[Debian-med-packaging] Bug#984145: gatb-core: ftbfs with GCC-11

Matthias Klose doko at debian.org
Wed Mar 3 16:12:38 GMT 2021


Package: src:gatb-core
Version: 1.4.2+dfsg-6
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/gatb-core_1.4.2+dfsg-6_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.

[...]
  _ZSt16__insertion_sortIN9__gnu_cxx17__normal_iteratorIPN4gatb4core8debruijn4impl11kmerIndiceTILm64EEESt6vectorIS7_SaIS7_EEEENS0_5__ops15_Iter_comp_iterINS5_10comparatorILm64EEEEEEvT_SI_T0_ at Base 1.4.2
  _ZSt16__insertion_sortIN9__gnu_cxx17__normal_iteratorIPN4gatb4core8debruijn4impl11kmerIndiceTILm96EEESt6vectorIS7_SaIS7_EEEENS0_5__ops15_Iter_comp_iterINS5_10comparatorILm96EEEEEEvT_SI_T0_ at Base 1.4.2
@@ -9397,13 +9488,13 @@
  _ZSt22__final_insertion_sortIPN4gatb4core5tools11collections4impl6Hash16INS2_4math8LargeIntILi2EEEiE4cellEN9__gnu_cxx5__ops15_Iter_comp_iterIPFbRKSA_SG_EEEEvT_SK_T0_ at Base 1.4.2
  _ZSt22__final_insertion_sortIPN4gatb4core5tools11collections4impl6Hash16INS2_4math8LargeIntILi3EEEiE4cellEN9__gnu_cxx5__ops15_Iter_comp_iterIPFbRKSA_SG_EEEEvT_SK_T0_ at Base 1.4.2
  _ZSt22__final_insertion_sortIPN4gatb4core5tools11collections4impl6Hash16INS2_4math8LargeIntILi4EEEiE4cellEN9__gnu_cxx5__ops15_Iter_comp_iterIPFbRKSA_SG_EEEEvT_SK_T0_ at Base 1.4.2
- _ZSt22__move_median_to_firstIN9__gnu_cxx17__normal_iteratorIPN4gatb4core8debruijn4impl11kmerIndiceTILm128EEESt6vectorIS7_SaIS7_EEEENS0_5__ops15_Iter_comp_iterINS5_10comparatorILm128EEEEEEvT_SI_SI_SI_T0_ at Base 1.4.2
- _ZSt22__move_median_to_firstIN9__gnu_cxx17__normal_iteratorIPN4gatb4core8debruijn4impl11kmerIndiceTILm64EEESt6vectorIS7_SaIS7_EEEENS0_5__ops15_Iter_comp_iterINS5_10comparatorILm64EEEEEEvT_SI_SI_SI_T0_ at Base 1.4.2
- _ZSt22__move_median_to_firstIN9__gnu_cxx17__normal_iteratorIPN4gatb4core8debruijn4impl11kmerIndiceTILm96EEESt6vectorIS7_SaIS7_EEEENS0_5__ops15_Iter_comp_iterINS5_10comparatorILm96EEEEEEvT_SI_SI_SI_T0_ at Base 1.4.2
- _ZSt22__move_median_to_firstIN9__gnu_cxx17__normal_iteratorIPSt4pairIS2_ImmEmESt6vectorIS4_SaIS4_EEEENS0_5__ops15_Iter_comp_iterIPFbRKS4_SD_EEEEvT_SH_SH_SH_T0_ at Base 1.4.2
- _ZSt22__move_median_to_firstIN9__gnu_cxx17__normal_iteratorIPmSt6vectorImSaImEEEENS0_5__ops15_Iter_comp_iterIN4gatb4core4kmer4impl11SortCommandILm128EE3CmpEEEEvT_SH_SH_SH_T0_ at Base 1.4.2
