--- Begin Message ---
Source: python-ete3
Version: 3.1.3+dfsg-1
Severity: serious
Justification: FTBFS
Tags: trixie sid ftbfs
User: lu...@debian.org
Usertags: ftbfs-20231212 ftbfs-trixie
Hi,
During a rebuild of all packages in sid, your package failed to build
on amd64.
Relevant part (hopefully):
> make[1]: Entering directory '/<<PKGBUILDDIR>>'
> # link to examples
> find .pybuild -name build -type d -exec ln -s /<<PKGBUILDDIR>>/examples \{\}
> \;
> dh_auto_test
> I: pybuild base:310: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build;
> python3.12 -m pytest -k "not test_ncbiquery and not test_ncbi_compare and not
> test_get_topology and not test_01tree_annotation and not
> test_00_update_database and not test_merged_id and not test_renderer"
> ete3/test/test_api.py
> ============================= test session starts
> ==============================
> platform linux -- Python 3.12.1, pytest-7.4.3, pluggy-1.3.0
> rootdir: /<<PKGBUILDDIR>>
> collected 53 items / 7 deselected / 46 selected
>
> ete3/test/test_api.py ..................................F....FF.....
> [100%]
>
> =================================== FAILURES
> ===================================
> _______________ Test_Coretype_ArrayTable.test_arraytable_parser
> ________________
>
> self = <ete3.test.test_arraytable.Test_Coretype_ArrayTable
> testMethod=test_arraytable_parser>
>
> def test_arraytable_parser(self):
> """ Tests reading numneric tables"""
> A = ArrayTable(expression)
> self.assertEqual(A.get_row_vector("A").tolist(), \
> [-1.23, -0.81, 1.79, 0.78,-0.42,-0.69, 0.58])
> self.assertEqual(A.get_several_row_vectors(["A","C"]).tolist(), \
> [[-1.23, -0.81, 1.79, 0.78, -0.42, -0.69, 0.58],
> [-2.19, 0.13, 0.65, -0.51, 0.52, 1.04, 0.36]])
>
> self.assertEqual(A.get_several_column_vectors(["col2",
> "col7"]).tolist(), \
> [[-0.81000000000000005, -0.93999999999999995,\
> 0.13, -0.97999999999999998,
> -0.82999999999999996,\
> -1.1100000000000001, -1.1699999999999999,\
> -1.25],
> [0.57999999999999996, 1.1200000000000001, \
> 0.35999999999999999, 0.93000000000000005, \
> 0.65000000000000002, 0.47999999999999998, \
> 0.26000000000000001, 0.77000000000000002]])
>
>
> self.assertEqual(A.get_column_vector("col4").tolist(), \
> [0.78000000000000003, 0.35999999999999999, \
> -0.51000000000000001, -0.76000000000000001,
> \
> 0.070000000000000007, -0.14000000000000001,
> \
> 0.23000000000000001, -0.29999999999999999])
>
> A.remove_column("col4")
> > self.assert_(A.get_column_vector("col4") is None )
> E AttributeError: 'Test_Coretype_ArrayTable' object has no attribute
> 'assert_'. Did you mean: 'assertIn'?
>
> ete3/test/test_arraytable.py:36: AttributeError
> _____________________ TestEvolEvolTree.test_labelling_tree
> _____________________
>
> self = <ete3.test.test_evol.TestEvolEvolTree testMethod=test_labelling_tree>
>
> def test_labelling_tree(self):
> tree = EvolTree (WRKDIR + 'tree.nw')
> tree.workdir = 'protamine/PRM1/paml/'
> random_swap(tree)
> tree.link_to_evol_model (WRKDIR + 'paml/fb/fb.out', 'fb')
> > self.assert_(check_annotation (tree))
> E AttributeError: 'TestEvolEvolTree' object has no attribute 'assert_'.
> Did you mean: 'assertIn'?
