[Debian-med-packaging] Testsuite fails when trying to upgrade Gubbins Debian package
Andreas Tille
andreas at an3as.eu
Wed Apr 20 18:07:22 UTC 2016
Hi Andrew,
I realised that there is a new release of gubbins. When I try to build
the package 10 tests are failing. I've attached the according log.
Could you give any hint what might be wrong here? Please note that
Debian switched to Python 3.5 if this might matter.
Kind regards
Andreas.
--
http://fam-tille.de
-------------- next part --------------
debian/rules override_dh_auto_test
make[1]: Entering directory '/build/gubbins-1.4.9'
dh_auto_test
make -j1 check VERBOSE=1
make[2]: Entering directory '/build/gubbins-1.4.9'
Making check in src
make[3]: Entering directory '/build/gubbins-1.4.9/src'
make run_all_tests
make[4]: Entering directory '/build/gubbins-1.4.9/src'
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o ../tests/run_all_tests-check_branch_sequences.o `test -f '../tests/check_branch_sequences.c' || echo './'`../tests/check_branch_sequences.c
../tests/check_branch_sequences.c: In function 'check_copy_and_concat_2d_integer_arrays':
../tests/check_branch_sequences.c:67:16: warning: implicit declaration of function 'copy_and_concat_2d_integer_arrays' [-Wimplicit-function-declaration]
output_size = copy_and_concat_2d_integer_arrays(block_coords, 3, block_coords_2, 2, block_coords_out) ;
^
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o ../tests/run_all_tests-check_gubbins.o `test -f '../tests/check_gubbins.c' || echo './'`../tests/check_gubbins.c
In file included from ../tests/check_gubbins.c:4:0:
../tests/check_gubbins.c: In function 'check_gubbins_no_recombinations':
../tests/check_gubbins.c:21:15: warning: implicit declaration of function 'number_of_recombinations_in_file' [-Wimplicit-function-declaration]
fail_unless(number_of_recombinations_in_file("../tests/data/no_recombinations.tre.tab") == 0);
^
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o ../tests/run_all_tests-check_parse_phylip.o `test -f '../tests/check_parse_phylip.c' || echo './'`../tests/check_parse_phylip.c
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o ../tests/run_all_tests-check_snp_searching.o `test -f '../tests/check_snp_searching.c' || echo './'`../tests/check_snp_searching.c
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o ../tests/run_all_tests-check_snp_sites.o `test -f '../tests/check_snp_sites.c' || echo './'`../tests/check_snp_sites.c
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o ../tests/run_all_tests-check_vcf_parsing.o `test -f '../tests/check_vcf_parsing.c' || echo './'`../tests/check_vcf_parsing.c
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o ../tests/run_all_tests-helper_methods.o `test -f '../tests/helper_methods.c' || echo './'`../tests/helper_methods.c
../tests/helper_methods.c: In function 'compare_files':
../tests/helper_methods.c:27:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(expected_buffer, sizeof(char), numbytes, expected_output_fh);
^
../tests/helper_methods.c:34:3: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
fread(actual_buffer, sizeof(char), numbytes, actual_output_fh);
^
gcc -DHAVE_CONFIG_H -I. -I.. -Wdate-time -D_FORTIFY_SOURCE=2 -I../tests -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -c -o ../tests/run_all_tests-run_all_tests.o `test -f '../tests/run_all_tests.c' || echo './'`../tests/run_all_tests.c
/bin/bash ../libtool --tag=CC --mode=link gcc -I../tests -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z,relro -Wl,-z,now -o run_all_tests ../tests/run_all_tests-check_branch_sequences.o ../tests/run_all_tests-check_gubbins.o ../tests/run_all_tests-check_parse_phylip.o ../tests/run_all_tests-check_snp_searching.o ../tests/run_all_tests-check_snp_sites.o ../tests/run_all_tests-check_vcf_parsing.o ../tests/run_all_tests-helper_methods.o ../tests/run_all_tests-run_all_tests.o -lcheck libgubbins.la -lz -lm -lrt -lsubunit
libtool: link: gcc -I../tests -pthread -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wl,-z -Wl,relro -Wl,-z -Wl,now -o .libs/run_all_tests ../tests/run_all_tests-check_branch_sequences.o ../tests/run_all_tests-check_gubbins.o ../tests/run_all_tests-check_parse_phylip.o ../tests/run_all_tests-check_snp_searching.o ../tests/run_all_tests-check_snp_sites.o ../tests/run_all_tests-check_vcf_parsing.o ../tests/run_all_tests-helper_methods.o ../tests/run_all_tests-run_all_tests.o -lcheck ./.libs/libgubbins.so -lz -lm -lrt -lsubunit -pthread
make[4]: Leaving directory '/build/gubbins-1.4.9/src'
make check-TESTS
make[4]: Entering directory '/build/gubbins-1.4.9/src'
make[5]: Entering directory '/build/gubbins-1.4.9/src'
PASS: run_all_tests
============================================================================
Testsuite summary for gubbins 1.4.9
============================================================================
# TOTAL: 1
# PASS: 1
# SKIP: 0
# XFAIL: 0
# FAIL: 0
# XPASS: 0
# ERROR: 0
============================================================================
make[5]: Leaving directory '/build/gubbins-1.4.9/src'
make[4]: Leaving directory '/build/gubbins-1.4.9/src'
make[3]: Leaving directory '/build/gubbins-1.4.9/src'
Making check in release
make[3]: Entering directory '/build/gubbins-1.4.9/release'
make[3]: Nothing to be done for 'check'.
