Package: src:ariba
Version: 2.14.7+ds-7
Severity: serious
Tags: ftbfs trixie sid
Dear maintainer:
During a rebuild of all packages in unstable, your package failed to build:
--------------------------------------------------------------------------------
[...]
debian/rules clean
dh clean --buildsystem=pybuild
debian/rules override_dh_auto_clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
rm -rf /<<PKGBUILDDIR>>/debian/man
dh_auto_clean --
I: pybuild base:311: python3.12 setup.py clean
/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:270: UserWarning:
Unknown distribution option: 'test_suite'
warnings.warn(msg)
/usr/lib/python3/dist-packages/setuptools/_distutils/dist.py:270: UserWarning:
Unknown distribution option: 'tests_require'
warnings.warn(msg)
running clean
removing '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build' (and everything
under it)
'build/bdist.linux-x86_64' does not exist -- can't clean it
[... snipped ...]
creating
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars
copying ariba/tests/data/cluster_test_full_run_multiple_vars/reads_2.fq ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars
copying ariba/tests/data/cluster_test_full_run_multiple_vars/for_reads.fa ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars
copying ariba/tests/data/cluster_test_full_run_multiple_vars/references.fa ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars
copying ariba/tests/data/cluster_test_full_run_multiple_vars/reads_1.fq ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_multiple_vars
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copying ariba/tests/data/cluster_test_full_run_partial_asmbly/reads_2.fq ->
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/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_varonly_gene_2
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->
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/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail
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/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail
copying ariba/tests/data/cluster_test_full_run_choose_ref_fail/references.fa ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail
copying ariba/tests/data/cluster_test_full_run_choose_ref_fail/reads_1.fq ->
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_test_full_run_choose_ref_fail
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/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc
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/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc
copying ariba/tests/data/cluster_full_run_smtls_snp_presabs_nonc/references.fa
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copying ariba/tests/data/cluster_test_init_no_reads_2/genes.fa ->
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running build_ext
building 'minimap_ariba' extension
creating build/temp.linux-x86_64-cpython-313/ariba/ext
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
-I/usr/include/minimap -I/usr/include/python3.13 -c ariba/ext/minimap_ariba.cpp
-o build/temp.linux-x86_64-cpython-313/ariba/ext/minimap_ariba.o
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared
-Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro
-Wl,-z,now -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection
-Wdate-time -D_FORTIFY_SOURCE=2
build/temp.linux-x86_64-cpython-313/ariba/ext/minimap_ariba.o
-L/usr/lib/x86_64-linux-gnu -o
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/minimap_ariba.cpython-313-x86_64-linux-gnu.so
-lz -lminimap
building 'fermilite_ariba' extension
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
-I/usr/include/python3.13 -c ariba/ext/fml-asm_ariba.cpp -o
build/temp.linux-x86_64-cpython-313/ariba/ext/fml-asm_ariba.o
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared
-Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro
-Wl,-z,now -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection
-Wdate-time -D_FORTIFY_SOURCE=2
build/temp.linux-x86_64-cpython-313/ariba/ext/fml-asm_ariba.o
-L/usr/lib/x86_64-linux-gnu -o
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/fermilite_ariba.cpython-313-x86_64-linux-gnu.so
-lz -lfml
building 'vcfcall_ariba' extension
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC
-I/usr/include/python3.13 -c ariba/ext/vcfcall_ariba.cpp -o
build/temp.linux-x86_64-cpython-313/ariba/ext/vcfcall_ariba.o
x86_64-linux-gnu-g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=.
