Control: clone -1 -2 Control: reassign -2 t-coffee 13.45.0.4846264+dfsg-1 Control: severity -2 serious Control: retitle -2 t-coffee regression -- segfaults for cases that files that worked with previous release
t-coffee is breaking python-biopython build. I ran the test in question w/ gdb and I observe a segfault from t_coffee's end. Starting program: /usr/bin/t_coffee -output clustalw_aln -infile Fasta/fa01 -outfile Fasta/tc_out.aln -type protein -outorder input -gapopen -2 -gapext -5 [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1". [Detaching after vfork from child process 231299] [Detaching after vfork from child process 231301] PROGRAM: T-COFFEE Version_13.45.0.4846264 (2020-09-21 17:25:40 - Revision 0818d8a - Build 619) -full_log S [0] -genepred_score S [0] nsd -run_name S [0] -mem_mode S [0] mem -extend D [1] 1 -extend_mode S [0] very_fast_triplet -max_n_pair D [0] 10 -seq_name_for_quadruplet S [0] all -compact S [0] default -clean S [0] no -do_self FL [0] 0 -do_normalise D [0] 1000 -template_file S [0] -setenv S [0] 0 -export S [0] 0 -template_mode S [0] -flip D [0] 0 -remove_template_file D [0] 0 -profile_template_file S [0] -in S [0] -seq S [0] -aln S [0] -method_limits S [0] -method S [0] -lib S [0] -profile S [0] -profile1 S [0] -profile2 S [0] -pdb S [0] -relax_lib D [0] 1 -filter_lib D [0] 0 -shrink_lib D [0] 0 -out_lib W_F [0] no -out_lib_mode S [0] primary -lib_only D [0] 0 -outseqweight W_F [0] no -seq_source S [0] ANY -cosmetic_penalty D [0] 0 -gapopen D [1] -2 -gapext D [1] -5 -fgapopen D [0] 0 -fgapext D [0] 0 -nomatch D [0] 0 -newtree W_F [0] default -tree W_F [0] NO -usetree R_F [0] -tree_mode S [0] nj -distance_matrix_mode S [0] ktup -distance_matrix_sim_mode S [0] idmat_sim1 -quicktree FL [0] 0 -outfile W_F [1] Fasta/tc_out.aln -maximise FL [1] 1 -output S [1] clustalw_aln -len D [0] 0 -infile R_F [1] Fasta/fa01 -matrix S [0] default -tg_mode D [0] 1 -profile_mode S [0] cw_profile_profile -profile_comparison S [0] profile -dp_mode S [0] linked_pair_wise -ktuple D [0] 1 -ndiag D [0] 0 -diag_threshold D [0] 0 -diag_mode D [0] 0 -sim_matrix S [0] vasiliky -transform S [0] -extend_seq FL [0] 0 -outorder S [1] input -inorder S [0] aligned -seqnos S [0] off -case S [0] keep -cpu D [0] 0 -ulimit D [0] -1 -maxnseq D [0] -1 -maxlen D [0] -1 -sample_dp D [0] 0 -weight S [0] default -seq_weight S [0] no -align FL [1] 1 -mocca FL [0] 0 -domain FL [0] 0 -start D [0] 0 -len D [0] 0 -scale D [0] 0 -mocca_interactive FL [0] 0 -method_evaluate_mode S [0] default -color_mode S [0] new -aln_line_length D [0] 0 -evaluate_mode S [0] triplet -get_type FL [0] 0 -clean_aln D [0] 0 -clean_threshold D [1] 1 -clean_iteration D [1] 1 -clean_evaluate_mode S [0] t_coffee_fast -extend_matrix FL [0] 0 -prot_min_sim D [0] 0 -prot_max_sim D [100] 100 -psiJ D [0] 3 -psitrim_mode S [0] regtrim -psitrim_tree S [0] codnd -psitrim D [100] 100 -prot_min_cov D [90] 90 -pdb_type S [0] d -pdb_min_sim D [35] 35 -pdb_max_sim D [100] 100 -pdb_min_cov D [50] 50 -pdb_blast_server W_F [0] EBI -blast W_F [0] -blast_server W_F [0] EBI -pdb_db W_F [0] pdb -protein_db W_F [0] uniref50 -method_log W_F [0] no -struc_to_use S [0] -cache W_F [0] use -print_cache FL [0] 0 -align_pdb_param_file W_F [0] no -align_pdb_hasch_mode W_F [0] hasch_ca_trace_bubble -external_aligner S [0] NO -msa_mode S [0] tree -et_mode S [0] et -master S [0] no -blast_nseq D [0] 0 -lalign_n_top D [0] 10 -iterate D [0] 0 -trim D [0] 0 -split D [0] 0 -trimfile S [0] default -split D [0] 0 -split_nseq_thres D [0] 0 -split_score_thres D [0] 0 -check_pdb_status D [0] 0 -clean_seq_name D [0] 0 -seq_to_keep S [0] -dpa_master_aln S [0] -dpa_maxnseq D [0] 0 -dpa_min_score1 D [0] -dpa_min_score2 D [0] -dpa_keep_tmpfile FL [0] 0 -dpa_debug D [0] 0 -multi_core S [0] templates_jobs_relax_msa_evaluate -n_core D [0] 1 -thread D [0] 1 -max_n_proc D [0] 1 -lib_list S [0] -prune_lib_mode S [0] 5 -tip S [0] none -rna_lib S [0] -no_warning D [0] 0 -run_local_script D [0] 0 -proxy S [0] unset -email S [0] -clean_overaln D [0] 0 -overaln_param S [0] -overaln_mode S [0] -overaln_model S [0] -overaln_threshold D [0] 0 -overaln_target D [0] 0 -overaln_P1 D [0] 0 -overaln_P2 D [0] 0 -overaln_P3 D [0] 0 -overaln_P4 D [0] 0 -exon_boundaries S [0] -display D [0] 100 INPUT FILES Input File (A) Fasta/fa01 Format fasta_aln Program received signal SIGSEGV, Segmentation fault. 