING: 1.4.2+dfsg-8# _ZTVSt23_Sp_counted_ptr_inplaceIN4gatb4core5tools11collections4impl6BooPHFINS2_4math8LargeIntILi1EEENS4_16AdaptatorDefaultIS8_EENS2_4misc4impl12ProgressNoneEE18iterator_adaptatorESaISF_ELN9__gnu_cxx12_Lock_policyE2EE at Base 1.4.2
+ _ZTVSt23_Sp_counted_ptr_inplaceIN4gatb4core5tools11collections4impl6BooPHFINS2_4math8LargeIntILi1EEENS4_16AdaptatorDefaultIS8_EENS2_4misc4impl12ProgressNoneEE18iterator_adaptatorESaIvELN9__gnu_cxx12_Lock_policyE2EE at Base 1.4.2+dfsg-8
+#MISSING: 1.4.2+dfsg-8# _ZTVSt23_Sp_counted_ptr_inplaceIN4gatb4core5tools11collections4impl6BooPHFINS2_4math8LargeIntILi2EEENS4_16AdaptatorDefaultIS8_EENS2_4misc4impl12ProgressNoneEE18iterator_adaptatorESaISF_ELN9__gnu_cxx12_Lock_policyE2EE at Base 1.4.2
+ _ZTVSt23_Sp_counted_ptr_inplaceIN4gatb4core5tools11collections4impl6BooPHFINS2_4math8LargeIntILi2EEENS4_16AdaptatorDefaultIS8_EENS2_4misc4impl12ProgressNoneEE18iterator_adaptatorESaIvELN9__gnu_cxx12_Lock_policyE2EE at Base 1.4.2+dfsg-8
+#MISSING: 1.4.2+dfsg-8# _ZTVSt23_Sp_counted_ptr_inplaceIN4gatb4core5tools11collections4impl6BooPHFINS2_4math8LargeIntILi3EEENS4_16AdaptatorDefaultIS8_EENS2_4misc4impl12ProgressNoneEE18iterator_adaptatorESaISF_ELN9__gnu_cxx12_Lock_policyE2EE at Base 1.4.2
+ _ZTVSt23_Sp_counted_ptr_inplaceIN4gatb4core5tools11collections4impl6BooPHFINS2_4math8LargeIntILi3EEENS4_16AdaptatorDefaultIS8_EENS2_4misc4impl12ProgressNoneEE18iterator_adaptatorESaIvELN9__gnu_cxx12_Lock_policyE2EE at Base 1.4.2+dfsg-8
+#MISSING: 1.4.2+dfsg-8# _ZTVSt23_Sp_counted_ptr_inplaceIN4gatb4core5tools11collections4impl6BooPHFINS2_4math8LargeIntILi4EEENS4_16AdaptatorDefaultIS8_EENS2_4misc4impl12ProgressNoneEE18iterator_adaptatorESaISF_ELN9__gnu_cxx12_Lock_policyE2EE at Base 1.4.2
+ _ZTVSt23_Sp_counted_ptr_inplaceIN4gatb4core5tools11collections4impl6BooPHFINS2_4math8LargeIntILi4EEENS4_16AdaptatorDefaultIS8_EENS2_4misc4impl12ProgressNoneEE18iterator_adaptatorESaIvELN9__gnu_cxx12_Lock_policyE2EE at Base 1.4.2+dfsg-8
+#MISSING: 1.4.2+dfsg-8# _ZTVSt23_Sp_counted_ptr_inplaceIN9__gnu_cxx17__normal_iteratorIPKmSt6vectorImSaImEEEESaIS7_ELNS0_12_Lock_policyE2EE at Base 1.4.2
+ _ZTVSt23_Sp_counted_ptr_inplaceIN9__gnu_cxx17__normal_iteratorIPKmSt6vectorImSaImEEEESaIvELNS0_12_Lock_policyE2EE at Base 1.4.2+dfsg-8
  _ZTVSt23_Sp_counted_ptr_inplaceINSt13__future_base11_Task_stateISt5_BindIFZN4gatb4core8debruijn4impl10prepare_ufILi128EEEvNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEPNS4_4bank5IBankEiRiiiRmmEUliE_St12_PlaceholderILi1EEEESaIiEFviEEESO_LN9__gnu_cxx12_Lock_policyE2EE at Base 1.4.2
  _ZTVSt23_Sp_counted_ptr_inplaceINSt13__future_base11_Task_stateISt5_BindIFZN4gatb4core8debruijn4impl10prepare_ufILi32EEEvNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEPNS4_4bank5IBankEiRiiiRmmEUliE_St12_PlaceholderILi1EEEESaIiEFviEEESO_LN9__gnu_cxx12_Lock_policyE2EE at Base 1.4.2