>
> ete3/test/test_evol.py:132: AttributeError
> _______________________ TestEvolEvolTree.test_load_model
> _______________________
>
> self = <ete3.test.test_evol.TestEvolEvolTree testMethod=test_load_model>
>
> def test_load_model(self):
> tree = EvolTree (WRKDIR + 'tree.nw')
> tree.workdir = 'protamine/PRM1/paml/'
> tree.link_to_evol_model (WRKDIR + 'paml/fb/fb.out', 'fb')
> tree.link_to_evol_model (WRKDIR + 'paml/M1/M1.out', 'M1')
> tree.link_to_evol_model (WRKDIR + 'paml/M2/M2.out', 'M2')
> tree.link_to_evol_model (WRKDIR + 'paml/M7/M7.out', 'M7')
> tree.link_to_evol_model (WRKDIR + 'paml/M8/M8.out', 'M8')
> tree.link_to_alignment (WRKDIR + 'alignments.fasta_ali')
> self.assertEqual(sorted(tree._models.keys()),
> sorted(['fb', 'M1', 'M2', 'M7', 'M8']))
> self.assertEqual(len (tree.get_evol_model('M2').branches), 194)
> self.assertEqual(tree.get_evol_model('fb').lnL, -3265.316569)
> > self.assert_('proportions' in str(tree.get_evol_model('M2')))
> E AttributeError: 'TestEvolEvolTree' object has no attribute 'assert_'.
> Did you mean: 'assertIn'?
>
> ete3/test/test_evol.py:114: AttributeError
> =============================== warnings summary
> ===============================
> ete3/coretype/tree.py:365
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/coretype/tree.py:365:
> SyntaxWarning: invalid escape sequence '\-'
> """
>
> ete3/coretype/tree.py:436
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/coretype/tree.py:436:
> SyntaxWarning: invalid escape sequence '\-'
> """Prunes the topology of a node to conserve only the selected list of
> leaf
>
> ete3/coretype/tree.py:1508
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/coretype/tree.py:1508:
> SyntaxWarning: invalid escape sequence '\-'
> """
>
> ete3/parser/newick.py:51
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/parser/newick.py:51:
> SyntaxWarning: invalid escape sequence '\['
> _ILEGAL_NEWICK_CHARS = ":;(),\[\]\t\n\r="
>
> ete3/parser/newick.py:54
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/parser/newick.py:54:
> SyntaxWarning: invalid escape sequence '\['
> _NHX_RE = "\[&&NHX:[^\]]*\]"
>
> ete3/parser/newick.py:55
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/parser/newick.py:55:
> SyntaxWarning: invalid escape sequence '\s'
> _FLOAT_RE = "\s*[+-]?\d+\.?\d*(?:[eE][-+]?\d+)?\s*"
>
> ete3/parser/newick.py:402
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/parser/newick.py:402:
> SyntaxWarning: invalid escape sequence '\s'
> matcher_str= '^\s*%s\s*%s\s*(%s)?\s*$' % (FIRST_MATCH, SECOND_MATCH,
> _NHX_RE)
>
> ete3/utils.py:82
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/utils.py:82:
> SyntaxWarning: invalid escape sequence '\['
> return re.sub("\\033\[[^m]+m", "", string)
>
> ete3/treeview/main.py:64
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/treeview/main.py:64:
> SyntaxWarning: invalid escape sequence '\d'
> _COLOR_MATCH = re.compile("^#[A-Fa-f\d]{6}$")
>
> ete3/treeview/main.py:712
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/treeview/main.py:712:
> SyntaxWarning: invalid escape sequence '\d'
> compatible_code = re.sub('font-size="(\d+)"', 'font-size="\\1pt"',
> compatible_code)
>
> ete3/treeview/main.py:714
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/treeview/main.py:714:
> SyntaxWarning: invalid escape sequence '\s'
> compatible_code = re.sub('<g [^>]+>\s*</g>', '', compatible_code)
>
> ete3/treeview/faces.py:159
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/treeview/faces.py:159:
> SyntaxWarning: invalid escape sequence '\_'
> """Base Face object. All Face types (i.e. TextFace, SeqMotifFace,
>
> ete3/parser/phylip.py:76
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/parser/phylip.py:76:
> SyntaxWarning: invalid escape sequence '\s'
> m = re.match("^\s*(\d+)\s+(\d+)",line)
>
> ete3/parser/phylip.py:108
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/parser/phylip.py:108:
> SyntaxWarning: invalid escape sequence '\s'
> SG.id2seq[id_counter] += re.sub("\s","", line)
>
> ete3/parser/phylip.py:123
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/parser/phylip.py:123:
> SyntaxWarning: invalid escape sequence '\s'
> seq = re.sub("\s","",m.groups()[1])
>
> ete3/parser/phylip.py:138
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/parser/phylip.py:138:
> SyntaxWarning: invalid escape sequence '\s'
> seq = re.sub("\s", "", line)
>
> ete3/phylo/phylotree.py:132
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/phylo/phylotree.py:132:
> SyntaxWarning: invalid escape sequence '\d'
> id_match = re.compile("([^0-9])?(\d+)([^0-9])?")
