[Debian-med-packaging] Bug#957254: gatb-core: ftbfs with GCC-10

Matthias Klose doko at debian.org
Fri Apr 17 12:01:00 BST 2020


Package: src:gatb-core
Version: 1.4.1+git20191209.9398f28+dfsg-3
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/gatb-core_1.4.1+git20191209.9398f28+dfsg-3_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

[...]
- _ZZN4gatb4core5tools11collections4impl12HashFunctorsINS1_4math8LargeIntILi3EEEE18generate_hash_seedEvE5rbase at Base 1.4.1+git20190813.a73b6dd+dfsg
- _ZZN4gatb4core5tools11collections4impl12HashFunctorsINS1_4math8LargeIntILi4EEEE18generate_hash_seedEvE5rbase at Base 1.4.1+git20190813.a73b6dd+dfsg
+#MISSING: 1.4.1+git20191209.9398f28+dfsg-3# _ZZN4gatb4core5tools11collections4impl12BloomFactory9singletonEvE8instance at Base 1.4.1+git20190813.a73b6dd+dfsg
+#MISSING: 1.4.1+git20191209.9398f28+dfsg-3# _ZZN4gatb4core5tools11collections4impl12HashFunctorsINS1_4math8LargeIntILi1EEEE18generate_hash_seedEvE5rbase at Base 1.4.1+git20190813.a73b6dd+dfsg
+#MISSING: 1.4.1+git20191209.9398f28+dfsg-3# _ZZN4gatb4core5tools11collections4impl12HashFunctorsINS1_4math8LargeIntILi2EEEE18generate_hash_seedEvE5rbase at Base 1.4.1+git20190813.a73b6dd+dfsg
+#MISSING: 1.4.1+git20191209.9398f28+dfsg-3# _ZZN4gatb4core5tools11collections4impl12HashFunctorsINS1_4math8LargeIntILi3EEEE18generate_hash_seedEvE5rbase at Base 1.4.1+git20190813.a73b6dd+dfsg
+#MISSING: 1.4.1+git20191209.9398f28+dfsg-3# _ZZN4gatb4core5tools11collections4impl12HashFunctorsINS1_4math8LargeIntILi4EEEE18generate_hash_seedEvE5rbase at Base 1.4.1+git20190813.a73b6dd+dfsg
  _ZZN4gatb4core5tools4math8LargeIntILi2EE7getNameEvE5first at Base 1.4.1+git20190813.a73b6dd+dfsg
  _ZZN4gatb4core5tools4math8LargeIntILi2EE7getNameEvE6buffer at Base 1.4.1+git20190813.a73b6dd+dfsg
  _ZZN4gatb4core5tools4math8LargeIntILi3EE7getNameEvE5first at Base 1.4.1+git20190813.a73b6dd+dfsg
@@ -16038,6 +16657,7 @@
  _ZZN4gatb4core6system4impl6System6memoryEvE8instance at Base 1.4.1+git20190813.a73b6dd+dfsg
  _ZZN4gatb4core6system4impl6System6threadEvE8instance at Base 1.4.1+git20190813.a73b6dd+dfsg
  _ZZN4gatb4core8debruijn4impl10prepare_ufILi128EEEvNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEPNS0_4bank5IBankEiRiiiRmmEN12RepartHashesclERKNSA_8SequenceE at Base 1.4.1+git20190813.a73b6dd+dfsg
+ _ZZN4gatb4core8debruijn4impl10prepare_ufILi32EEEvNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEPNS0_4bank5IBankEiRiiiRmmEN12RepartHashesclERKNSA_8SequenceE at Base 1.4.1+git20191209.9398f28+dfsg-3
  _ZZN4gatb4core8debruijn4impl10prepare_ufILi64EEEvNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEPNS0_4bank5IBankEiRiiiRmmEN12RepartHashesclERKNSA_8SequenceE at Base 1.4.1+git20190813.a73b6dd+dfsg