-fstack-protector-strong -fstack-clash-protection -Wformat
-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -shared
-Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro
-Wl,-z,now -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection
-Wdate-time -D_FORTIFY_SOURCE=2
build/temp.linux-x86_64-cpython-313/ariba/ext/vcfcall_ariba.o
-L/usr/lib/x86_64-linux-gnu -o
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/vcfcall_ariba.cpython-313-x86_64-linux-gnu.so
running build_scripts
creating build/scripts-3.13
copying and adjusting scripts/ariba -> build/scripts-3.13
changing mode of build/scripts-3.13/ariba from 644 to 755
dh_auto_test -O--buildsystem=pybuild
I: pybuild base:311: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build;
python3.12 -m pytest -k "not test_load_fasta_files_and_write_clusters_file"
============================= test session starts ==============================
platform linux -- Python 3.12.9, pytest-8.3.4, pluggy-1.5.0
rootdir: /<<PKGBUILDDIR>>
plugins: typeguard-4.4.1
collected 356 items / 1 deselected / 355 selected
ariba/tests/aln_to_metadata_test.py .................... [ 5%]
ariba/tests/assembly_compare_test.py ................ [ 10%]
ariba/tests/assembly_test.py ..F...... [ 12%]
ariba/tests/assembly_variants_test.py ........... [ 15%]
ariba/tests/bam_parse_test.py ...... [ 17%]
ariba/tests/card_record_test.py ........ [ 19%]
ariba/tests/cdhit_test.py ................ [ 24%]
ariba/tests/cluster_test.py ............................. [ 32%]
ariba/tests/clusters_test.py ................ [ 36%]
ariba/tests/common_test.py .. [ 37%]
ariba/tests/external_progs_test.py . [ 37%]
ariba/tests/faidx_test.py . [ 38%]
ariba/tests/flag_test.py ....... [ 40%]
ariba/tests/histogram_test.py .... [ 41%]
ariba/tests/link_test.py ......... [ 43%]
ariba/tests/mapping_test.py ....... [ 45%]
ariba/tests/megares_data_finder_test.py .. [ 46%]
ariba/tests/megares_zip_parser_test.py ..... [ 47%]
ariba/tests/mic_plotter_test.py ............. [ 51%]
ariba/tests/mlst_profile_test.py .... [ 52%]
ariba/tests/mlst_reporter_test.py ..... [ 53%]
ariba/tests/pubmlst_getter_test.py ... [ 54%]
ariba/tests/pubmlst_ref_preparer_test.py . [ 54%]
ariba/tests/read_filter_test.py . [ 55%]
ariba/tests/read_store_test.py ....... [ 57%]
ariba/tests/ref_genes_getter_test.py . [ 57%]
ariba/tests/ref_preparer_test.py ..... [ 58%]
ariba/tests/ref_seq_chooser_test.py ....... [ 60%]
ariba/tests/reference_data_test.py .............................. [ 69%]
ariba/tests/report_filter_test.py ................. [ 74%]
ariba/tests/report_flag_expander_test.py . [ 74%]
ariba/tests/samtools_variants_test.py ....... [ 76%]
ariba/tests/scaffold_graph_test.py ..... [ 77%]
ariba/tests/sequence_metadata_test.py ..... [ 79%]
ariba/tests/sequence_variant_test.py ....... [ 81%]
ariba/tests/summary_cluster_test.py ....................... [ 87%]
ariba/tests/summary_cluster_variant_test.py .... [ 88%]
ariba/tests/summary_sample_test.py .... [ 89%]
ariba/tests/summary_test.py .................... [ 95%]
ariba/tests/tb_test.py ....... [ 97%]
ariba/tests/test_refdata_query.py ..... [ 98%]
ariba/tests/versions_test.py . [ 99%]
ariba/tests/vfdb_parser_test.py ... [100%]
=================================== FAILURES ===================================
____________________ TestAssembly.test_assemble_with_spades ____________________
self = <ariba.tests.assembly_test.TestAssembly
testMethod=test_assemble_with_spades>
@unittest.skipUnless(extern_progs.exe('spades'), "Spades assembler is
optional and is not configured")
def test_assemble_with_spades(self):
'''test _assemble_with_spades'''
reads1 = os.path.join(data_dir,
'assembly_test_assemble_with_spades_reads_1.fq')
reads2 = os.path.join(data_dir,
'assembly_test_assemble_with_spades_reads_2.fq')
tmp_dir = 'tmp.test_assemble_with_spades'
tmp_log = 'tmp.test_assemble_with_spades.log'
with open(tmp_log, 'w') as tmp_log_fh:
print('First line', file=tmp_log_fh)
common.rmtree(tmp_dir)
#using spades_options=" --only-assembler" because error correction
cannot determine quality offset on this
#artificial dataset
a = assembly.Assembly(reads1, reads2, 'not needed', 'not needed',
tmp_dir, 'not_needed_for_this_test.fa',
'not_needed_for_this_test.bam', tmp_log_fh,
'not needed',
assembler="spades", spades_options="
--only-assembler")
a._assemble_with_spades()
> self.assertTrue(a.assembled_ok)
E AssertionError: False is not true
ariba/tests/assembly_test.py:128: AssertionError
----------------------------- Captured stderr call -----------------------------
WARNING: I tried to get the version of spades with: "/usr/bin/spades.py
--version" and the output didn't match this regular expression:
"SPAdes.*v([0-9\.]+)"
The following command failed with exit code 4
['/usr/bin/spades.py', '-t', '1', '--pe1-1',
'/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_test_assemble_with_spades_reads_1.fq',
'--pe1-2',
'/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_test_assemble_with_spades_reads_2.fq',
'-o',
'/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/tmp.test_assemble_with_spades/Assemble',
'--only-assembler']
The output was:
== Warning == No assembly mode was specified! If you intend to assemble
high-coverage multi-cell/isolate data, use '--isolate' option.