make[3]: Leaving directory '/build/gubbins-1.4.9/release'
make[3]: Entering directory '/build/gubbins-1.4.9'
make[3]: Leaving directory '/build/gubbins-1.4.9'
make[2]: Leaving directory '/build/gubbins-1.4.9'
cd python && \
python3 setup.py test
running test
running egg_info
creating gubbins.egg-info
writing requirements to gubbins.egg-info/requires.txt
writing top-level names to gubbins.egg-info/top_level.txt
writing gubbins.egg-info/PKG-INFO
writing dependency_links to gubbins.egg-info/dependency_links.txt
writing manifest file 'gubbins.egg-info/SOURCES.txt'
reading manifest file 'gubbins.egg-info/SOURCES.txt'
writing manifest file 'gubbins.egg-info/SOURCES.txt'
running build_ext
test_get_sequence_names_from_alignment (test_alignment_python_methods.TestAlignmentPythonMethods) ... ok
test_number_of_sequences_in_alignment (test_alignment_python_methods.TestAlignmentPythonMethods) ... ok
test_reconvert_fasta_file (test_alignment_python_methods.TestAlignmentPythonMethods) ... /usr/lib/python3/dist-packages/Bio/AlignIO/__init__.py:374: PendingDeprecationWarning: generator '_SeqIO_to_alignment_iterator' raised StopIteration
for a in i:
ok
test_reinsert_gaps_into_fasta_file (test_alignment_python_methods.TestAlignmentPythonMethods) ... ok
test_get_recombination_files (test_converging_recombinations.TestConvergingRecombinations) ... ok
test_multiple_files_have_one_match (test_converging_recombinations.TestConvergingRecombinations) ... ok
test_reading_embl_file (test_converging_recombinations.TestConvergingRecombinations) ... ok
test_two_files_are_different (test_converging_recombinations.TestConvergingRecombinations) ... ok
test_two_files_are_same (test_converging_recombinations.TestConvergingRecombinations) ... ok
test_change_window_size (test_external_dependancies.TestExternalDependancies) ... ERROR
test_delete_files_based_on_list_of_regexes (test_external_dependancies.TestExternalDependancies) ... ok
test_fasttree_default_output_names (test_external_dependancies.TestExternalDependancies) ... ERROR
test_hybrid_default_output_names (test_external_dependancies.TestExternalDependancies) ... ERROR
test_pairwise_comparison (test_external_dependancies.TestExternalDependancies) ... /bin/sh: 1: fastml: not found
ERROR
test_parse_and_run (test_external_dependancies.TestExternalDependancies) ... ERROR
test_recombination_convergence (test_external_dependancies.TestExternalDependancies) ... ERROR
test_rename_final_output (test_external_dependancies.TestExternalDependancies) ... ERROR
test_rename_final_output_fasttree (test_external_dependancies.TestExternalDependancies) ... ERROR
test_rename_final_output_hybrid (test_external_dependancies.TestExternalDependancies) ... ERROR
test_robinson_foulds_convergence (test_external_dependancies.TestExternalDependancies) ... ERROR
test_use_bundled_exec (test_external_dependancies.TestExternalDependancies) ... ok
test_which (test_external_dependancies.TestExternalDependancies) ... ok
test_custom_fastml_2_installed (test_fastml.TestFastml) ... ok
test_fastml_2_installed (test_fastml.TestFastml) ... ok
test_fastml_3_installed (test_fastml.TestFastml) ... ok
test_no_fastml_installed (test_fastml.TestFastml) ... ok
test_filter_out_alignments_with_too_much_missing_data (test_pre_process_fasta.TestPreProcessFasta) ... ok
test_input_file_with_all_duplicate_sequences (test_pre_process_fasta.TestPreProcessFasta) ... ok
test_input_file_with_multiple_duplicate_sequences (test_pre_process_fasta.TestPreProcessFasta) ... ok
test_input_file_with_no_duplicate_sequences (test_pre_process_fasta.TestPreProcessFasta) ... ok
test_input_file_with_one_duplicate_sequences (test_pre_process_fasta.TestPreProcessFasta) ... ok
test_fasttree_current_tree_name (test_string_construction.TestStringConstruction) ... ok
test_fasttree_fastml_command (test_string_construction.TestStringConstruction) ... ok
test_fasttree_gubbins_command (test_string_construction.TestStringConstruction) ... ok
