Hi,
I've recently upgraded t-coffee after a longish discussion with Hamid
(in CC) who found out that t-coffee should switch off optimisation
(which is also the case in the binaries provided upstream).
Seems there are other issues with latest upstream.
I wonder whether it might be the best "fix" to revert the move to
the new version and switch back to the old version. In any case
the failure in question should be added to t-coffee autopkgtest.
Kind regards
Andreas.
Am Mon, Oct 24, 2022 at 01:08:31PM +0530 schrieb Nilesh Patra:
> 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 <[email protected]> wrote:
> > Source: python-biopython
> > Version: 1.79+dfsg-3
> > Severity: serious
> > Justification: FTBFS
> > Tags: bookworm sid ftbfs
> > User: [email protected]
> > 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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