Command line: /usr/libexec/spades/spades.py -t 1 --pe1-1
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_test_assemble_with_spades_reads_1.fq
--pe1-2
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_test_assemble_with_spades_reads_2.fq
-o
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/tmp.test_assemble_with_spades/Assemble
--only-assembler
System information:
SPAdes version: 4.0.0
Python version: 3.13.2
OS: Linux-6.1.0-31-amd64-x86_64-with-glibc2.40
Output dir:
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/tmp.test_assemble_with_spades/Assemble
Mode: ONLY assembling (without read error correction)
Debug mode is turned OFF
Dataset parameters:
Standard mode
For multi-cell/isolate data we recommend to use '--isolate' option; for
single-cell MDA data use '--sc'; for metagenomic data use '--meta'; for RNA-Seq
use '--rna'.
Reads:
Library number: 1, library type: paired-end
orientation: fr
left reads:
['/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_test_assemble_with_spades_reads_1.fq']
right reads:
['/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_test_assemble_with_spades_reads_2.fq']
interlaced reads: not specified
single reads: not specified
merged reads: not specified
Assembly parameters:
k: automatic selection based on read length
Repeat resolution is enabled
Mismatch careful mode is turned OFF
MismatchCorrector will be SKIPPED
Coverage cutoff is turned OFF
Assembly graph output will use GFA v1.2 format
Other parameters:
Dir for temp files:
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/tmp.test_assemble_with_spades/Assemble/tmp
Threads: 1
Memory limit (in Gb): 3
======= SPAdes pipeline started. Log can be found here:
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/tmp.test_assemble_with_spades/Assemble/spades.log
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_test_assemble_with_spades_reads_1.fq:
max reads length: 76
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/tests/data/assembly_test_assemble_with_spades_reads_2.fq:
max reads length: 76
Reads length: 76
===== Before start started.
===== Assembling started.
===== K21 started.
== Running: /usr/libexec/spades/spades-core
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/tmp.test_assemble_with_spades/Assemble/K21/configs/config.info
Exception caught
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/tmp.test_assemble_with_spades/Assemble/K21/configs/config.info(3):
cannot open include file simplification.info
== Error == system call for: "['/usr/libexec/spades/spades-core',
'/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/tmp.test_assemble_with_spades/Assemble/K21/configs/config.info']"
finished abnormally, OS return value: 4
None
In case you have troubles running SPAdes, you can report an issue on our GitHub
repository github.com/ablab/spades
Please provide us with params.txt and spades.log files from the output
directory.
SPAdes log can be found here:
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/tmp.test_assemble_with_spades/Assemble/spades.log
Thank you for using SPAdes! If you use it in your research, please cite:
Prjibelski, A., Antipov, D., Meleshko, D., Lapidus, A. and Korobeynikov, A.,
2020. Using SPAdes de novo assembler. Current protocols in bioinformatics,
70(1), p.e102.