  _ZTVSt23_Sp_counted_ptr_inplaceINSt13__future_base11_Task_stateISt5_BindIFZN4gatb4core8debruijn4impl10prepare_ufILi64EEEvNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEPNS4_4bank5IBankEiRiiiRmmEUliE_St12_PlaceholderILi1EEEESaIiEFviEEESO_LN9__gnu_cxx12_Lock_policyE2EE at Base 1.4.2
@@ -13366,12 +13510,18 @@
  _ZTVSt23_Sp_counted_ptr_inplaceINSt13__future_base11_Task_stateISt5_BindIFZN4gatb4core8debruijn4impl6bcalm2ILm64EEEvPNS4_5tools7storage4impl7StorageENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiiiiibEUliE1_St12_PlaceholderILi1EEEESaIiEFviEEESO_LN9__gnu_cxx12_Lock_policyE2EE at Base 1.4.2
  _ZTVSt23_Sp_counted_ptr_inplaceINSt13__future_base11_Task_stateISt5_BindIFZN4gatb4core8debruijn4impl6bcalm2ILm96EEEvPNS4_5tools7storage4impl7StorageENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiiiiibEUliE0_St12_PlaceholderILi1EEEESaIiEFviEEESO_LN9__gnu_cxx12_Lock_policyE2EE at Base 1.4.2
  _ZTVSt23_Sp_counted_ptr_inplaceINSt13__future_base11_Task_stateISt5_BindIFZN4gatb4core8debruijn4impl6bcalm2ILm96EEEvPNS4_5tools7storage4impl7StorageENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiiiiibEUliE1_St12_PlaceholderILi1EEEESaIiEFviEEESO_LN9__gnu_cxx12_Lock_policyE2EE at Base 1.4.2
- _ZTVSt23_Sp_counted_ptr_inplaceIPKN4gatb4core5tools4math8LargeIntILi1EEESaIS7_ELN9__gnu_cxx12_Lock_policyE2EE at Base 1.4.2
- _ZTVSt23_Sp_counted_ptr_inplaceIPKN4gatb4core5tools4math8LargeIntILi2EEESaIS7_ELN9__gnu_cxx12_Lock_policyE2EE at Base 1.4.2
- _ZTVSt23_Sp_counted_ptr_inplaceIPKN4gatb4core5tools4math8LargeIntILi3EEESaIS7_ELN9__gnu_cxx12_Lock_policyE2EE at Base 1.4.2
- _ZTVSt23_Sp_counted_ptr_inplaceIPKN4gatb4core5tools4math8LargeIntILi4EEESaIS7_ELN9__gnu_cxx12_Lock_policyE2EE at Base 1.4.2
- _ZTVSt23_Sp_counted_ptr_inplaceIPKmSaIS1_ELN9__gnu_cxx12_Lock_policyE2EE at Base 1.4.2
- _ZTVSt23_Sp_counted_ptr_inplaceISt13packaged_taskIFviEESaIS2_ELN9__gnu_cxx12_Lock_policyE2EE at Base 1.4.2
+#MISSING: 1.4.2+dfsg-8# _ZTVSt23_Sp_counted_ptr_inplaceIPKN4gatb4core5tools4math8LargeIntILi1EEESaIS7_ELN9__gnu_cxx12_Lock_policyE2EE at Base 1.4.2
+ _ZTVSt23_Sp_counted_ptr_inplaceIPKN4gatb4core5tools4math8LargeIntILi1EEESaIvELN9__gnu_cxx12_Lock_policyE2EE at Base 1.4.2+dfsg-8
+#MISSING: 1.4.2+dfsg-8# _ZTVSt23_Sp_counted_ptr_inplaceIPKN4gatb4core5tools4math8LargeIntILi2EEESaIS7_ELN9__gnu_cxx12_Lock_policyE2EE at Base 1.4.2
+ _ZTVSt23_Sp_counted_ptr_inplaceIPKN4gatb4core5tools4math8LargeIntILi2EEESaIvELN9__gnu_cxx12_Lock_policyE2EE at Base 1.4.2+dfsg-8
+#MISSING: 1.4.2+dfsg-8# _ZTVSt23_Sp_counted_ptr_inplaceIPKN4gatb4core5tools4math8LargeIntILi3EEESaIS7_ELN9__gnu_cxx12_Lock_policyE2EE at Base 1.4.2