>
> ete3/phylo/phylotree.py:188
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/phylo/phylotree.py:188:
> SyntaxWarning: invalid escape sequence '\d'
> id_match = re.compile("([^0-9])(\d+)([^0-9])")
>
> ete3/evol/parser/codemlparser.py:74
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/evol/parser/codemlparser.py:74:
> SyntaxWarning: invalid escape sequence '\('
> k = int(re.sub ('.* \(K=([0-9]+)\)\n', '\\1', line))
>
> ete3/evol/parser/codemlparser.py:78
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/evol/parser/codemlparser.py:78:
> SyntaxWarning: invalid escape sequence '\d'
> re.match ('^[a-z]+.*(\d+\.\d{5} *){'+ str(k) +'}', line):
>
> ete3/evol/parser/codemlparser.py:82
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/evol/parser/codemlparser.py:82:
> SyntaxWarning: invalid escape sequence '\d'
> classes[var] = [float(v) for v in re.findall('\d+\.\d{5}', line)]
>
> ete3/evol/parser/codemlparser.py:86
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/evol/parser/codemlparser.py:86:
> SyntaxWarning: invalid escape sequence '\d'
> k = int(re.sub('.*for (\d+) classes.*\n', '\\1', line))
>
> ete3/evol/parser/codemlparser.py:92
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/evol/parser/codemlparser.py:92:
> SyntaxWarning: invalid escape sequence '\d'
> k = int(re.sub('.*for (\d+) classes.*\n', '\\1', line))
>
> ete3/evol/parser/codemlparser.py:217
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/evol/parser/codemlparser.py:217:
> SyntaxWarning: invalid escape sequence '\('
> model._tree = EvolTree (re.findall ('\(.*\);', ''.join(all_lines))[2])
>
> ete3/evol/parser/codemlparser.py:227
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/evol/parser/codemlparser.py:227:
> SyntaxWarning: invalid escape sequence '\d'
> line = list(map (float, re.findall ('\d\.\d+', all_lines [i+j+1])))
>
> ete3/evol/parser/codemlparser.py:240
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/evol/parser/codemlparser.py:240:
> SyntaxWarning: invalid escape sequence '\d'
> line = re.sub ('.* np: *(\d+)\): +(-\d+\.\d+).*',
>
> ete3/evol/parser/codemlparser.py:245
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/evol/parser/codemlparser.py:245:
> SyntaxWarning: invalid escape sequence '\d'
> line = re.sub ('.* np: *(\d+)\): +(nan).*',
>
> ete3/evol/parser/codemlparser.py:252
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/evol/parser/codemlparser.py:252:
> SyntaxWarning: invalid escape sequence '\d'
> labels = re.findall ('\d+\.\.\d+', line + ' ')
>
> ete3/evol/parser/codemlparser.py:258
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/evol/parser/codemlparser.py:258:
> SyntaxWarning: invalid escape sequence '\d'
> model.stats ['kappa'] = float (re.sub ('.*(\d+\.\d+).*',
>
> ete3/evol/parser/codemlparser.py:264
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/evol/parser/codemlparser.py:264:
> SyntaxWarning: invalid escape sequence '\d'
> if not re.match (' +\d+\.\.\d+ +\d+\.\d+ ', line):
>
> ete3/evol/parser/codemlparser.py:265
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/evol/parser/codemlparser.py:265:
> SyntaxWarning: invalid escape sequence '\d'
> if re.match (' +( +\d+\.\d+){8}', all_lines [i+1]):
>
> ete3/evol/evoltree.py:468
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/evol/evoltree.py:468:
> SyntaxWarning: invalid escape sequence '\['
> nwk += sub('\[&&NHX:mark=([ #0-9.]*)\]', r'\1',
>
> ete3/evol/evoltree.py:471
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/evol/evoltree.py:471:
> SyntaxWarning: invalid escape sequence '\['
> nwk = sub('\[&&NHX:mark=([ #0-9.]*)\]', r'\1',
>
> ete3/tools/utils.py:28
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/tools/utils.py:28:
> SyntaxWarning: invalid escape sequence '\['
> return re.sub("\\033\[[^m]+m", "", string)
>
> ete3/evol/model.py:367
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/evol/model.py:367:
> SyntaxWarning: invalid escape sequence '\.'