0x0000555555675e73 in ?? () On Sun, 23 Oct 2022 14:50:27 +0200 Lucas Nussbaum <lu...@debian.org> wrote: > Source: python-biopython > Version: 1.79+dfsg-3 > Severity: serious > Justification: FTBFS > Tags: bookworm sid ftbfs > User: lu...@debian.org > Usertags: ftbfs-20221023 ftbfs-bookworm > > Hi, > > During a rebuild of all packages in sid, your package failed to build > on amd64. > > > Relevant part (hopefully): > > make[1]: Entering directory '/<<PKGBUILDDIR>>' > > mkdir -p Tests_avoid > > for avoid in PAML_tools EmbossPhylipNew MSAProbs_tool NACCESS_tool > > PopGen_GenePop PopGen_GenePop_EasyController XXmotif_tool PDB_ResidueDepth > > mmtf mmtf_online BioSQL_MySQLdb BioSQL_psycopg2 \ > > ; do \ > > mv Tests/test_${avoid}.py Tests_avoid ; \ > > done > > mv: cannot stat 'Tests/test_NACCESS_tool.py': No such file or directory > > # For the doc package we need a clean testsuite without all the remaining > > files. So keep a clean copy here > > mkdir -p debian/tmp_tests > > cp -a Tests debian/tmp_tests > > # remove duplicated file > > rm -f debian/tmp_tests/Tests/Quality/example.fastq.gz > > # We also keep the tests we need to avoid for later inspection > > cp -a Tests_avoid debian/tmp_tests > > # in the Debian package dialign it is not needed to set DIALIGN2_DIR but > > the test is verifying this dir > > # to run the EMBOSS test test_Emboss also requires to have the environment > > variable EMBOSS_ROOT set > > LC_ALL=C.UTF-8 dh_auto_test -- --test --system=custom \ > > --test-args='set -e; \ > > mkdir -p {build_dir}/home; \ > > mkdir -p {build_dir}/Doc/examples; \ > > cp -a Doc/Tutorial.tex {build_dir}/Doc; \ > > cp -a Doc/Tutorial {build_dir}/Doc; \ > > cp -a Doc/examples {build_dir}/Doc; \ > > cp -a Tests {build_dir}; \ > > cd {build_dir}/Tests; \ > > env DIALIGN2_DIR=/usr/share/dialign > > EMBOSS_ROOT=/usr/lib/emboss HOME={build_dir}/home {interpreter} > > run_tests.py --offline' > > pybuild --test -i python{version} -p 3.10 --test --system=custom > > "--test-args=set -e; \\\ > > mkdir -p {build_dir}/home; \\\ > > mkdir -p {build_dir}/Doc/examples; \\\ > > cp -a Doc/Tutorial.tex {build_dir}/Doc; \\\ > > cp -a Doc/Tutorial {build_dir}/Doc; \\\ > > cp -a Doc/examples {build_dir}/Doc; \\\ > > cp -a Tests {build_dir}; \\\ > > cd {build_dir}/Tests; \\\ > > env DIALIGN2_DIR=/usr/share/dialign > > EMBOSS_ROOT=/usr/lib/emboss HOME={build_dir}/home {interpreter} > > run_tests.py --offline" > > I: pybuild base:240: set -e; \ > > mkdir -p > > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/home; \ > > mkdir -p > > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/Doc/examples; \ > > cp -a Doc/Tutorial.tex > > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/Doc; \ > > cp -a Doc/Tutorial > > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/Doc; \ > > cp -a Doc/examples > > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/Doc; \ > > cp -a Tests > > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build; \ > > cd > > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/Tests; \ > > env DIALIGN2_DIR=/usr/share/dialign > > EMBOSS_ROOT=/usr/lib/emboss > > HOME=/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/home python3.10 > > run_tests.py --offline > > /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/Tests/run_tests.py:33: > > DeprecationWarning: The distutils package is deprecated and slated for > > removal in Python 3.12. Use setuptools or check PEP 632 for potential > > alternatives -- Best, Nilesh
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