- _ZSt22__move_median_to_firstIN9__gnu_cxx17__normal_iteratorIPmSt6vectorImSaImEEEENS0_5__ops15_Iter_comp_iterIN4gatb4core4kmer4impl11SortCommandILm64EE3CmpEEEEvT_SH_SH_SH_T0_ at Base 1.4.2
- _ZSt22__move_median_to_firstIN9__gnu_cxx17__normal_iteratorIPmSt6vectorImSaImEEEENS0_5__ops15_Iter_comp_iterIN4gatb4core4kmer4impl11SortCommandILm96EE3CmpEEEEvT_SH_SH_SH_T0_ at Base 1.4.2
+#MISSING: 1.4.2+dfsg-6# _ZSt22__move_median_to_firstIN9__gnu_cxx17__normal_iteratorIPN4gatb4core8debruijn4impl11kmerIndiceTILm128EEESt6vectorIS7_SaIS7_EEEENS0_5__ops15_Iter_comp_iterINS5_10comparatorILm128EEEEEEvT_SI_SI_SI_T0_ at Base 1.4.2
+#MISSING: 1.4.2+dfsg-6# _ZSt22__move_median_to_firstIN9__gnu_cxx17__normal_iteratorIPN4gatb4core8debruijn4impl11kmerIndiceTILm64EEESt6vectorIS7_SaIS7_EEEENS0_5__ops15_Iter_comp_iterINS5_10comparatorILm64EEEEEEvT_SI_SI_SI_T0_ at Base 1.4.2
+#MISSING: 1.4.2+dfsg-6# _ZSt22__move_median_to_firstIN9__gnu_cxx17__normal_iteratorIPN4gatb4core8debruijn4impl11kmerIndiceTILm96EEESt6vectorIS7_SaIS7_EEEENS0_5__ops15_Iter_comp_iterINS5_10comparatorILm96EEEEEEvT_SI_SI_SI_T0_ at Base 1.4.2
+#MISSING: 1.4.2+dfsg-6# _ZSt22__move_median_to_firstIN9__gnu_cxx17__normal_iteratorIPSt4pairIS2_ImmEmESt6vectorIS4_SaIS4_EEEENS0_5__ops15_Iter_comp_iterIPFbRKS4_SD_EEEEvT_SH_SH_SH_T0_ at Base 1.4.2
+#MISSING: 1.4.2+dfsg-6# _ZSt22__move_median_to_firstIN9__gnu_cxx17__normal_iteratorIPmSt6vectorImSaImEEEENS0_5__ops15_Iter_comp_iterIN4gatb4core4kmer4impl11SortCommandILm128EE3CmpEEEEvT_SH_SH_SH_T0_ at Base 1.4.2
+#MISSING: 1.4.2+dfsg-6# _ZSt22__move_median_to_firstIN9__gnu_cxx17__normal_iteratorIPmSt6vectorImSaImEEEENS0_5__ops15_Iter_comp_iterIN4gatb4core4kmer4impl11SortCommandILm64EE3CmpEEEEvT_SH_SH_SH_T0_ at Base 1.4.2
+#MISSING: 1.4.2+dfsg-6# _ZSt22__move_median_to_firstIN9__gnu_cxx17__normal_iteratorIPmSt6vectorImSaImEEEENS0_5__ops15_Iter_comp_iterIN4gatb4core4kmer4impl11SortCommandILm96EE3CmpEEEEvT_SH_SH_SH_T0_ at Base 1.4.2
  _ZSt23__copy_move_backward_a1ILb1EPN4gatb4core8debruijn4impl6NodeNtINS3_6Node_tINS1_5tools4math15IntegerTemplateIN5boost3mpl7vector4IN4mpl_4int_ILi32EEENSD_ILi64EEENSD_ILi96EEENSD_ILi128EEEEEEEEEEESL_EN9__gnu_cxx11__enable_ifIXsrSt23__is_random_access_iterIT0_NSt15iterator_traitsISQ_E17iterator_categoryEE7__valueESt15_Deque_iteratorIT1_RSW_PSW_EE6__typeESQ_SQ_SZ_ at Base 1.4.2