> if sub('\..*', '', model) in AVAIL:
>
> ete3/evol/model.py:368
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/evol/model.py:368:
> SyntaxWarning: invalid escape sequence '\.'
> return model, AVAIL [sub('\..*', '', model)]
>
> ete3/webplugin/webapp.py:44
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/webplugin/webapp.py:44:
> DeprecationWarning: 'cgi' is deprecated and slated for removal in Python 3.13
> import cgi
>
> ete3/phylomedb/phylomeDB3.py:75
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/phylomedb/phylomeDB3.py:75:
> SyntaxWarning: invalid escape sequence '\w'
> ID_PATTERN = re.compile("^[Pp][Hh][Yy]\w{7}(_\w{2,7})?$")
>
> ete3/phylomedb/phylomeDB3.py:153
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/phylomedb/phylomeDB3.py:153:
> SyntaxWarning: invalid escape sequence '\w'
> m = re.search("Phy(\w{7})_[\w\d]+", name)
>
> ete3/phylomedb/phylomeDB3.py:500
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/phylomedb/phylomeDB3.py:500:
> SyntaxWarning: invalid escape sequence '\w'
> QUERY_OLD_REGEXP_FILTER = "^\w{3}\d{1,}$"
>
> ete3/phylomedb/phylomeDB3.py:756
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/phylomedb/phylomeDB3.py:756:
> SyntaxWarning: invalid escape sequence '\w'
> QUERY_GEN_REGEXP_FILTER = "^[\w\d\-_,;:.|#@\/\\\()'<>!]+$"
>
> ete3/phylomedb/phylomeDB3.py:757
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/phylomedb/phylomeDB3.py:757:
> SyntaxWarning: invalid escape sequence '\w'
> QUERY_OLD_REGEXP_FILTER = "^\w{3}\d{1,}$"
>
> ete3/phylomedb/phylomeDB3.py:758
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/phylomedb/phylomeDB3.py:758:
> SyntaxWarning: invalid escape sequence '\w'
> QUERY_INT_REGEXP_FILTER = "^[Pp][Hh][Yy]\w{7}(_\w{2,7})?$"
>
> .pybuild/cpython3_3.12_ete3/build/ete3/test/test_api.py::TestEvolEvolTree::test_call_histface
> .pybuild/cpython3_3.12_ete3/build/ete3/test/test_api.py::TestEvolEvolTree::test_pickling
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/evol/parser/codemlparser.py:304:
> UserWarning: WARNING: labelling does not correspond (bad tree?)!!
> Getting them from
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/test/ete_evol_data//protamine/PRM1/paml/M2/M2.out
> warn('WARNING: labelling does not correspond (bad tree?)!!\n' + \
>
> .pybuild/cpython3_3.12_ete3/build/ete3/test/test_api.py::TestEvolEvolTree::test_deep_copy
> .pybuild/cpython3_3.12_ete3/build/ete3/test/test_api.py::TestEvolEvolTree::test_labelling_tree
> .pybuild/cpython3_3.12_ete3/build/ete3/test/test_api.py::TestEvolEvolTree::test_load_model
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/evol/parser/codemlparser.py:304:
> UserWarning: WARNING: labelling does not correspond (bad tree?)!!
> Getting them from
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/test/ete_evol_data//protamine/PRM1/paml/fb/fb.out
> warn('WARNING: labelling does not correspond (bad tree?)!!\n' + \
>
> .pybuild/cpython3_3.12_ete3/build/ete3/test/test_api.py::TestEvolEvolTree::test_get_most_likely
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/evol/parser/codemlparser.py:304:
> UserWarning: WARNING: labelling does not correspond (bad tree?)!!
> Getting them from
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build/ete3/test/ete_evol_data//protamine/PRM1/paml/M1/M1.out
> warn('WARNING: labelling does not correspond (bad tree?)!!\n' + \
>
> -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
> =========================== short test summary info
> ============================
> FAILED ete3/test/test_api.py::Test_Coretype_ArrayTable::test_arraytable_parser
> FAILED ete3/test/test_api.py::TestEvolEvolTree::test_labelling_tree -
> Attribu...
