[Debian-med-packaging] Bug#1114369: seqan-raptor: FTBFS: dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2

Fri Sep 5 19:26:04 BST 2025

Package: src:seqan-raptor
Version: 3.0.1+ds-9
Severity: serious
Tags: ftbfs forky sid

Dear maintainer:

During a rebuild of all packages in unstable, your package failed to build.

Below you will find how the build ends (probably the most relevant part,
but not necessarily). If required, the full build log is available here:

https://people.debian.org/~sanvila/build-logs/202509/

About the archive rebuild: The build was made on virtual machines from AWS,
using sbuild and a reduced chroot with only build-essential packages.

If you could not reproduce the bug please contact me privately, as I
am willing to provide ssh access to a virtual machine where the bug is
fully reproducible.

If this is really a bug in one of the build-depends, please use
reassign and add an affects on src:seqan-raptor, so that this is still
visible in the BTS web page for this package.

Thanks.

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[...]
 debian/rules clean
dh clean
   debian/rules override_dh_auto_clean-arch
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_clean
dh_auto_clean --sourcedirectory=test/unit --builddirectory build_unit
#dh_auto_clean --sourcedirectory=test/performance --builddirectory build_performance
#dh_auto_clean --sourcedirectory=test/header --builddirectory build_header
dh_auto_clean --sourcedirectory=test/snippet --builddirectory build_snippet
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
   debian/rules override_dh_auto_clean-indep
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_clean --indep --builddir doc_build
make[1]: Leaving directory '/<<PKGBUILDDIR>>'

[... snipped ...]

