Source: gudhi
Version: 3.4.0+dfsg-1
Severity: serious
Justification: FTBFS on amd64
Tags: bullseye sid ftbfs
Usertags: ftbfs-20201226 ftbfs-bullseye
Hi,
During a rebuild of all packages in sid, your package failed to build
on amd64.
Relevant part (hopefully):
> cd /<<PKGBUILDDIR>>/build/userversion/src/Tangential_complex/benchmark &&
> /usr/bin/c++ -DBOOST_ALL_DYN_LINK -DBOOST_ALL_NO_LIB
> -DBOOST_RESULT_OF_USE_DECLTYPE -DBOOST_SYSTEM_NO_DEPRECATED
> -DCGAL_EIGEN3_ENABLED -DCGAL_USE_GMPXX=1 -DGUDHI_USE_TBB -DNOMINMAX
> -I/<<PKGBUILDDIR>>/build/userversion -I/<<PKGBUILDDIR>>/src/common/include
> -I/<<PKGBUILDDIR>>/src/Alpha_complex/include
> -I/<<PKGBUILDDIR>>/src/Bitmap_cubical_complex/include
> -I/<<PKGBUILDDIR>>/src/Bottleneck_distance/include
> -I/<<PKGBUILDDIR>>/src/Collapse/include
> -I/<<PKGBUILDDIR>>/src/Contraction/include
> -I/<<PKGBUILDDIR>>/src/Cech_complex/include
> -I/<<PKGBUILDDIR>>/src/Hasse_complex/include
> -I/<<PKGBUILDDIR>>/src/Persistence_representations/include
> -I/<<PKGBUILDDIR>>/src/Persistent_cohomology/include
> -I/<<PKGBUILDDIR>>/src/Rips_complex/include
> -I/<<PKGBUILDDIR>>/src/Simplex_tree/include
> -I/<<PKGBUILDDIR>>/src/Skeleton_blocker/include
> -I/<<PKGBUILDDIR>>/src/Spatial_searching/include
> -I/<<PKGBUILDDIR>>/src/Subsampling/include
> -I/<<PKGBUILDDIR>>/src/Tangential_complex/include
> -I/<<PKGBUILDDIR>>/src/Toplex_map/include
> -I/<<PKGBUILDDIR>>/src/Witness_complex/include
> -I/<<PKGBUILDDIR>>/src/Nerve_GIC/include -isystem /usr/include/eigen3 -g -O2
> -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
> -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -pedantic
> -frounding-math -std=gnu++14 -o
> CMakeFiles/Tangential_complex_benchmark.dir/benchmark_tc.cpp.o -c
> /<<PKGBUILDDIR>>/src/Tangential_complex/benchmark/benchmark_tc.cpp
> In file included from
> /<<PKGBUILDDIR>>/src/Tangential_complex/benchmark/benchmark_tc.cpp:30:
> /<<PKGBUILDDIR>>/src/Tangential_complex/include/gudhi/Tangential_complex/Simplicial_complex.h:
> In member function ‘void
> Gudhi::tangential_complex::internal::Simplicial_complex::collapse(int, bool)’:
> /<<PKGBUILDDIR>>/src/Tangential_complex/include/gudhi/Tangential_complex/Simplicial_complex.h:154:37:
> warning: comparison of integer expressions of different signedness:
> ‘boost::container::dtl::flat_tree<long unsigned int,
> boost::move_detail::identity<long unsigned int>, std::less<long unsigned
> int>, void>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
> 154 | GUDHI_CHECK(it_Cf->size() == max_simplex_dim + 1,
> | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
> /<<PKGBUILDDIR>>/src/common/include/gudhi/Debug_utils.h:23:44: note: in
> definition of macro ‘GUDHI_CHECK’
> 23 | #define GUDHI_CHECK(expression, excpt) ((expression) ? (void) 0 :
> (throw excpt))
> | ^~~~~~~~~~
> In file included from
> /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22,
> from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23,
> from
> /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14,
> from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42,
> from
> /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25,
> from /usr/include/boost/smart_ptr/shared_ptr.hpp:29,
> from /usr/include/boost/shared_ptr.hpp:17,
> from /usr/include/CGAL/Object.h:32,
> from /usr/include/CGAL/kernel_basic.h:25,
> from /usr/include/CGAL/basic.h:35,
> from /usr/include/CGAL/Combination_enumerator.h:18,
> from
> /<<PKGBUILDDIR>>/src/Tangential_complex/include/gudhi/Tangential_complex/utilities.h:15,
> from
> /<<PKGBUILDDIR>>/src/Tangential_complex/include/gudhi/Tangential_complex/Simplicial_complex.h:15,
> from
> /<<PKGBUILDDIR>>/src/Tangential_complex/include/gudhi/Tangential_complex.h:16,
> from
> /<<PKGBUILDDIR>>/src/Tangential_complex/benchmark/benchmark_tc.cpp:32:
> /usr/include/boost/function_output_iterator.hpp: At global scope:
> /usr/include/boost/function_output_iterator.hpp:14:1: note: ‘#pragma message:
> This header is deprecated. Use <boost/iterator/function_output_iterator.hpp>
> instead.’