> FAILED ete3/test/test_api.py::TestEvolEvolTree::test_load_model -
> AttributeEr...
> =========== 3 failed, 43 passed, 7 deselected, 49 warnings in 3.46s
> ============
> E: pybuild pybuild:395: test: plugin distutils failed with: exit code=1: cd
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.12_ete3/build; python3.12 -m pytest -k
> "not test_ncbiquery and not test_ncbi_compare and not test_get_topology and
> not test_01tree_annotation and not test_00_update_database and not
> test_merged_id and not test_renderer" ete3/test/test_api.py
> I: pybuild base:310: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_ete3/build;
> python3.11 -m pytest -k "not test_ncbiquery and not test_ncbi_compare and not
> test_get_topology and not test_01tree_annotation and not
> test_00_update_database and not test_merged_id and not test_renderer"
> ete3/test/test_api.py
> ============================= test session starts
> ==============================
> platform linux -- Python 3.11.7, pytest-7.4.3, pluggy-1.3.0
> rootdir: /<<PKGBUILDDIR>>
> collected 53 items / 7 deselected / 46 selected
>
> ete3/test/test_api.py ..............................................
> [100%]
>
> =============================== warnings summary
> ===============================
> ete3/coretype/tree.py:365
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_ete3/build/ete3/coretype/tree.py:365:
> DeprecationWarning: invalid escape sequence '\-'
> """
>
> ete3/coretype/tree.py:436
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_ete3/build/ete3/coretype/tree.py:436:
> DeprecationWarning: invalid escape sequence '\-'
> """Prunes the topology of a node to conserve only the selected list of
> leaf
>
> ete3/coretype/tree.py:1508
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_ete3/build/ete3/coretype/tree.py:1508:
> DeprecationWarning: invalid escape sequence '\-'
> """
>
> ete3/parser/newick.py:51
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_ete3/build/ete3/parser/newick.py:51:
> DeprecationWarning: invalid escape sequence '\['
> _ILEGAL_NEWICK_CHARS = ":;(),\[\]\t\n\r="
>
> ete3/parser/newick.py:54
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_ete3/build/ete3/parser/newick.py:54:
> DeprecationWarning: invalid escape sequence '\['
> _NHX_RE = "\[&&NHX:[^\]]*\]"
>
> ete3/parser/newick.py:55
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_ete3/build/ete3/parser/newick.py:55:
> DeprecationWarning: invalid escape sequence '\s'
> _FLOAT_RE = "\s*[+-]?\d+\.?\d*(?:[eE][-+]?\d+)?\s*"
>
> ete3/parser/newick.py:402
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_ete3/build/ete3/parser/newick.py:402:
> DeprecationWarning: invalid escape sequence '\s'
> matcher_str= '^\s*%s\s*%s\s*(%s)?\s*$' % (FIRST_MATCH, SECOND_MATCH,
> _NHX_RE)
>
> ete3/utils.py:82
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_ete3/build/ete3/utils.py:82:
> DeprecationWarning: invalid escape sequence '\['
> return re.sub("\\033\[[^m]+m", "", string)
>
> ete3/treeview/main.py:64
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_ete3/build/ete3/treeview/main.py:64:
> DeprecationWarning: invalid escape sequence '\d'
> _COLOR_MATCH = re.compile("^#[A-Fa-f\d]{6}$")
>
> ete3/treeview/main.py:712
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_ete3/build/ete3/treeview/main.py:712:
> DeprecationWarning: invalid escape sequence '\d'
> compatible_code = re.sub('font-size="(\d+)"', 'font-size="\\1pt"',
> compatible_code)
>
> ete3/treeview/main.py:714
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_ete3/build/ete3/treeview/main.py:714:
> DeprecationWarning: invalid escape sequence '\s'
> compatible_code = re.sub('<g [^>]+>\s*</g>', '', compatible_code)
>
> ete3/treeview/faces.py:159
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_ete3/build/ete3/treeview/faces.py:159:
> DeprecationWarning: invalid escape sequence '\_'
> """Base Face object. All Face types (i.e. TextFace, SeqMotifFace,
>
> ete3/parser/phylip.py:76
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_ete3/build/ete3/parser/phylip.py:76:
> DeprecationWarning: invalid escape sequence '\s'
> m = re.match("^\s*(\d+)\s+(\d+)",line)
>
> ete3/parser/phylip.py:108
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_ete3/build/ete3/parser/phylip.py:108:
> DeprecationWarning: invalid escape sequence '\s'
> SG.id2seq[id_counter] += re.sub("\s","", line)
>
> ete3/parser/phylip.py:123
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_ete3/build/ete3/parser/phylip.py:123:
> DeprecationWarning: invalid escape sequence '\s'
> seq = re.sub("\s","",m.groups()[1])
>
> ete3/parser/phylip.py:138
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_ete3/build/ete3/parser/phylip.py:138:
> DeprecationWarning: invalid escape sequence '\s'
> seq = re.sub("\s", "", line)
>
> ete3/phylo/phylotree.py:132
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_ete3/build/ete3/phylo/phylotree.py:132:
> DeprecationWarning: invalid escape sequence '\d'
> id_match = re.compile("([^0-9])?(\d+)([^0-9])?")