Generating code for file call_parallel_on_bins.hpp...
Generating code for file dna4_traits.hpp...
Generating code for file file_reader.hpp...
Generating code for file hierarchical_interleaved_bloom_filter.hpp...
Generating code for file index.hpp...
Generating code for file raptor_layout.hpp...
Generating code for file compute_minimiser.hpp...
Generating code for file cutoff.hpp...
Generating code for file raptor.hpp...
Generating code for file do_parallel.hpp...
Generating code for file load_index.hpp...
Generating code for file search.hpp...
Generating code for file search_hibf.hpp...
Generating code for file search_ibf.hpp...
Generating code for file search_partitioned_ibf.hpp...
Generating code for file search_singular_ibf.hpp...
Generating code for file sync_out.hpp...
Generating code for file strong_types.hpp...
Generating code for file forward_strand_minimiser.hpp...
Generating code for file logspace.hpp...
Generating code for file multiple_error_model.hpp...
Generating code for file one_error_model.hpp...
Generating code for file one_indirect_error_model.hpp...
Generating code for file pascal_row.hpp...
Generating code for file precompute_correction.hpp...
Generating code for file precompute_threshold.hpp...
Generating code for file threshold.hpp...
Generating code for file threshold_parameters.hpp...
Generating code for file index_upgrader.hpp...
Generating code for file upgrade.hpp...
Generating code for file version.hpp...
Parsing code for file LICENSE.md...
Parsing code for file build_parsing.cpp...
Parsing code for file compute_bin_size.cpp...
Parsing code for file init_shared_meta.cpp...
Parsing code for file parse_bin_path.cpp...
Parsing code for file prepare_parsing.cpp...
Parsing code for file search_parsing.cpp...
Parsing code for file upgrade_parsing.cpp...
Parsing code for file build_ibf.cpp...
Parsing code for file bin_size_in_bits.cpp...
Parsing code for file chopper_build.cpp...
Parsing code for file compute_kmers.cpp...
Parsing code for file construct_ibf.cpp...
Parsing code for file create_ibfs_from_chopper_pack.cpp...
Parsing code for file hierarchical_build.cpp...
Parsing code for file insert_into_ibf.cpp...
Parsing code for file loop_over_children.cpp...
Parsing code for file parse_chopper_pack_header.cpp...
Parsing code for file parse_chopper_pack_line.cpp...
Parsing code for file read_chopper_pack_file.cpp...
Parsing code for file update_parent_kmers.cpp...
Parsing code for file update_user_bins.cpp...
Parsing code for file max_count_per_partition.cpp...
Parsing code for file raptor_build.cpp...
Parsing code for file CMakeLists.txt...
Parsing code for file CMakeLists.txt...
Parsing code for file CMakeLists.txt...
Parsing code for file CMakeLists.txt...
Parsing code for file CMakeLists.txt...
Parsing code for file CMakeLists.txt...
Parsing code for file CMakeLists.txt...
Parsing code for file CMakeLists.txt...
Parsing code for file CMakeLists.txt...
Parsing code for file raptor_layout.cpp...
Parsing code for file compute_minimiser.cpp...
Parsing code for file raptor.cpp...
Parsing code for file raptor_search.cpp...
Parsing code for file search_hibf.cpp...
Parsing code for file search_ibf.cpp...
Parsing code for file search_partitioned_ibf.cpp...
Parsing code for file multiple_error_model.cpp...
Parsing code for file one_error_model.cpp...
Parsing code for file one_indirect_error_model.cpp...
Parsing code for file pascal_row.cpp...
Parsing code for file precompute_correction.cpp...
Parsing code for file precompute_threshold.cpp...
Parsing code for file raptor_upgrade.cpp...
Generating file documentation...
Generating docs for file adjust_seed.hpp...
Generating docs for file build_arguments.hpp...
Generating docs for file build_parsing.hpp...
Generating docs for file compute_bin_size.hpp...
Generating docs for file init_shared_meta.hpp...
Generating docs for file memory_usage.hpp...
Generating docs for file parse_bin_path.hpp...
Generating docs for file prepare_arguments.hpp...
Generating docs for file prepare_parsing.hpp...
Generating docs for file search_arguments.hpp...
Generating docs for file search_parsing.hpp...
Generating docs for file shared.hpp...
Generating docs for file timer.hpp...
Generating docs for file upgrade_arguments.hpp...
Generating docs for file upgrade_parsing.hpp...
Generating docs for file validators.hpp...
Generating docs for file build_ibf.hpp...
Generating docs for file emplace_iterator.hpp...
Generating docs for file bin_size_in_bits.hpp...
Generating docs for file build_data.hpp...
Generating docs for file chopper_build.hpp...
Generating docs for file chopper_pack_record.hpp...
Generating docs for file compute_kmers.hpp...
Generating docs for file construct_ibf.hpp...
Generating docs for file create_ibfs_from_chopper_pack.hpp...
Generating docs for file hierarchical_build.hpp...
Generating docs for file insert_into_ibf.hpp...
Generating docs for file loop_over_children.hpp...
Generating docs for file node_data.hpp...
Generating docs for file parse_chopper_pack_header.hpp...
Generating docs for file parse_chopper_pack_line.hpp...
Generating docs for file read_chopper_pack_file.hpp...
Generating docs for file update_parent_kmers.hpp...
Generating docs for file update_user_bins.hpp...
Generating docs for file index_factory.hpp...
Generating docs for file max_count_per_partition.hpp...
Generating docs for file partition_config.hpp...
Generating docs for file raptor_build.hpp...
Generating docs for file store_index.hpp...
Generating docs for file call_parallel_on_bins.hpp...
Generating docs for file dna4_traits.hpp...
Generating docs for file file_reader.hpp...
Generating docs for file hierarchical_interleaved_bloom_filter.hpp...
Generating docs for file index.hpp...
Generating docs for file raptor_layout.hpp...
Generating docs for file compute_minimiser.hpp...
Generating docs for file cutoff.hpp...
Generating docs for file raptor.hpp...
Generating docs for file do_parallel.hpp...
Generating docs for file load_index.hpp...
Generating docs for file search.hpp...
Generating docs for file search_hibf.hpp...
Generating docs for file search_ibf.hpp...
Generating docs for file search_partitioned_ibf.hpp...
Generating docs for file search_singular_ibf.hpp...
Generating docs for file sync_out.hpp...
Generating docs for file strong_types.hpp...
Generating docs for file forward_strand_minimiser.hpp...
Generating docs for file logspace.hpp...
Generating docs for file multiple_error_model.hpp...
Generating docs for file one_error_model.hpp...
Generating docs for file one_indirect_error_model.hpp...
Generating docs for file pascal_row.hpp...
Generating docs for file precompute_correction.hpp...
Generating docs for file precompute_threshold.hpp...
Generating docs for file threshold.hpp...