> 14 |
> BOOST_HEADER_DEPRECATED("<boost/iterator/function_output_iterator.hpp>")
> | ^~~~~~~~~~~~~~~~~~~~~~~
> In file included from
> /<<PKGBUILDDIR>>/src/Tangential_complex/benchmark/benchmark_tc.cpp:51:
> /usr/include/tbb/task_scheduler_init.h:21:154: note: ‘#pragma message: TBB
> Warning: tbb/task_scheduler_init.h is deprecated. For details, please see
> Deprecated Features appendix in the TBB reference manual.’
> 21 | #pragma message("TBB Warning: tbb/task_scheduler_init.h is
> deprecated. For details, please see Deprecated Features appendix in the TBB
> reference manual.")
> |
>
> ^
> In file included from
> /<<PKGBUILDDIR>>/src/Tangential_complex/benchmark/benchmark_tc.cpp:53:
> /<<PKGBUILDDIR>>/src/Tangential_complex/benchmark/XML_exporter.h: In member
> function ‘bool Streaming_XML_exporter<value_type>::add_element(const
> Element&)’:
> /<<PKGBUILDDIR>>/src/Tangential_complex/benchmark/XML_exporter.h:160:32:
> warning: ‘std::ios_base::streampos’ is deprecated: use 'std::streampos'
> instead [-Wdeprecated-declarations]
> 160 | std::ofstream::streampos pos = m_xml_fstream.tellp();
> | ^~~
> In file included from /usr/include/c++/10/ios:42,
> from /usr/include/c++/10/ostream:38,
> from /usr/include/c++/10/iostream:39,
> from
> /<<PKGBUILDDIR>>/src/common/include/gudhi/Debug_utils.h:13,
> from
> /<<PKGBUILDDIR>>/src/Tangential_complex/benchmark/benchmark_tc.cpp:30:
> /usr/include/c++/10/bits/ios_base.h:499:28: note: declared here
> 499 | typedef std::streampos streampos
> | ^~~~~~~~~
> In file included from
> /<<PKGBUILDDIR>>/src/Tangential_complex/benchmark/benchmark_tc.cpp:32:
> /<<PKGBUILDDIR>>/src/Tangential_complex/include/gudhi/Tangential_complex.h:
> In instantiation of ‘Gudhi::tangential_complex::Tangential_complex<Kernel_,
> DimensionTag, Concurrency_tag, Triangulation_>::Tr_vertex_handle
> Gudhi::tangential_complex::Tangential_complex<Kernel_, DimensionTag,
> Concurrency_tag, Triangulation_>::compute_star(std::size_t, const Point&,
> const Tangent_space_basis&,
> Gudhi::tangential_complex::Tangential_complex<Kernel_, DimensionTag,
> Concurrency_tag, Triangulation_>::Triangulation&, bool) [with Kernel_ =
> CGAL::Epick_d<CGAL::Dynamic_dimension_tag>; DimensionTag =
> CGAL::Dynamic_dimension_tag; Concurrency_tag = CGAL::Parallel_tag;
> Triangulation_ = CGAL::Default;
> Gudhi::tangential_complex::Tangential_complex<Kernel_, DimensionTag,
> Concurrency_tag, Triangulation_>::Tr_vertex_handle =
> CGAL::internal::CC_iterator<CGAL::Compact_container<CGAL::Triangulation_vertex<CGAL::Regular_triangulation_traits_adapter<CGAL::Epick_d<CGAL::Dynamic_dimension_tag>
> >, Gudhi::tangential_complex::Vertex_data,
> CGAL::Triangulation_ds_vertex<CGAL::Triangulation_data_structure<CGAL::Dynamic_dimension_tag,
>
> CGAL::Triangulation_vertex<CGAL::Regular_triangulation_traits_adapter<CGAL::Epick_d<CGAL::Dynamic_dimension_tag>
> >, Gudhi::tangential_complex::Vertex_data, CGAL::Default>,
> CGAL::Triangulation_full_cell<CGAL::Regular_triangulation_traits_adapter<CGAL::Epick_d<CGAL::Dynamic_dimension_tag>