>
> ete3/phylo/phylotree.py:188
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_ete3/build/ete3/phylo/phylotree.py:188:
> DeprecationWarning: invalid escape sequence '\d'
> id_match = re.compile("([^0-9])(\d+)([^0-9])")
>
> ete3/evol/parser/codemlparser.py:74
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_ete3/build/ete3/evol/parser/codemlparser.py:74:
> DeprecationWarning: invalid escape sequence '\('
> k = int(re.sub ('.* \(K=([0-9]+)\)\n', '\\1', line))
>
> ete3/evol/parser/codemlparser.py:78
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_ete3/build/ete3/evol/parser/codemlparser.py:78:
> DeprecationWarning: invalid escape sequence '\d'
> re.match ('^[a-z]+.*(\d+\.\d{5} *){'+ str(k) +'}', line):
>
> ete3/evol/parser/codemlparser.py:82
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_ete3/build/ete3/evol/parser/codemlparser.py:82:
> DeprecationWarning: invalid escape sequence '\d'
> classes[var] = [float(v) for v in re.findall('\d+\.\d{5}', line)]
>
> ete3/evol/parser/codemlparser.py:86
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_ete3/build/ete3/evol/parser/codemlparser.py:86:
> DeprecationWarning: invalid escape sequence '\d'
> k = int(re.sub('.*for (\d+) classes.*\n', '\\1', line))
>
> ete3/evol/parser/codemlparser.py:92
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_ete3/build/ete3/evol/parser/codemlparser.py:92:
> DeprecationWarning: invalid escape sequence '\d'
> k = int(re.sub('.*for (\d+) classes.*\n', '\\1', line))
>
> ete3/evol/parser/codemlparser.py:217
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_ete3/build/ete3/evol/parser/codemlparser.py:217:
> DeprecationWarning: invalid escape sequence '\('
> model._tree = EvolTree (re.findall ('\(.*\);', ''.join(all_lines))[2])
>
> ete3/evol/parser/codemlparser.py:227
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_ete3/build/ete3/evol/parser/codemlparser.py:227:
> DeprecationWarning: invalid escape sequence '\d'
> line = list(map (float, re.findall ('\d\.\d+', all_lines [i+j+1])))
>
> ete3/evol/parser/codemlparser.py:240
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_ete3/build/ete3/evol/parser/codemlparser.py:240:
> DeprecationWarning: invalid escape sequence '\d'
> line = re.sub ('.* np: *(\d+)\): +(-\d+\.\d+).*',
>
> ete3/evol/parser/codemlparser.py:245
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_ete3/build/ete3/evol/parser/codemlparser.py:245:
> DeprecationWarning: invalid escape sequence '\d'
> line = re.sub ('.* np: *(\d+)\): +(nan).*',
>
> ete3/evol/parser/codemlparser.py:252
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_ete3/build/ete3/evol/parser/codemlparser.py:252:
> DeprecationWarning: invalid escape sequence '\d'
> labels = re.findall ('\d+\.\.\d+', line + ' ')
>
> ete3/evol/parser/codemlparser.py:258
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_ete3/build/ete3/evol/parser/codemlparser.py:258:
> DeprecationWarning: invalid escape sequence '\d'
> model.stats ['kappa'] = float (re.sub ('.*(\d+\.\d+).*',
>
> ete3/evol/parser/codemlparser.py:264
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_ete3/build/ete3/evol/parser/codemlparser.py:264:
> DeprecationWarning: invalid escape sequence '\d'
> if not re.match (' +\d+\.\.\d+ +\d+\.\d+ ', line):
>
> ete3/evol/parser/codemlparser.py:265
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_ete3/build/ete3/evol/parser/codemlparser.py:265:
> DeprecationWarning: invalid escape sequence '\d'