doi.org/10.1002/cpbi.102
=============================== warnings summary ===============================
ariba/__init__.py:1
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/__init__.py:1:
DeprecationWarning: pkg_resources is deprecated as an API. See
https://setuptools.pypa.io/en/latest/pkg_resources.html
from pkg_resources import get_distribution
../../../../../../usr/lib/python3/dist-packages/pyfastaq/__init__.py:3
/usr/lib/python3/dist-packages/pyfastaq/__init__.py:3: DeprecationWarning:
Unimplemented abstract methods {'read_text', 'locate_file'}
__version__ = Distribution().from_name('pyfastaq').version
.pybuild/cpython3_3.12_ariba/build/ariba/tests/mic_plotter_test.py::TestMicPlotter::test_get_colours
.pybuild/cpython3_3.12_ariba/build/ariba/tests/mic_plotter_test.py::TestMicPlotter::test_get_colours
.pybuild/cpython3_3.12_ariba/build/ariba/tests/mic_plotter_test.py::TestMicPlotter::test_get_colours
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/mic_plotter.py:222:
MatplotlibDeprecationWarning: The get_cmap function was deprecated in
Matplotlib 3.7 and will be removed two minor releases later. Use
``matplotlib.colormaps[name]`` or ``matplotlib.colormaps.get_cmap(obj)``
instead.
cmap = cmx.get_cmap(colormap)
.pybuild/cpython3_3.12_ariba/build/ariba/tests/mic_plotter_test.py::TestMicPlotter::test_get_colours
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build/ariba/mic_plotter.py:206:
MatplotlibDeprecationWarning: The get_cmap function was deprecated in
Matplotlib 3.7 and will be removed two minor releases later. Use
``matplotlib.colormaps[name]`` or ``matplotlib.colormaps.get_cmap(obj)``
instead.
cmap = cmx.get_cmap(colormap)
-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
=========================== short test summary info ============================
FAILED ariba/tests/assembly_test.py::TestAssembly::test_assemble_with_spades
=========== 1 failed, 354 passed, 1 deselected, 6 warnings in 36.28s ===========
E: pybuild pybuild:389: test: plugin distutils failed with: exit code=1: cd
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ariba/build; python3.12 -m pytest -k
"not test_load_fasta_files_and_write_clusters_file"
I: pybuild base:311: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build;
python3.13 -m pytest
============================= test session starts ==============================
platform linux -- Python 3.13.2, pytest-8.3.4, pluggy-1.5.0
rootdir: /<<PKGBUILDDIR>>
plugins: typeguard-4.4.1
collected 356 items
ariba/tests/aln_to_metadata_test.py .................... [ 5%]
ariba/tests/assembly_compare_test.py ................ [ 10%]
ariba/tests/assembly_test.py ..F...... [ 12%]
ariba/tests/assembly_variants_test.py ........... [ 15%]
ariba/tests/bam_parse_test.py ...... [ 17%]
ariba/tests/card_record_test.py ........ [ 19%]
ariba/tests/cdhit_test.py ................ [ 24%]
ariba/tests/cluster_test.py ............................. [ 32%]
ariba/tests/clusters_test.py ................ [ 36%]
ariba/tests/common_test.py .. [ 37%]
ariba/tests/external_progs_test.py . [ 37%]
ariba/tests/faidx_test.py . [ 37%]
ariba/tests/flag_test.py ....... [ 39%]
ariba/tests/histogram_test.py .... [ 41%]
ariba/tests/link_test.py ......... [ 43%]
ariba/tests/mapping_test.py ....... [ 45%]
ariba/tests/megares_data_finder_test.py .. [ 46%]
ariba/tests/megares_zip_parser_test.py ..... [ 47%]
ariba/tests/mic_plotter_test.py ............. [ 51%]
ariba/tests/mlst_profile_test.py .... [ 52%]
ariba/tests/mlst_reporter_test.py ..... [ 53%]
ariba/tests/pubmlst_getter_test.py ... [ 54%]
ariba/tests/pubmlst_ref_preparer_test.py .. [ 55%]
ariba/tests/read_filter_test.py . [ 55%]
ariba/tests/read_store_test.py ....... [ 57%]
ariba/tests/ref_genes_getter_test.py . [ 57%]