test_fasttree_previous_tree_name (test_string_construction.TestStringConstruction) ... ok
test_fasttree_regex_for_file_deletions (test_string_construction.TestStringConstruction) ... ok
test_fasttree_tree_building_command (test_string_construction.TestStringConstruction) ... ok
test_generate_fastml_command (test_string_construction.TestStringConstruction) ... ok
test_raxml_base_name (test_string_construction.TestStringConstruction) ... ok
test_raxml_current_tree_name (test_string_construction.TestStringConstruction) ... ok
test_raxml_fastml_command (test_string_construction.TestStringConstruction) ... ok
test_raxml_gubbins_command (test_string_construction.TestStringConstruction) ... ok
test_raxml_previous_tree (test_string_construction.TestStringConstruction) ... ok
test_raxml_previous_tree_name (test_string_construction.TestStringConstruction) ... ok
test_raxml_regex_for_file_deletions (test_string_construction.TestStringConstruction) ... ok
test_raxml_regex_for_file_deletions_10 (test_string_construction.TestStringConstruction) ... ok
test_raxml_tree_building_command (test_string_construction.TestStringConstruction) ... ok
test_rename_files (test_string_construction.TestStringConstruction) ... ok
test_starting_files_regex (test_string_construction.TestStringConstruction) ... ok
test_translation_of_fasttree_filenames_to_final_filenames (test_string_construction.TestStringConstruction) ... ok
test_translation_of_raxml_filenames_to_final_filenames (test_string_construction.TestStringConstruction) ... ok
test_create_pairwise_newick_tree (test_tree_python_methods.TestTreePythonMethods) ... ok
test_filter_out_removed_taxa_from_tree_and_return_new_file (test_tree_python_methods.TestTreePythonMethods) ... /usr/lib/python3/dist-packages/dendropy/dataio/newickreader.py:317: PendingDeprecationWarning: generator 'NewickReader.tree_iter' raised StopIteration
tree_factory=tree_factory):
ok
test_has_tree_been_seen_before (test_tree_python_methods.TestTreePythonMethods) ... ok
test_internal_node_taxons_removed_when_used_as_starting_tree (test_tree_python_methods.TestTreePythonMethods) ... ok
test_remove_internal_node_labels (test_tree_python_methods.TestTreePythonMethods) ... ok
test_reroot_tree (test_tree_python_methods.TestTreePythonMethods) ... ok
test_reroot_tree_at_midpoint (test_tree_python_methods.TestTreePythonMethods) ... ok
test_reroot_tree_with_outgroup (test_tree_python_methods.TestTreePythonMethods) ... ok
test_reroot_tree_with_outgroups (test_tree_python_methods.TestTreePythonMethods) ... ok
test_reroot_tree_with_outgroups_all_in_different_clade (test_tree_python_methods.TestTreePythonMethods) ... ok
test_reroot_tree_with_outgroups_all_in_one_clade (test_tree_python_methods.TestTreePythonMethods) ... ok
test_reroot_tree_with_outgroups_all_in_one_clade_large (test_tree_python_methods.TestTreePythonMethods) ... ok
test_reroot_tree_with_outgroups_with_two_mixed_clades (test_tree_python_methods.TestTreePythonMethods) ... ok
test_robinson_foulds_distance (test_tree_python_methods.TestTreePythonMethods) ... ok
test_split_all_non_bi_nodes (test_tree_python_methods.TestTreePythonMethods) ... ok
test_are_all_sequence_names_unique (test_validate_fasta_input.TestValidateInputFastaFile) ... ok
test_are_all_sequences_the_same_length (test_validate_fasta_input.TestValidateInputFastaFile) ... ok
test_are_there_enough_sequences_to_build_a_tree (test_validate_fasta_input.TestValidateInputFastaFile) ... ok
test_does_each_sequence_have_a_name (test_validate_fasta_input.TestValidateInputFastaFile) ... ok
test_does_the_sequence_have_sensible_characters (test_validate_fasta_input.TestValidateInputFastaFile) ... ok
test_input_file_exists (test_validate_fasta_input.TestValidateInputFastaFile) ... ok
test_valid_fasta_file (test_validate_fasta_input.TestValidateInputFastaFile) ... ok
test_are_all_names_unique (test_validate_starting_tree.TestValidationOfStartingTree) ... ok