> if re.match (' +( +\d+\.\d+){8}', all_lines [i+1]):
>
> ete3/evol/evoltree.py:468
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_ete3/build/ete3/evol/evoltree.py:468:
> DeprecationWarning: invalid escape sequence '\['
> nwk += sub('\[&&NHX:mark=([ #0-9.]*)\]', r'\1',
>
> ete3/evol/evoltree.py:471
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_ete3/build/ete3/evol/evoltree.py:471:
> DeprecationWarning: invalid escape sequence '\['
> nwk = sub('\[&&NHX:mark=([ #0-9.]*)\]', r'\1',
>
> ete3/tools/utils.py:28
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_ete3/build/ete3/tools/utils.py:28:
> DeprecationWarning: invalid escape sequence '\['
> return re.sub("\\033\[[^m]+m", "", string)
>
> ete3/evol/model.py:367
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_ete3/build/ete3/evol/model.py:367:
> DeprecationWarning: invalid escape sequence '\.'
> if sub('\..*', '', model) in AVAIL:
>
> ete3/evol/model.py:368
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_ete3/build/ete3/evol/model.py:368:
> DeprecationWarning: invalid escape sequence '\.'
> return model, AVAIL [sub('\..*', '', model)]
>
> ete3/webplugin/webapp.py:44
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_ete3/build/ete3/webplugin/webapp.py:44:
> DeprecationWarning: 'cgi' is deprecated and slated for removal in Python 3.13
> import cgi
>
> ete3/phylomedb/phylomeDB3.py:75
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_ete3/build/ete3/phylomedb/phylomeDB3.py:75:
> DeprecationWarning: invalid escape sequence '\w'
> ID_PATTERN = re.compile("^[Pp][Hh][Yy]\w{7}(_\w{2,7})?$")
>
> ete3/phylomedb/phylomeDB3.py:153
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_ete3/build/ete3/phylomedb/phylomeDB3.py:153:
> DeprecationWarning: invalid escape sequence '\w'
> m = re.search("Phy(\w{7})_[\w\d]+", name)
>
> ete3/phylomedb/phylomeDB3.py:500
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_ete3/build/ete3/phylomedb/phylomeDB3.py:500:
> DeprecationWarning: invalid escape sequence '\w'
> QUERY_OLD_REGEXP_FILTER = "^\w{3}\d{1,}$"
>
> ete3/phylomedb/phylomeDB3.py:756
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_ete3/build/ete3/phylomedb/phylomeDB3.py:756:
> DeprecationWarning: invalid escape sequence '\w'
> QUERY_GEN_REGEXP_FILTER = "^[\w\d\-_,;:.|#@\/\\\()'<>!]+$"
>
> ete3/phylomedb/phylomeDB3.py:757
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_ete3/build/ete3/phylomedb/phylomeDB3.py:757:
> DeprecationWarning: invalid escape sequence '\w'
> QUERY_OLD_REGEXP_FILTER = "^\w{3}\d{1,}$"
>
> ete3/phylomedb/phylomeDB3.py:758
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_ete3/build/ete3/phylomedb/phylomeDB3.py:758:
> DeprecationWarning: invalid escape sequence '\w'
> QUERY_INT_REGEXP_FILTER = "^[Pp][Hh][Yy]\w{7}(_\w{2,7})?$"
>
> .pybuild/cpython3_3.11_ete3/build/ete3/test/test_api.py::Test_Coretype_ArrayTable::test_arraytable_parser
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_ete3/build/ete3/test/test_arraytable.py:36:
> DeprecationWarning: Please use assertTrue instead.
> self.assert_(A.get_column_vector("col4") is None )
>
> .pybuild/cpython3_3.11_ete3/build/ete3/test/test_api.py::TestEvolEvolTree::test_call_histface
> .pybuild/cpython3_3.11_ete3/build/ete3/test/test_api.py::TestEvolEvolTree::test_pickling
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_ete3/build/ete3/evol/parser/codemlparser.py:304:
> UserWarning: WARNING: labelling does not correspond (bad tree?)!!