+ _ZTVSt23_Sp_counted_ptr_inplaceIPKN4gatb4core5tools4math8LargeIntILi3EEESaIvELN9__gnu_cxx12_Lock_policyE2EE at Base 1.4.2+dfsg-8
+#MISSING: 1.4.2+dfsg-8# _ZTVSt23_Sp_counted_ptr_inplaceIPKN4gatb4core5tools4math8LargeIntILi4EEESaIS7_ELN9__gnu_cxx12_Lock_policyE2EE at Base 1.4.2
+ _ZTVSt23_Sp_counted_ptr_inplaceIPKN4gatb4core5tools4math8LargeIntILi4EEESaIvELN9__gnu_cxx12_Lock_policyE2EE at Base 1.4.2+dfsg-8
+#MISSING: 1.4.2+dfsg-8# _ZTVSt23_Sp_counted_ptr_inplaceIPKmSaIS1_ELN9__gnu_cxx12_Lock_policyE2EE at Base 1.4.2
+ _ZTVSt23_Sp_counted_ptr_inplaceIPKmSaIvELN9__gnu_cxx12_Lock_policyE2EE at Base 1.4.2+dfsg-8
+#MISSING: 1.4.2+dfsg-8# _ZTVSt23_Sp_counted_ptr_inplaceISt13packaged_taskIFviEESaIS2_ELN9__gnu_cxx12_Lock_policyE2EE at Base 1.4.2
+ _ZTVSt23_Sp_counted_ptr_inplaceISt13packaged_taskIFviEESaIvELN9__gnu_cxx12_Lock_policyE2EE at Base 1.4.2+dfsg-8
  _ZTVZNK4gatb4core8debruijn4impl13GraphTemplateINS2_6Node_tINS0_5tools4math15IntegerTemplateIN5boost3mpl7vector4IN4mpl_4int_ILi32EEENSC_ILi64EEENSC_ILi96EEENSC_ILi128EEEEEEEEENS2_6Edge_tISJ_EENS8_7variantINS8_6detail7variant13over_sequenceINS9_6l_itemINSB_5long_ILl4EEENS2_9GraphDataILm32EEENSQ_INSR_ILl3EEENST_ILm64EEENSQ_INSR_ILl2EEENST_ILm96EEENSQ_INSR_ILl1EEENST_ILm128EEENS9_5l_endEEEEEEEEEEEJEEEE9neighborsESt23_Rb_tree_const_iteratorINS2_15BranchingNode_tISJ_EEES1C_E3Cmd at Base 1.4.2
  _ZTVZNK4gatb4core8debruijn4impl13GraphTemplateINS2_6Node_tINS0_5tools4math8LargeIntILi1EEEEENS2_6Edge_tIS9_EEN5boost7variantINS2_9GraphDataILm32EEEJEEEE9neighborsESt23_Rb_tree_const_iteratorINS2_15BranchingNode_tIS9_EEESL_E3Cmd at Base 1.4.2
  _ZTVZNK4gatb4core8debruijn4impl13GraphTemplateINS2_6Node_tINS0_5tools4math8LargeIntILi2EEEEENS2_6Edge_tIS9_EEN5boost7variantINS2_9GraphDataILm64EEEJEEEE9neighborsESt23_Rb_tree_const_iteratorINS2_15BranchingNode_tIS9_EEESL_E3Cmd at Base 1.4.2
@@ -16031,7 +16181,7 @@
  _ZZN4gatb4core5tools4misc4impl10StringLine15getDefaultWidthEvE5value at Base 1.4.2
  _ZZN4gatb4core5tools4misc4impl11LibraryInfo7getInfoEvE9singleton at Base 1.4.2
  _ZZN4gatb4core5tools4misc4impl8HostInfo7getInfoEvE9singleton at Base 1.4.2
- _ZZN4gatb4core5tools7storage4impl12StorageTools9singletonEvE8instance at Base 1.4.2
+#MISSING: 1.4.2+dfsg-8# _ZZN4gatb4core5tools7storage4impl12StorageTools9singletonEvE8instance at Base 1.4.2
  _ZZN4gatb4core5tools7storage4impl18StorageHDF5Factory13GlobalSynchro9singletonEvE8instance at Base 1.4.2
  _ZZN4gatb4core5tools7storage4impl23CollectionDataHDF5PatchINS0_4kmer4impl4KmerILm128EE5CountEE12checkCleanupEvE4MASK at Base 1.4.2
  _ZZN4gatb4core5tools7storage4impl23CollectionDataHDF5PatchINS0_4kmer4impl4KmerILm32EE5CountEE12checkCleanupEvE4MASK at Base 1.4.2
dh_makeshlibs: error: failing due to earlier errors
make: *** [debian/rules:15: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2