ariba/tests/ref_preparer_test.py ..... [ 58%]
ariba/tests/ref_seq_chooser_test.py ....... [ 60%]
ariba/tests/reference_data_test.py .............................. [ 69%]
ariba/tests/report_filter_test.py ................. [ 74%]
ariba/tests/report_flag_expander_test.py . [ 74%]
ariba/tests/samtools_variants_test.py ....... [ 76%]
ariba/tests/scaffold_graph_test.py ..... [ 77%]
ariba/tests/sequence_metadata_test.py ..... [ 79%]
ariba/tests/sequence_variant_test.py ....... [ 81%]
ariba/tests/summary_cluster_test.py ....................... [ 87%]
ariba/tests/summary_cluster_variant_test.py .... [ 88%]
ariba/tests/summary_sample_test.py .... [ 89%]
ariba/tests/summary_test.py .................... [ 95%]
ariba/tests/tb_test.py ....... [ 97%]
ariba/tests/test_refdata_query.py ..... [ 98%]
ariba/tests/versions_test.py . [ 99%]
ariba/tests/vfdb_parser_test.py ... [100%]
=================================== FAILURES ===================================
____________________ TestAssembly.test_assemble_with_spades ____________________
self = <ariba.tests.assembly_test.TestAssembly
testMethod=test_assemble_with_spades>
@unittest.skipUnless(extern_progs.exe('spades'), "Spades assembler is
optional and is not configured")
def test_assemble_with_spades(self):
'''test _assemble_with_spades'''
reads1 = os.path.join(data_dir,
'assembly_test_assemble_with_spades_reads_1.fq')
reads2 = os.path.join(data_dir,
'assembly_test_assemble_with_spades_reads_2.fq')
tmp_dir = 'tmp.test_assemble_with_spades'
tmp_log = 'tmp.test_assemble_with_spades.log'
with open(tmp_log, 'w') as tmp_log_fh:
print('First line', file=tmp_log_fh)
common.rmtree(tmp_dir)
#using spades_options=" --only-assembler" because error correction
cannot determine quality offset on this
#artificial dataset
a = assembly.Assembly(reads1, reads2, 'not needed', 'not needed',
tmp_dir, 'not_needed_for_this_test.fa',
'not_needed_for_this_test.bam', tmp_log_fh,
'not needed',
assembler="spades", spades_options="
--only-assembler")
a._assemble_with_spades()
> self.assertTrue(a.assembled_ok)
E AssertionError: False is not true
ariba/tests/assembly_test.py:128: AssertionError
----------------------------- Captured stderr call -----------------------------
WARNING: I tried to get the version of spades with: "/usr/bin/spades.py
--version" and the output didn't match this regular expression:
"SPAdes.*v([0-9\.]+)"
The following command failed with exit code 4
['/usr/bin/spades.py', '-t', '1', '--pe1-1',
'/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_test_assemble_with_spades_reads_1.fq',
'--pe1-2',
'/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_test_assemble_with_spades_reads_2.fq',
'-o',
'/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/tmp.test_assemble_with_spades/Assemble',
'--only-assembler']
The output was:
== Warning == No assembly mode was specified! If you intend to assemble
high-coverage multi-cell/isolate data, use '--isolate' option.
Command line: /usr/libexec/spades/spades.py -t 1 --pe1-1
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_test_assemble_with_spades_reads_1.fq
--pe1-2
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_test_assemble_with_spades_reads_2.fq
-o
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/tmp.test_assemble_with_spades/Assemble
--only-assembler
System information:
SPAdes version: 4.0.0
Python version: 3.13.2
OS: Linux-6.1.0-31-amd64-x86_64-with-glibc2.40
Output dir:
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/tmp.test_assemble_with_spades/Assemble
Mode: ONLY assembling (without read error correction)
Debug mode is turned OFF
Dataset parameters:
Standard mode
For multi-cell/isolate data we recommend to use '--isolate' option; for
single-cell MDA data use '--sc'; for metagenomic data use '--meta'; for RNA-Seq
use '--rna'.