  _ZSt23__copy_move_backward_a1ILb1EPN4gatb4core8debruijn4impl6NodeNtINS3_6Node_tINS1_5tools4math8LargeIntILi1EEEEEEESB_EN9__gnu_cxx11__enable_ifIXsrSt23__is_random_access_iterIT0_NSt15iterator_traitsISG_E17iterator_categoryEE7__valueESt15_Deque_iteratorIT1_RSM_PSM_EE6__typeESG_SG_SP_ at Base 1.4.2
  _ZSt23__copy_move_backward_a1ILb1EPN4gatb4core8debruijn4impl6NodeNtINS3_6Node_tINS1_5tools4math8LargeIntILi2EEEEEEESB_EN9__gnu_cxx11__enable_ifIXsrSt23__is_random_access_iterIT0_NSt15iterator_traitsISG_E17iterator_categoryEE7__valueESt15_Deque_iteratorIT1_RSM_PSM_EE6__typeESG_SG_SP_ at Base 1.4.2
@@ -9421,7 +9512,15 @@
  _ZSt4copyISt15_Deque_iteratorIN4gatb4core8debruijn4impl6NodeNtINS4_6Node_tINS2_5tools4math8LargeIntILi2EEEEEEERKSC_PSD_ES0_ISC_RSC_PSC_EET0_T_SL_SK_ at Base 1.4.2
  _ZSt4copyISt15_Deque_iteratorIN4gatb4core8debruijn4impl6NodeNtINS4_6Node_tINS2_5tools4math8LargeIntILi3EEEEEEERKSC_PSD_ES0_ISC_RSC_PSC_EET0_T_SL_SK_ at Base 1.4.2
  _ZSt4copyISt15_Deque_iteratorIN4gatb4core8debruijn4impl6NodeNtINS4_6Node_tINS2_5tools4math8LargeIntILi4EEEEEEERKSC_PSD_ES0_ISC_RSC_PSC_EET0_T_SL_SK_ at Base 1.4.2
+ _ZSt4moveISt15_Deque_iteratorIN4gatb4core8debruijn4impl6NodeNtINS4_6Node_tINS2_5tools4math15IntegerTemplateIN5boost3mpl7vector4IN4mpl_4int_ILi32EEENSE_ILi64EEENSE_ILi96EEENSE_ILi128EEEEEEEEEEERSM_PSM_ESP_ET0_T_SR_SQ_ at Base 1.4.2+dfsg-6
+ _ZSt4moveISt15_Deque_iteratorIN4gatb4core8debruijn4impl6NodeNtINS4_6Node_tINS2_5tools4math8LargeIntILi1EEEEEEERSC_PSC_ESF_ET0_T_SH_SG_ at Base 1.4.2+dfsg-6
+ _ZSt4moveISt15_Deque_iteratorIN4gatb4core8debruijn4impl6NodeNtINS4_6Node_tINS2_5tools4math8LargeIntILi2EEEEEEERSC_PSC_ESF_ET0_T_SH_SG_ at Base 1.4.2+dfsg-6
+ _ZSt4moveISt15_Deque_iteratorIN4gatb4core8debruijn4impl6NodeNtINS4_6Node_tINS2_5tools4math8LargeIntILi3EEEEEEERSC_PSC_ESF_ET0_T_SH_SG_ at Base 1.4.2+dfsg-6
+ _ZSt4moveISt15_Deque_iteratorIN4gatb4core8debruijn4impl6NodeNtINS4_6Node_tINS2_5tools4math8LargeIntILi4EEEEEEERSC_PSC_ESF_ET0_T_SH_SG_ at Base 1.4.2+dfsg-6
+ _ZSt4swapIN4gatb4core8debruijn4impl11kmerIndiceTILm128EEEENSt9enable_ifIXsrSt6__and_IJSt6__not_ISt15__is_tuple_likeIT_EESt21is_move_constructibleISA_ESt18is_move_assignableISA_EEE5valueEvE4typeERSA_SK_ at Base 1.4.2+dfsg-6
+ _ZSt4swapIN4gatb4core8debruijn4impl11kmerIndiceTILm96EEEENSt9enable_ifIXsrSt6__and_IJSt6__not_ISt15__is_tuple_likeIT_EESt21is_move_constructibleISA_ESt18is_move_assignableISA_EEE5valueEvE4typeERSA_SK_ at Base 1.4.2+dfsg-6