> >, CGAL::No_full_cell_data, CGAL::Default> > > >, CGAL::Default,
> CGAL::Default, CGAL::Default>, false>; std::size_t = long unsigned int;
> Gudhi::tangential_complex::Tangential_complex<Kernel_, DimensionTag,
> Concurrency_tag, Triangulation_>::Point =
> CGAL::Wrap::Point_d<CGAL::Epick_d<CGAL::Dynamic_dimension_tag> >;
> Gudhi::tangential_complex::Tangential_complex<Kernel_, DimensionTag,
> Concurrency_tag, Triangulation_>::Tangent_space_basis =
> Gudhi::tangential_complex::internal::Basis<CGAL::Epick_d<CGAL::Dynamic_dimension_tag>
> >; Gudhi::tangential_complex::Tangential_complex<Kernel_, DimensionTag,
> Concurrency_tag, Triangulation_>::Triangulation =
> CGAL::Regular_triangulation<CGAL::Epick_d<CGAL::Dynamic_dimension_tag>,
> CGAL::Triangulation_data_structure<CGAL::Dynamic_dimension_tag,
> CGAL::Triangulation_vertex<CGAL::Regular_triangulation_traits_adapter<CGAL::Epick_d<CGAL::Dynamic_dimension_tag>
> >, Gudhi::tangential_complex::Vertex_data, CGAL::Default>,
> CGAL::Triangulation_full_cell<CGAL::Regular_triangulation_traits_adapter<CGAL::Epick_d<CGAL::Dynamic_dimension_tag>
> >, CGAL::No_full_cell_data, CGAL::Default> > >]’:
> /<<PKGBUILDDIR>>/src/Tangential_complex/include/gudhi/Tangential_complex.h:1137:43:
> required from ‘void Gudhi::tangential_complex::Tangential_complex<Kernel_,
> DimensionTag, Concurrency_tag,
> Triangulation_>::compute_tangent_triangulation(std::size_t, bool) [with
> Kernel_ = CGAL::Epick_d<CGAL::Dynamic_dimension_tag>; DimensionTag =
> CGAL::Dynamic_dimension_tag; Concurrency_tag = CGAL::Parallel_tag;
> Triangulation_ = CGAL::Default; std::size_t = long unsigned int]’
> /<<PKGBUILDDIR>>/src/Tangential_complex/include/gudhi/Tangential_complex.h:365:57:
> required from ‘void Gudhi::tangential_complex::Tangential_complex<Kernel_,
> DimensionTag, Concurrency_tag, Triangulation_>::compute_tangential_complex()
> [with Kernel_ = CGAL::Epick_d<CGAL::Dynamic_dimension_tag>; DimensionTag =
> CGAL::Dynamic_dimension_tag; Concurrency_tag = CGAL::Parallel_tag;
> Triangulation_ = CGAL::Default]’
> /<<PKGBUILDDIR>>/src/Tangential_complex/benchmark/benchmark_tc.cpp:366:33:
> required from here
> /<<PKGBUILDDIR>>/src/Tangential_complex/include/gudhi/Tangential_complex.h:957:40:
> error: no type named ‘Power_center_d’ in
> ‘Gudhi::tangential_complex::Tangential_complex<CGAL::Epick_d<CGAL::Dynamic_dimension_tag>,
> CGAL::Dynamic_dimension_tag, CGAL::Parallel_tag>::Tr_traits’ {aka ‘class
> CGAL::Regular_triangulation_traits_adapter<CGAL::Epick_d<CGAL::Dynamic_dimension_tag>
> >’}
> 957 | typename Tr_traits::Power_center_d power_center =
> local_tr_traits.power_center_d_object();
> | ^~~~~~~~~~~~
> /<<PKGBUILDDIR>>/src/Tangential_complex/include/gudhi/Tangential_complex.h:957:40:
> error: no type named ‘Power_center_d’ in
> ‘Gudhi::tangential_complex::Tangential_complex<CGAL::Epick_d<CGAL::Dynamic_dimension_tag>,
> CGAL::Dynamic_dimension_tag, CGAL::Parallel_tag>::Tr_traits’ {aka ‘class