Reads:
Library number: 1, library type: paired-end
orientation: fr
left reads:
['/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_test_assemble_with_spades_reads_1.fq']
right reads:
['/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_test_assemble_with_spades_reads_2.fq']
interlaced reads: not specified
single reads: not specified
merged reads: not specified
Assembly parameters:
k: automatic selection based on read length
Repeat resolution is enabled
Mismatch careful mode is turned OFF
MismatchCorrector will be SKIPPED
Coverage cutoff is turned OFF
Assembly graph output will use GFA v1.2 format
Other parameters:
Dir for temp files:
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/tmp.test_assemble_with_spades/Assemble/tmp
Threads: 1
Memory limit (in Gb): 3
======= SPAdes pipeline started. Log can be found here:
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/tmp.test_assemble_with_spades/Assemble/spades.log
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_test_assemble_with_spades_reads_1.fq:
max reads length: 76
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/tests/data/assembly_test_assemble_with_spades_reads_2.fq:
max reads length: 76
Reads length: 76
===== Before start started.
===== Assembling started.
===== K21 started.
== Running: /usr/libexec/spades/spades-core
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/tmp.test_assemble_with_spades/Assemble/K21/configs/config.info
Exception caught
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/tmp.test_assemble_with_spades/Assemble/K21/configs/config.info(3):
cannot open include file simplification.info
== Error == system call for: "['/usr/libexec/spades/spades-core',
'/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/tmp.test_assemble_with_spades/Assemble/K21/configs/config.info']"
finished abnormally, OS return value: 4
None
In case you have troubles running SPAdes, you can report an issue on our GitHub
repository github.com/ablab/spades
Please provide us with params.txt and spades.log files from the output
directory.
SPAdes log can be found here:
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/tmp.test_assemble_with_spades/Assemble/spades.log
Thank you for using SPAdes! If you use it in your research, please cite:
Prjibelski, A., Antipov, D., Meleshko, D., Lapidus, A. and Korobeynikov, A.,
2020. Using SPAdes de novo assembler. Current protocols in bioinformatics,
70(1), p.e102.
doi.org/10.1002/cpbi.102
=============================== warnings summary ===============================
ariba/__init__.py:1
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/__init__.py:1:
DeprecationWarning: pkg_resources is deprecated as an API. See
https://setuptools.pypa.io/en/latest/pkg_resources.html
from pkg_resources import get_distribution
../../../../../../usr/lib/python3/dist-packages/pyfastaq/__init__.py:3
/usr/lib/python3/dist-packages/pyfastaq/__init__.py:3: DeprecationWarning:
Unimplemented abstract methods {'read_text', 'locate_file'}
__version__ = Distribution().from_name('pyfastaq').version
.pybuild/cpython3_3.13_ariba/build/ariba/tests/mic_plotter_test.py::TestMicPlotter::test_get_colours
.pybuild/cpython3_3.13_ariba/build/ariba/tests/mic_plotter_test.py::TestMicPlotter::test_get_colours
.pybuild/cpython3_3.13_ariba/build/ariba/tests/mic_plotter_test.py::TestMicPlotter::test_get_colours
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/mic_plotter.py:222:
MatplotlibDeprecationWarning: The get_cmap function was deprecated in
Matplotlib 3.7 and will be removed two minor releases later. Use
``matplotlib.colormaps[name]`` or ``matplotlib.colormaps.get_cmap(obj)``
instead.
cmap = cmx.get_cmap(colormap)
.pybuild/cpython3_3.13_ariba/build/ariba/tests/mic_plotter_test.py::TestMicPlotter::test_get_colours
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build/ariba/mic_plotter.py:206:
MatplotlibDeprecationWarning: The get_cmap function was deprecated in
Matplotlib 3.7 and will be removed two minor releases later. Use
``matplotlib.colormaps[name]`` or ``matplotlib.colormaps.get_cmap(obj)``
instead.
cmap = cmx.get_cmap(colormap)
-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
=========================== short test summary info ============================
FAILED ariba/tests/assembly_test.py::TestAssembly::test_assemble_with_spades
================== 1 failed, 355 passed, 6 warnings in 35.92s ==================
E: pybuild pybuild:389: test: plugin distutils failed with: exit code=1: cd
/<<PKGBUILDDIR>>/.pybuild/cpython3_3.13_ariba/build; python3.13 -m pytest
dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p "3.12
3.13" returned exit code 13
make: *** [debian/rules:16: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2
--------------------------------------------------------------------------------
The above is just how the build ends and not necessarily the most relevant part.
If required, the full build log is available here:
https://people.debian.org/~sanvila/build-logs/202502/
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:ariba, so that this is still
visible in the BTS web page for this package.
Thanks.
