[Debian-med-packaging] Bug#1022307: python-biopython: FTBFS: mv: cannot stat 'Tests/test_NACCESS_tool.py': No such file or directory
Nilesh Patra
nilesh at debian.org
Mon Oct 24 08:38:31 BST 2022
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 <lucas at debian.org> wrote:
> Source: python-biopython
> Version: 1.79+dfsg-3
> Severity: serious
> Justification: FTBFS
> Tags: bookworm sid ftbfs
> User: lucas at 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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