  _ZZN4gatb4core8debruijn4impl10prepare_ufILi96EEEvNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEPNS0_4bank5IBankEiRiiiRmmEN12RepartHashesclERKNSA_8SequenceE at Base 1.4.1+git20190813.a73b6dd+dfsg
  _ZZN4gatb4core8debruijn4impl13GraphTemplateINS2_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_endEEEEEEEEEEEJEEEE19precomputeAdjacencyEjbENKUlRSJ_E_clES19_ at Base 1.4.1+git20190813.a73b6dd+dfsg
@@ -16055,12 +16675,15 @@
  _ZZN4gatb4core8debruijn4impl15SimplificationsINS2_13GraphTemplateINS2_6Node_tINS0_5tools4math8LargeIntILi2EEEEENS2_6Edge_tISA_EEN5boost7variantINS2_9GraphDataILm64EEEJEEEEESA_SC_E10removeTipsEvENKUlRSA_E_clESK_ at Base 1.4.1+git20190813.a73b6dd+dfsg
  _ZZN4gatb4core8debruijn4impl15SimplificationsINS2_13GraphTemplateINS2_6Node_tINS0_5tools4math8LargeIntILi2EEEEENS2_6Edge_tISA_EEN5boost7variantINS2_9GraphDataILm64EEEJEEEEESA_SC_E12removeBulgesEvENKUlRSA_E_clESK_ at Base 1.4.1+git20190813.a73b6dd+dfsg
  _ZZN4gatb4core8debruijn4impl15SimplificationsINS2_13GraphTemplateINS2_6Node_tINS0_5tools4math8LargeIntILi2EEEEENS2_6Edge_tISA_EEN5boost7variantINS2_9GraphDataILm64EEEJEEEEESA_SC_E26removeErroneousConnectionsEvENKUlRSA_E_clESK_ at Base 1.4.1+git20190813.a73b6dd+dfsg
+ _ZZN4gatb4core8debruijn4impl15SimplificationsINS2_13GraphTemplateINS2_6Node_tINS0_5tools4math8LargeIntILi2EEEEENS2_6Edge_tISA_EEN5boost7variantINS2_9GraphDataILm64EEEJEEEEESA_SC_E35heuristic_most_covered_path_unitigsENS2_9DirectionERSA_SL_iRSt3setISA_St4lessISA_ESaISA_EERiRSt6vectorIiSaIiEESW_RdjPSA_bRmENKUlSL_E_clESL_ at Base 1.4.1+git20191209.9398f28+dfsg-3
  _ZZN4gatb4core8debruijn4impl15SimplificationsINS2_13GraphTemplateINS2_6Node_tINS0_5tools4math8LargeIntILi3EEEEENS2_6Edge_tISA_EEN5boost7variantINS2_9GraphDataILm96EEEJEEEEESA_SC_E10removeTipsEvENKUlRSA_E_clESK_ at Base 1.4.1+git20190813.a73b6dd+dfsg
  _ZZN4gatb4core8debruijn4impl15SimplificationsINS2_13GraphTemplateINS2_6Node_tINS0_5tools4math8LargeIntILi3EEEEENS2_6Edge_tISA_EEN5boost7variantINS2_9GraphDataILm96EEEJEEEEESA_SC_E12removeBulgesEvENKUlRSA_E_clESK_ at Base 1.4.1+git20190813.a73b6dd+dfsg
  _ZZN4gatb4core8debruijn4impl15SimplificationsINS2_13GraphTemplateINS2_6Node_tINS0_5tools4math8LargeIntILi3EEEEENS2_6Edge_tISA_EEN5boost7variantINS2_9GraphDataILm96EEEJEEEEESA_SC_E26removeErroneousConnectionsEvENKUlRSA_E_clESK_ at Base 1.4.1+git20190813.a73b6dd+dfsg
+ _ZZN4gatb4core8debruijn4impl15SimplificationsINS2_13GraphTemplateINS2_6Node_tINS0_5tools4math8LargeIntILi3EEEEENS2_6Edge_tISA_EEN5boost7variantINS2_9GraphDataILm96EEEJEEEEESA_SC_E35heuristic_most_covered_path_unitigsENS2_9DirectionERSA_SL_iRSt3setISA_St4lessISA_ESaISA_EERiRSt6vectorIiSaIiEESW_RdjPSA_bRmENKUlSL_E_clESL_ at Base 1.4.1+git20191209.9398f28+dfsg-3