> Getting them from
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_ete3/build/ete3/test/ete_evol_data//protamine/PRM1/paml/M2/M2.out
> warn('WARNING: labelling does not correspond (bad tree?)!!\n' + \
>
> .pybuild/cpython3_3.11_ete3/build/ete3/test/test_api.py::TestEvolEvolTree::test_deep_copy
> .pybuild/cpython3_3.11_ete3/build/ete3/test/test_api.py::TestEvolEvolTree::test_labelling_tree
> .pybuild/cpython3_3.11_ete3/build/ete3/test/test_api.py::TestEvolEvolTree::test_load_model
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_ete3/build/ete3/evol/parser/codemlparser.py:304:
> UserWarning: WARNING: labelling does not correspond (bad tree?)!!
> Getting them from
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_ete3/build/ete3/test/ete_evol_data//protamine/PRM1/paml/fb/fb.out
> warn('WARNING: labelling does not correspond (bad tree?)!!\n' + \
>
> .pybuild/cpython3_3.11_ete3/build/ete3/test/test_api.py::TestEvolEvolTree::test_get_most_likely
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_ete3/build/ete3/evol/parser/codemlparser.py:304:
> UserWarning: WARNING: labelling does not correspond (bad tree?)!!
> Getting them from
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_ete3/build/ete3/test/ete_evol_data//protamine/PRM1/paml/M1/M1.out
> warn('WARNING: labelling does not correspond (bad tree?)!!\n' + \
>
> .pybuild/cpython3_3.11_ete3/build/ete3/test/test_api.py::TestEvolEvolTree::test_labelling_tree
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_ete3/build/ete3/test/test_evol.py:132:
> DeprecationWarning: Please use assertTrue instead.
> self.assert_(check_annotation (tree))
>
> .pybuild/cpython3_3.11_ete3/build/ete3/test/test_api.py::TestEvolEvolTree::test_load_model
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_ete3/build/ete3/test/test_evol.py:114:
> DeprecationWarning: Please use assertTrue instead.
> self.assert_('proportions' in str(tree.get_evol_model('M2')))
>
> .pybuild/cpython3_3.11_ete3/build/ete3/test/test_api.py::TestEvolEvolTree::test_load_model
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_ete3/build/ete3/test/test_evol.py:115:
> DeprecationWarning: Please use assertTrue instead.
> self.assert_('p2=' in str(tree.get_evol_model('M2')))
>
> .pybuild/cpython3_3.11_ete3/build/ete3/test/test_api.py::TestEvolEvolTree::test_load_model
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_ete3/build/ete3/test/test_evol.py:116:
> DeprecationWarning: Please use assertTrue instead.
> self.assert_('proportions' not in str(tree.get_evol_model('fb')))
>
> .pybuild/cpython3_3.11_ete3/build/ete3/test/test_api.py::TestEvolEvolTree::test_load_model
>
> /<<PKGBUILDDIR>>/.pybuild/cpython3_3.11_ete3/build/ete3/test/test_evol.py:117:
> DeprecationWarning: Please use assertTrue instead.
> self.assert_(' #193' in str(tree.get_evol_model('fb')))
>
> -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
> ================ 46 passed, 7 deselected, 55 warnings in 3.59s
> =================
> dh_auto_test: error: pybuild --test -i python{version} -p "3.12 3.11"
> returned exit code 13
The full build log is available from:
http://qa-logs.debian.net/2023/12/12/python-ete3_3.1.3+dfsg-1_unstable.log
All bugs filed during this archive rebuild are listed at:
https://bugs.debian.org/cgi-bin/pkgreport.cgi?tag=ftbfs-20231212;users=lu...@debian.org
or:
https://udd.debian.org/bugs/?release=na&merged=ign&fnewerval=7&flastmodval=7&fusertag=only&fusertagtag=ftbfs-20231212&fusertaguser=lu...@debian.org&allbugs=1&cseverity=1&ctags=1&caffected=1#results
A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
If you reassign this bug to another package, please mark it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects
If you fail to reproduce this, please provide a build log and diff it with mine
so that we can identify if something relevant changed in the meantime.
--- End Message ---