Generating docs for file threshold_parameters.hpp...
Generating docs for file index_upgrader.hpp...
Generating docs for file upgrade.hpp...
Generating docs for file version.hpp...
Generating docs for file build_parsing.cpp...
Generating docs for file compute_bin_size.cpp...
Generating docs for file init_shared_meta.cpp...
Generating docs for file parse_bin_path.cpp...
Generating docs for file prepare_parsing.cpp...
Generating docs for file search_parsing.cpp...
Generating docs for file upgrade_parsing.cpp...
Generating docs for file build_ibf.cpp...
Generating docs for file bin_size_in_bits.cpp...
Generating docs for file chopper_build.cpp...
Generating docs for file compute_kmers.cpp...
Generating docs for file construct_ibf.cpp...
Generating docs for file create_ibfs_from_chopper_pack.cpp...
Generating docs for file hierarchical_build.cpp...
Generating docs for file insert_into_ibf.cpp...
Generating docs for file loop_over_children.cpp...
Generating docs for file parse_chopper_pack_header.cpp...
Generating docs for file parse_chopper_pack_line.cpp...
Generating docs for file read_chopper_pack_file.cpp...
Generating docs for file update_parent_kmers.cpp...
Generating docs for file update_user_bins.cpp...
Generating docs for file max_count_per_partition.cpp...
Generating docs for file raptor_build.cpp...
Generating docs for file raptor_layout.cpp...
Generating docs for file compute_minimiser.cpp...
Generating docs for file raptor.cpp...
Generating docs for file raptor_search.cpp...
Generating docs for file search_hibf.cpp...
Generating docs for file search_ibf.cpp...
Generating docs for file search_partitioned_ibf.cpp...
Generating docs for file multiple_error_model.cpp...
Generating docs for file one_error_model.cpp...
Generating docs for file one_indirect_error_model.cpp...
Generating docs for file pascal_row.cpp...
Generating docs for file precompute_correction.cpp...
Generating docs for file precompute_threshold.cpp...
Generating docs for file raptor_upgrade.cpp...
Generating page documentation...
Generating docs for page setup...
Generating docs for page tutorial_first_steps...
Generating docs for page tutorial_layout...
Generating docs for page tutorial_index...
Generating docs for page tutorial_search...
Generating docs for page md__2build_2seqan-raptor-no1zBt_2seqan-raptor-3_80_81_09ds_2LICENSE...
Generating docs for page md__2build_2seqan-raptor-no1zBt_2seqan-raptor-3_80_81_09ds_2CHANGELOG...
Generating group documentation...
Generating class documentation...
Generating concept documentation...
Generating module documentation...
Generating namespace documentation...
Generating docs for compound raptor::bin_validator...
Generating docs for compound raptor::build_arguments...
Generating docs for compound raptor::cutoff...
Generating docs for compound raptor::dna4_traits...
Generating docs for compound raptor::emplace_iterator...
Generating docs for compound raptor::file_reader...
Generating docs for compound raptor::file_reader< file_types::minimiser >...
Generating docs for compound raptor::file_reader< file_types::sequence >...
Generating docs for compound raptor::hierarchical_interleaved_bloom_filter...
Generating docs for nested compound raptor::hierarchical_interleaved_bloom_filter::counting_agent_type...
Generating docs for nested compound raptor::hierarchical_interleaved_bloom_filter::membership_agent_type...
Generating docs for nested compound raptor::hierarchical_interleaved_bloom_filter::user_bins...
Generating docs for compound raptor::index_factory...
Generating docs for compound raptor::index_upgrader...
Generating docs for compound raptor::output_directory_validator...
Generating docs for compound raptor::output_file_validator...
Generating docs for compound raptor::partition_config...
Generating docs for compound raptor::positive_integer_validator...
Generating docs for compound raptor::power_of_two_validator...
Generating docs for compound raptor::prepare_arguments...
Generating docs for compound raptor::raptor_index...
Generating docs for compound raptor::search_arguments...
Generating docs for compound raptor::sequence_file_validator...
Generating docs for compound raptor::size_validator...
Generating docs for compound raptor::sync_out...
Generating docs for compound raptor::timer...
Generating docs for compound raptor::upgrade_arguments...
Generating docs for compound raptor::window...
Generating docs for namespace raptor::hibf
Generating docs for compound raptor::hibf::build_data...
Generating docs for compound raptor::hibf::chopper_pack_record...
Generating docs for compound raptor::hibf::node_data...
Generating docs for concept raptor::index_structure::compressible_from...
Generating docs for concept raptor::index_structure::is_ibf...
Generating docs for concept raptor::index_structure::is_hibf...
Generating docs for concept raptor::index_structure::is_compressed...
Generating docs for compound raptor::logspace::add_fn...
Generating docs for compound raptor::threshold::forward_strand_minimiser...
Generating docs for compound raptor::threshold::threshold...
Generating docs for compound raptor::threshold::threshold_parameters...
Generating graph info page...
Generating directory documentation...
Generating index page...
Generating page index...
Generating namespace member index...
Generating concept index...
Generating annotated compound index...
Generating alphabetical compound index...
Generating hierarchical class index...
Generating member index...
Generating file index...
Generating file member index...
Generating example index...
finalizing index lists...
writing tag file...
Running plantuml with JAVA...
type lookup cache used 2392/65536 hits=11424 misses=2675
symbol lookup cache used 2956/65536 hits=16171 misses=2956
finished...
make[4]: Leaving directory '/<<PKGBUILDDIR>>/doc_build'
[100%] Built target doc
make[3]: Leaving directory '/<<PKGBUILDDIR>>/doc_build'
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/doc_build/CMakeFiles 0
make[2]: Leaving directory '/<<PKGBUILDDIR>>/doc_build'
cd doc_build/latex && /usr/bin/make
make[2]: Entering directory '/<<PKGBUILDDIR>>/doc_build/latex'
rm -f *.ps *.dvi *.aux *.toc *.idx *.ind *.ilg *.log *.out *.brf *.blg *.bbl refman.pdf
pdflatex refman
This is pdfTeX, Version 3.141592653-2.6-1.40.28 (TeX Live 2025/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
(./refman.tex
LaTeX2e <2025-06-01> patch level 1
L3 programming layer <2025-07-19>

make[2]: *** [Makefile:12: refman.pdf] Error 1
make[2]: Leaving directory '/<<PKGBUILDDIR>>/doc_build/latex'
make[1]: *** [debian/rules:52: override_dh_auto_build-indep] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:13: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
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