  _ZZN4gatb4core8debruijn4impl15SimplificationsINS2_13GraphTemplateINS2_6Node_tINS0_5tools4math8LargeIntILi4EEEEENS2_6Edge_tISA_EEN5boost7variantINS2_9GraphDataILm128EEEJEEEEESA_SC_E10removeTipsEvENKUlRSA_E_clESK_ at Base 1.4.1+git20190813.a73b6dd+dfsg
  _ZZN4gatb4core8debruijn4impl15SimplificationsINS2_13GraphTemplateINS2_6Node_tINS0_5tools4math8LargeIntILi4EEEEENS2_6Edge_tISA_EEN5boost7variantINS2_9GraphDataILm128EEEJEEEEESA_SC_E12removeBulgesEvENKUlRSA_E_clESK_ at Base 1.4.1+git20190813.a73b6dd+dfsg
  _ZZN4gatb4core8debruijn4impl15SimplificationsINS2_13GraphTemplateINS2_6Node_tINS0_5tools4math8LargeIntILi4EEEEENS2_6Edge_tISA_EEN5boost7variantINS2_9GraphDataILm128EEEJEEEEESA_SC_E26removeErroneousConnectionsEvENKUlRSA_E_clESK_ at Base 1.4.1+git20190813.a73b6dd+dfsg
+ _ZZN4gatb4core8debruijn4impl15SimplificationsINS2_13GraphTemplateINS2_6Node_tINS0_5tools4math8LargeIntILi4EEEEENS2_6Edge_tISA_EEN5boost7variantINS2_9GraphDataILm128EEEJEEEEESA_SC_E35heuristic_most_covered_path_unitigsENS2_9DirectionERSA_SL_iRSt3setISA_St4lessISA_ESaISA_EERiRSt6vectorIiSaIiEESW_RdjPSA_bRmENKUlSL_E_clESL_ at Base 1.4.1+git20191209.9398f28+dfsg-3
  _ZZN4gatb4core8debruijn4impl15SimplificationsINS2_20GraphUnitigsTemplateILm128EEENS2_6NodeGUENS2_6EdgeGUEE10removeTipsEvENKUlRS6_E_clES9_ at Base 1.4.1+git20190813.a73b6dd+dfsg
  _ZZN4gatb4core8debruijn4impl15SimplificationsINS2_20GraphUnitigsTemplateILm128EEENS2_6NodeGUENS2_6EdgeGUEE12removeBulgesEvENKUlRS6_E_clES9_ at Base 1.4.1+git20190813.a73b6dd+dfsg
  _ZZN4gatb4core8debruijn4impl15SimplificationsINS2_20GraphUnitigsTemplateILm128EEENS2_6NodeGUENS2_6EdgeGUEE26removeErroneousConnectionsEvENKUlRS6_E_clES9_ at Base 1.4.1+git20190813.a73b6dd+dfsg
@@ -16076,19 +16699,19 @@
  _ZZN4gatb4core8debruijn4impl5bglueILm128EEEvPNS0_5tools7storage4impl7StorageENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiiibbENKUlRKNS0_4bank8SequenceEE1_clESI_ at Base 1.4.1+git20191130.664696c+dfsg
  _ZZN4gatb4core8debruijn4impl5bglueILm128EEEvPNS0_5tools7storage4impl7StorageENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiiibbENKUlRKNS0_4bank8SequenceEE_clESI_ at Base 1.4.1+git20191130.664696c+dfsg
  _ZZN4gatb4core8debruijn4impl5bglueILm128EEEvPNS0_5tools7storage4impl7StorageENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiiibbENKUlRKSE_SG_bbRNS0_4kmer4impl4KmerILm128EE13KmerCanonicalESM_RbE0_clESG_SG_bbSM_SM_SN_ at Base 1.4.1+git20191130.664696c+dfsg
- _ZZN4gatb4core8debruijn4impl5bglueILm128EEEvPNS0_5tools7storage4impl7StorageENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiiibbENKUliE2_clEi at Base 1.4.1+git20191130.664696c+dfsg
+#MISSING: 1.4.1+git20191209.9398f28+dfsg-3# _ZZN4gatb4core8debruijn4impl5bglueILm128EEEvPNS0_5tools7storage4impl7StorageENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiiibbENKUliE2_clEi at Base 1.4.1+git20191130.664696c+dfsg