> CGAL::Regular_triangulation_traits_adapter<CGAL::Epick_d<CGAL::Dynamic_dimension_tag>
> >’}
> In file included from
> /<<PKGBUILDDIR>>/src/Tangential_complex/benchmark/benchmark_tc.cpp:30:
> /<<PKGBUILDDIR>>/src/Tangential_complex/include/gudhi/Tangential_complex.h:
> In instantiation of ‘void
> Gudhi::tangential_complex::Tangential_complex<Kernel_, DimensionTag,
> Concurrency_tag, Triangulation_>::update_star(std::size_t) [with Kernel_ =
> CGAL::Epick_d<CGAL::Dynamic_dimension_tag>; DimensionTag =
> CGAL::Dynamic_dimension_tag; Concurrency_tag = CGAL::Parallel_tag;
> Triangulation_ = CGAL::Default; std::size_t = long unsigned int]’:
> /<<PKGBUILDDIR>>/src/Tangential_complex/include/gudhi/Tangential_complex.h:1150:5:
> required from ‘void Gudhi::tangential_complex::Tangential_complex<Kernel_,
> DimensionTag, Concurrency_tag,
> Triangulation_>::compute_tangent_triangulation(std::size_t, bool) [with
> Kernel_ = CGAL::Epick_d<CGAL::Dynamic_dimension_tag>; DimensionTag =
> CGAL::Dynamic_dimension_tag; Concurrency_tag = CGAL::Parallel_tag;
> Triangulation_ = CGAL::Default; std::size_t = long unsigned int]’
> /<<PKGBUILDDIR>>/src/Tangential_complex/include/gudhi/Tangential_complex.h:365:57:
> required from ‘void Gudhi::tangential_complex::Tangential_complex<Kernel_,
> DimensionTag, Concurrency_tag, Triangulation_>::compute_tangential_complex()
> [with Kernel_ = CGAL::Epick_d<CGAL::Dynamic_dimension_tag>; DimensionTag =
> CGAL::Dynamic_dimension_tag; Concurrency_tag = CGAL::Parallel_tag;
> Triangulation_ = CGAL::Default]’
> /<<PKGBUILDDIR>>/src/Tangential_complex/benchmark/benchmark_tc.cpp:366:33:
> required from here
> /<<PKGBUILDDIR>>/src/Tangential_complex/include/gudhi/Tangential_complex.h:1180:43:
> warning: comparison of integer expressions of different signedness:
> ‘boost::container::dtl::flat_tree<long unsigned int,
> boost::move_detail::identity<long unsigned int>, std::less<long unsigned
> int>, void>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
> 1180 | GUDHI_CHECK(incident_simplex.size() == cur_dim_plus_1 - 1,
> /<<PKGBUILDDIR>>/src/common/include/gudhi/Debug_utils.h:23:44: note: in
> definition of macro ‘GUDHI_CHECK’
> 23 | #define GUDHI_CHECK(expression, excpt) ((expression) ? (void) 0 :
> (throw excpt))
> | ^~~~~~~~~~
> In file included from
> /<<PKGBUILDDIR>>/src/Tangential_complex/benchmark/benchmark_tc.cpp:32:
> /<<PKGBUILDDIR>>/src/Tangential_complex/include/gudhi/Tangential_complex.h:
> In instantiation of ‘void
> Gudhi::tangential_complex::Tangential_complex<Kernel_, DimensionTag,
> Concurrency_tag, Triangulation_>::refresh_tangent_triangulation(std::size_t,
> const Points_ds&, bool) [with Kernel_ =
> CGAL::Epick_d<CGAL::Dynamic_dimension_tag>; DimensionTag =
> CGAL::Dynamic_dimension_tag; Concurrency_tag = CGAL::Parallel_tag;
> Triangulation_ = CGAL::Default; std::size_t = long unsigned int;
> Gudhi::tangential_complex::Tangential_complex<Kernel_, DimensionTag,
> Concurrency_tag, Triangulation_>::Points_ds =
> Gudhi::spatial_searching::Kd_tree_search<CGAL::Epick_d<CGAL::Dynamic_dimension_tag>,