test_do_the_names_match_the_fasta_file (test_validate_starting_tree.TestValidationOfStartingTree) ... ok
test_is_it_a_valid_newick_tree (test_validate_starting_tree.TestValidationOfStartingTree) ... ok
======================================================================
ERROR: test_change_window_size (test_external_dependancies.TestExternalDependancies)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/build/gubbins-1.4.9/python/gubbins/tests/test_external_dependancies.py", line 34, in test_change_window_size
gubbins_runner.parse_and_run()
File "/build/gubbins-1.4.9/python/gubbins/common.py", line 143, in parse_and_run
if GubbinsCommon.which(FASTML_EXEC) is None:
File "/build/gubbins-1.4.9/python/gubbins/common.py", line 889, in which
executable = program.split(" ")
AttributeError: 'NoneType' object has no attribute 'split'
======================================================================
ERROR: test_fasttree_default_output_names (test_external_dependancies.TestExternalDependancies)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/build/gubbins-1.4.9/python/gubbins/tests/test_external_dependancies.py", line 124, in test_fasttree_default_output_names
gubbins_runner.parse_and_run()
File "/build/gubbins-1.4.9/python/gubbins/common.py", line 143, in parse_and_run
if GubbinsCommon.which(FASTML_EXEC) is None:
File "/build/gubbins-1.4.9/python/gubbins/common.py", line 889, in which
executable = program.split(" ")
AttributeError: 'NoneType' object has no attribute 'split'
======================================================================
ERROR: test_hybrid_default_output_names (test_external_dependancies.TestExternalDependancies)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/build/gubbins-1.4.9/python/gubbins/tests/test_external_dependancies.py", line 142, in test_hybrid_default_output_names
gubbins_runner.parse_and_run()
File "/build/gubbins-1.4.9/python/gubbins/common.py", line 143, in parse_and_run
if GubbinsCommon.which(FASTML_EXEC) is None:
File "/build/gubbins-1.4.9/python/gubbins/common.py", line 889, in which
executable = program.split(" ")
AttributeError: 'NoneType' object has no attribute 'split'
======================================================================
ERROR: test_pairwise_comparison (test_external_dependancies.TestExternalDependancies)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/build/gubbins-1.4.9/python/gubbins/tests/test_external_dependancies.py", line 174, in test_pairwise_comparison
common.GubbinsCommon.pairwise_comparison('gubbins/tests/data/pairwise.aln','gubbins/tests/data/pairwise.aln','../src/gubbins','gubbins/tests/data/pairwise.aln','fastml -mg -qf -b ','pairwise')
File "/build/gubbins-1.4.9/python/gubbins/common.py", line 849, in pairwise_comparison
sys.exit("Failed while running fastML")
SystemExit: Failed while running fastML
======================================================================
ERROR: test_parse_and_run (test_external_dependancies.TestExternok
======================================================================
ERROR: test_change_window_size (test_external_dependancies.TestExternalDependancies)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/build/gubbins-1.4.9/python/gubbins/tests/test_external_dependancies.py", line 34, in test_change_window_size
gubbins_runner.parse_and_run()
File "/build/gubbins-1.4.9/python/gubbins/common.py", line 143, in parse_and_run
if GubbinsCommon.which(FASTML_EXEC) is None:
File "/build/gubbins-1.4.9/python/gubbins/common.py", line 889, in which
executable = program.split(" ")
AttributeError: 'NoneType' object has no attribute 'split'
======================================================================
ERROR: test_fasttree_default_output_names (test_external_dependancies.TestExternalDependancies)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/build/gubbins-1.4.9/python/gubbins/tests/test_external_dependancies.py", line 124, in test_fasttree_default_output_names