  _ZZN4gatb4core8debruijn4impl5bglueILm32EEEvPNS0_5tools7storage4impl7StorageENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiiibbENKUlRKNS0_4bank8SequenceEE1_clESI_ at Base 1.4.1+git20191130.664696c+dfsg
  _ZZN4gatb4core8debruijn4impl5bglueILm32EEEvPNS0_5tools7storage4impl7StorageENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiiibbENKUlRKNS0_4bank8SequenceEE_clESI_ at Base 1.4.1+git20191130.664696c+dfsg
  _ZZN4gatb4core8debruijn4impl5bglueILm32EEEvPNS0_5tools7storage4impl7StorageENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiiibbENKUlRKSE_SG_bbRNS0_4kmer4impl4KmerILm32EE13KmerCanonicalESM_RbE0_clESG_SG_bbSM_SM_SN_ at Base 1.4.1+git20191130.664696c+dfsg
- _ZZN4gatb4core8debruijn4impl5bglueILm32EEEvPNS0_5tools7storage4impl7StorageENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiiibbENKUliE2_clEi at Base 1.4.1+git20191130.664696c+dfsg
+#MISSING: 1.4.1+git20191209.9398f28+dfsg-3# _ZZN4gatb4core8debruijn4impl5bglueILm32EEEvPNS0_5tools7storage4impl7StorageENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiiibbENKUliE2_clEi at Base 1.4.1+git20191130.664696c+dfsg
  _ZZN4gatb4core8debruijn4impl5bglueILm64EEEvPNS0_5tools7storage4impl7StorageENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiiibbENKUlRKNS0_4bank8SequenceEE1_clESI_ at Base 1.4.1+git20191130.664696c+dfsg
  _ZZN4gatb4core8debruijn4impl5bglueILm64EEEvPNS0_5tools7storage4impl7StorageENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiiibbENKUlRKNS0_4bank8SequenceEE_clESI_ at Base 1.4.1+git20191130.664696c+dfsg
  _ZZN4gatb4core8debruijn4impl5bglueILm64EEEvPNS0_5tools7storage4impl7StorageENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiiibbENKUlRKSE_SG_bbRNS0_4kmer4impl4KmerILm64EE13KmerCanonicalESM_RbE0_clESG_SG_bbSM_SM_SN_ at Base 1.4.1+git20191130.664696c+dfsg
- _ZZN4gatb4core8debruijn4impl5bglueILm64EEEvPNS0_5tools7storage4impl7StorageENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiiibbENKUliE2_clEi at Base 1.4.1+git20191130.664696c+dfsg
+#MISSING: 1.4.1+git20191209.9398f28+dfsg-3# _ZZN4gatb4core8debruijn4impl5bglueILm64EEEvPNS0_5tools7storage4impl7StorageENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiiibbENKUliE2_clEi at Base 1.4.1+git20191130.664696c+dfsg
  _ZZN4gatb4core8debruijn4impl5bglueILm96EEEvPNS0_5tools7storage4impl7StorageENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiiibbENKUlRKNS0_4bank8SequenceEE1_clESI_ at Base 1.4.1+git20191130.664696c+dfsg
  _ZZN4gatb4core8debruijn4impl5bglueILm96EEEvPNS0_5tools7storage4impl7StorageENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiiibbENKUlRKNS0_4bank8SequenceEE_clESI_ at Base 1.4.1+git20191130.664696c+dfsg