  _ZSt6__sortIN9__gnu_cxx17__normal_iteratorIPSt4pairIS2_ImmEmESt6vectorIS4_SaIS4_EEEENS0_5__ops15_Iter_comp_iterIPFbRKS4_SD_EEEEvT_SH_T0_ at Base 1.4.2
+ _ZSt9call_onceIMNSt13__future_base13_State_baseV2EFvPSt8functionIFSt10unique_ptrINS0_12_Result_baseENS4_8_DeleterEEvEEPbEJPS1_S9_SA_EEvRSt9once_flagOT_DpOT0_ at Base 1.4.2+dfsg-6
  _ZSt9iter_swapIN9__gnu_cxx17__normal_iteratorIPSt4pairIiN4gatb4core8debruijn4impl6Edge_tINS6_6Node_tINS4_5tools4math15IntegerTemplateIN5boost3mpl7vector4IN4mpl_4int_ILi32EEENSG_ILi64EEENSG_ILi96EEENSG_ILi128EEEEEEEEEEEESt6vectorISP_SaISP_EEEESU_EvT_T0_ at Base 1.4.2
  _ZStltIiN4gatb4core8debruijn4impl6Edge_tINS3_6Node_tINS1_5tools4math15IntegerTemplateIN5boost3mpl7vector4IN4mpl_4int_ILi32EEENSD_ILi64EEENSD_ILi96EEENSD_ILi128EEEEEEEEEEEEbRKSt4pairIT_T0_ESR_ at Base 1.4.2
  _ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EEOS8_PKS5_ at Base 1.4.2
@@ -16052,15 +16151,15 @@
  _ZZN4gatb4core8debruijn4impl15SimplificationsINS2_13GraphTemplateINS2_6Node_tINS0_5tools4math8LargeIntILi2EEEEENS2_6Edge_tISA_EEN5boost7variantINS2_9GraphDataILm64EEEJEEEEESA_SC_E10removeTipsEvENKUlRSA_E_clESK_ at Base 1.4.2
  _ZZN4gatb4core8debruijn4impl15SimplificationsINS2_13GraphTemplateINS2_6Node_tINS0_5tools4math8LargeIntILi2EEEEENS2_6Edge_tISA_EEN5boost7variantINS2_9GraphDataILm64EEEJEEEEESA_SC_E12removeBulgesEvENKUlRSA_E_clESK_ at Base 1.4.2
  _ZZN4gatb4core8debruijn4impl15SimplificationsINS2_13GraphTemplateINS2_6Node_tINS0_5tools4math8LargeIntILi2EEEEENS2_6Edge_tISA_EEN5boost7variantINS2_9GraphDataILm64EEEJEEEEESA_SC_E26removeErroneousConnectionsEvENKUlRSA_E_clESK_ at Base 1.4.2
- _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 1.4.2
+#MISSING: 1.4.2+dfsg-6# _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 1.4.2
  _ZZN4gatb4core8debruijn4impl15SimplificationsINS2_13GraphTemplateINS2_6Node_tINS0_5tools4math8LargeIntILi3EEEEENS2_6Edge_tISA_EEN5boost7variantINS2_9GraphDataILm96EEEJEEEEESA_SC_E10removeTipsEvENKUlRSA_E_clESK_ at Base 1.4.2
  _ZZN4gatb4core8debruijn4impl15SimplificationsINS2_13GraphTemplateINS2_6Node_tINS0_5tools4math8LargeIntILi3EEEEENS2_6Edge_tISA_EEN5boost7variantINS2_9GraphDataILm96EEEJEEEEESA_SC_E12removeBulgesEvENKUlRSA_E_clESK_ at Base 1.4.2
  _ZZN4gatb4core8debruijn4impl15SimplificationsINS2_13GraphTemplateINS2_6Node_tINS0_5tools4math8LargeIntILi3EEEEENS2_6Edge_tISA_EEN5boost7variantINS2_9GraphDataILm96EEEJEEEEESA_SC_E26removeErroneousConnectionsEvENKUlRSA_E_clESK_ at Base 1.4.2