> std::vector<CGAL::Wrap::Point_d<CGAL::Epick_d<CGAL::Dynamic_dimension_tag>
> >,
> std::allocator<CGAL::Wrap::Point_d<CGAL::Epick_d<CGAL::Dynamic_dimension_tag>
> > > > >]’:
> /<<PKGBUILDDIR>>/src/Tangential_complex/include/gudhi/Tangential_complex.h:844:57:
> required from ‘void Gudhi::tangential_complex::Tangential_complex<Kernel_,
> DimensionTag, Concurrency_tag,
> Triangulation_>::refresh_tangential_complex(const Point_indices_range&) [with
> Point_indices_range = std::vector<long unsigned int>; Kernel_ =
> CGAL::Epick_d<CGAL::Dynamic_dimension_tag>; DimensionTag =
> CGAL::Dynamic_dimension_tag; Concurrency_tag = CGAL::Parallel_tag;
> Triangulation_ = CGAL::Default]’
> /<<PKGBUILDDIR>>/src/Tangential_complex/include/gudhi/Tangential_complex.h:485:65:
> required from ‘Gudhi::tangential_complex::Tangential_complex<Kernel_,
> DimensionTag, Concurrency_tag, Triangulation_>::Fix_inconsistencies_info
> Gudhi::tangential_complex::Tangential_complex<Kernel_, DimensionTag,
> Concurrency_tag,
> Triangulation_>::fix_inconsistencies_using_perturbation(double, double) [with
> Kernel_ = CGAL::Epick_d<CGAL::Dynamic_dimension_tag>; DimensionTag =
> CGAL::Dynamic_dimension_tag; Concurrency_tag = CGAL::Parallel_tag;
> Triangulation_ = CGAL::Default]’
> /<<PKGBUILDDIR>>/src/Tangential_complex/benchmark/benchmark_tc.cpp:402:86:
> required from here
> /<<PKGBUILDDIR>>/src/Tangential_complex/include/gudhi/Tangential_complex.h:1103:34:
> error: no type named ‘Power_distance_d’ in
> ‘Gudhi::tangential_complex::Tangential_complex<CGAL::Epick_d<CGAL::Dynamic_dimension_tag>,
> CGAL::Dynamic_dimension_tag, CGAL::Parallel_tag>::K’ {aka ‘struct
> CGAL::Epick_d<CGAL::Dynamic_dimension_tag>’}
> 1103 | typename K::Power_distance_d k_power_dist =
> m_k.power_distance_d_object();
> | ^~~~~~~~~~~~
> /<<PKGBUILDDIR>>/src/Tangential_complex/include/gudhi/Tangential_complex.h:1103:34:
> error: no type named ‘Power_distance_d’ in
> ‘Gudhi::tangential_complex::Tangential_complex<CGAL::Epick_d<CGAL::Dynamic_dimension_tag>,
> CGAL::Dynamic_dimension_tag, CGAL::Parallel_tag>::K’ {aka ‘struct
> CGAL::Epick_d<CGAL::Dynamic_dimension_tag>’}
> make[4]: ***
> [src/Tangential_complex/benchmark/CMakeFiles/Tangential_complex_benchmark.dir/build.make:85:
>
> src/Tangential_complex/benchmark/CMakeFiles/Tangential_complex_benchmark.dir/benchmark_tc.cpp.o]
> Error 1
The full build log is available from:
http://qa-logs.debian.net/2020/12/26/gudhi_3.4.0+dfsg-1_unstable.log
A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
If you reassign this bug to another package, please marking it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects
If you fail to reproduce this, please provide a build log and diff it with me
so that we can identify if something relevant changed in the meantime.
About the archive rebuild: The rebuild was done on EC2 VM instances from
Amazon Web Services, using a clean, minimal and up-to-date chroot. Every
failed build was retried once to eliminate random failures.