  _ZZN4gatb4core8debruijn4impl5bglueILm96EEEvPNS0_5tools7storage4impl7StorageENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiiibbENKUlRKSE_SG_bbRNS0_4kmer4impl4KmerILm96EE13KmerCanonicalESM_RbE0_clESG_SG_bbSM_SM_SN_ at Base 1.4.1+git20191130.664696c+dfsg
- _ZZN4gatb4core8debruijn4impl5bglueILm96EEEvPNS0_5tools7storage4impl7StorageENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiiibbENKUliE2_clEi at Base 1.4.1+git20191130.664696c+dfsg
+#MISSING: 1.4.1+git20191209.9398f28+dfsg-3# _ZZN4gatb4core8debruijn4impl5bglueILm96EEEvPNS0_5tools7storage4impl7StorageENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiiibbENKUliE2_clEi at Base 1.4.1+git20191130.664696c+dfsg
  _ZZN4gatb4core8debruijn4impl6bcalm2ILm128EEEvPNS0_5tools7storage4impl7StorageENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiiiiibEN19InsertTravellerKmerclERKNS0_4bank8SequenceE at Base 1.4.1+git20190813.a73b6dd+dfsg
  _ZZN4gatb4core8debruijn4impl6bcalm2ILm128EEEvPNS0_5tools7storage4impl7StorageENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiiiiibENKUliE1_clEi at Base 1.4.1+git20190813.a73b6dd+dfsg
  _ZZN4gatb4core8debruijn4impl6bcalm2ILm32EEEvPNS0_5tools7storage4impl7StorageENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiiiiibEN19InsertTravellerKmerclERKNS0_4bank8SequenceE at Base 1.4.1+git20190813.a73b6dd+dfsg
@@ -16361,6 +16984,8 @@
  _ZZNK4gatb4core8debruijn4impl20cached_nodes_visitorINS2_6Node_tINS0_5tools4math8LargeIntILi4EEEEENS2_6Edge_tIS9_EEN5boost7variantINS2_9GraphDataILm128EEEJEEEEclILm128EEEPNS5_2dp14ISmartIteratorIS9_EERKNSE_IXT_EEEENK18CachedNodeIterator4rankEv at Base 1.4.1+git20190813.a73b6dd+dfsg
  _ZZNK4gatb4core8debruijn4impl20cached_nodes_visitorINS2_6Node_tINS0_5tools4math8LargeIntILi4EEEEENS2_6Edge_tIS9_EEN5boost7variantINS2_9GraphDataILm128EEEJEEEEclILm128EEEPNS5_2dp14ISmartIteratorIS9_EERKNSE_IXT_EEEENK18CachedNodeIterator4sizeEv at Base 1.4.1+git20190813.a73b6dd+dfsg
  _ZZNSt19_Sp_make_shared_tag5_S_tiEvE5__tag at Base 1.4.1+git20190813.a73b6dd+dfsg
+ _ZZNSt8__detail18__to_chars_10_implIjEEvPcjT_E8__digits at Base 1.4.1+git20191209.9398f28+dfsg-3
+ _ZZNSt8__detail18__to_chars_10_implImEEvPcjT_E8__digits at Base 1.4.1+git20191209.9398f28+dfsg-3
  _ZZSt9call_onceIMNSt13__future_base13_State_baseV2EFvPSt8functionIFSt10unique_ptrINS0_12_Result_baseENS4_8_DeleterEEvEEPbEJPS1_S9_SA_EEvRSt9once_flagOT_DpOT0_ENUlvE0_4_FUNEv at Base 1.4.1+git20190813.a73b6dd+dfsg
  bin2NT at Base 1.4.1+git20190813.a73b6dd+dfsg
  bin2NTrev at Base 1.4.1+git20190813.a73b6dd+dfsg
dh_makeshlibs: error: failing due to earlier errors
make: *** [debian/rules:15: binary] Error 25
dpkg-buildpackage: error: fakeroot debian/rules binary subprocess returned exit status 2



More information about the Debian-med-packaging mailing list