- _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 1.4.2
+#MISSING: 1.4.2+dfsg-6# _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 1.4.2
  _ZZN4gatb4core8debruijn4impl15SimplificationsINS2_13GraphTemplateINS2_6Node_tINS0_5tools4math8LargeIntILi4EEEEENS2_6Edge_tISA_EEN5boost7variantINS2_9GraphDataILm128EEEJEEEEESA_SC_E10removeTipsEvENKUlRSA_E_clESK_ at Base 1.4.2
  _ZZN4gatb4core8debruijn4impl15SimplificationsINS2_13GraphTemplateINS2_6Node_tINS0_5tools4math8LargeIntILi4EEEEENS2_6Edge_tISA_EEN5boost7variantINS2_9GraphDataILm128EEEJEEEEESA_SC_E12removeBulgesEvENKUlRSA_E_clESK_ at Base 1.4.2
  _ZZN4gatb4core8debruijn4impl15SimplificationsINS2_13GraphTemplateINS2_6Node_tINS0_5tools4math8LargeIntILi4EEEEENS2_6Edge_tISA_EEN5boost7variantINS2_9GraphDataILm128EEEJEEEEESA_SC_E26removeErroneousConnectionsEvENKUlRSA_E_clESK_ at Base 1.4.2
- _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 1.4.2
+#MISSING: 1.4.2+dfsg-6# _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 1.4.2
  _ZZN4gatb4core8debruijn4impl15SimplificationsINS2_20GraphUnitigsTemplateILm128EEENS2_6NodeGUENS2_6EdgeGUEE10removeTipsEvENKUlRS6_E_clES9_ at Base 1.4.2
  _ZZN4gatb4core8debruijn4impl15SimplificationsINS2_20GraphUnitigsTemplateILm128EEENS2_6NodeGUENS2_6EdgeGUEE12removeBulgesEvENKUlRS6_E_clES9_ at Base 1.4.2
  _ZZN4gatb4core8debruijn4impl15SimplificationsINS2_20GraphUnitigsTemplateILm128EEENS2_6NodeGUENS2_6EdgeGUEE26removeErroneousConnectionsEvENKUlRS6_E_clES9_ at Base 1.4.2
@@ -16359,7 +16458,7 @@
  _ZZNSt19_Sp_make_shared_tag5_S_tiEvE5__tag at Base 1.4.2
  _ZZNSt8__detail18__to_chars_10_implIjEEvPcjT_E8__digits at Base 1.4.2
  _ZZNSt8__detail18__to_chars_10_implImEEvPcjT_E8__digits at Base 1.4.2
- _ZZSt9call_onceIMNSt13__future_base13_State_baseV2EFvPSt8functionIFSt10unique_ptrINS0_12_Result_baseENS4_8_DeleterEEvEEPbEJPS1_S9_SA_EEvRSt9once_flagOT_DpOT0_ENUlvE0_4_FUNEv at Base 1.4.2
+#MISSING: 1.4.2+dfsg-6# _ZZSt9call_onceIMNSt13__future_base13_State_baseV2EFvPSt8functionIFSt10unique_ptrINS0_12_Result_baseENS4_8_DeleterEEvEEPbEJPS1_S9_SA_EEvRSt9once_flagOT_DpOT0_ENUlvE0_4_FUNEv at Base 1.4.2
  bin2NT at Base 1.4.2
  bin2NTrev at Base 1.4.2
  binrev 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



More information about the Debian-med-packaging mailing list