gubbins_runner.parse_and_run()
File "/build/gubbins-1.4.9/python/gubbins/common.py", line 143, in parse_and_run
if GubbinsCommon.which(FASTML_EXEC) is None:
File "/build/gubbins-1.4.9/python/gubbins/common.py", line 889, in which
executable = program.split(" ")
AttributeError: 'NoneType' object has no attribute 'split'
======================================================================
ERROR: test_hybrid_default_output_names (test_external_dependancies.TestExternalDependancies)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/build/gubbins-1.4.9/python/gubbins/tests/test_external_dependancies.py", line 142, in test_hybrid_default_output_names
gubbins_runner.parse_and_run()
File "/build/gubbins-1.4.9/python/gubbins/common.py", line 143, in parse_and_run
if GubbinsCommon.which(FASTML_EXEC) is None:
File "/build/gubbins-1.4.9/python/gubbins/common.py", line 889, in which
executable = program.split(" ")
AttributeError: 'NoneType' object has no attribute 'split'
======================================================================
ERROR: test_pairwise_comparison (test_external_dependancies.TestExternalDependancies)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/build/gubbins-1.4.9/python/gubbins/tests/test_external_dependancies.py", line 174, in test_pairwise_comparison
common.GubbinsCommon.pairwise_comparison('gubbins/tests/data/pairwise.aln','gubbins/tests/data/pairwise.aln','../src/gubbins','gubbins/tests/data/pairwise.aln','fastml -mg -qf -b ','pairwise')
File "/build/gubbins-1.4.9/python/gubbins/common.py", line 849, in pairwise_comparison
sys.exit("Failed while running fastML")
SystemExit: Failed while running fastML
======================================================================
ERROR: test_parse_and_run (test_external_dependancies.TestExternalDependancies)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/build/gubbins-1.4.9/python/gubbins/tests/test_external_dependancies.py", line 160, in test_parse_and_run
gubbins_runner.parse_and_run()
File "/build/gubbins-1.4.9/python/gubbins/common.py", line 143, in parse_and_run
if GubbinsCommon.which(FASTML_EXEC) is None:
File "/build/gubbins-1.4.9/python/gubbins/common.py", line 889, in which
executable = program.split(" ")
AttributeError: 'NoneType' object has no attribute 'split'
======================================================================
ERROR: test_recombination_convergence (test_external_dependancies.TestExternalDependancies)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/build/gubbins-1.4.9/python/gubbins/tests/test_external_dependancies.py", line 68, in test_recombination_convergence
gubbins_runner.parse_and_run()
File "/build/gubbins-1.4.9/python/gubbins/common.py", line 143, in parse_and_run
if GubbinsCommon.which(FASTML_EXEC) is None:
File "/build/gubbins-1.4.9/python/gubbins/common.py", line 889, in which
executable = program.split(" ")
AttributeErrodebian/rules:23: recipe for target 'override_dh_auto_test' failed
make[1]: *** [override_dh_auto_test] Error 1
make[1]: Leaving directory '/build/gubbins-1.4.9'
debian/rules:14: recipe for target 'build' failed
make: *** [build] Error 2
dpkg-buildpackage: error: debian/rules build gave error exit status 2
I: copying local configuration
E: Failed autobuilding of package
W: no hooks of type C found -- ignoring
I: unmounting dev/pts filesystem
I: unmounting run/shm filesystem
I: unmounting proc filesystem
common.py", line 143, in parse_and_run
if GubbinsCommon.which(FASTML_EXEC) is None:
File "/build/gubbins-1.4.9/python/gubbins/common.py", line 889, in which
executable = program.split(" ")
AttributeError: 'NoneType' object has no attribute 'split'
======================================================================
ERROR: test_rename_final_output_fasttree (test_external_dependancies.TestExternalDependancies)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/build/gubbins-1.4.9/python/gubbins/tests/test_external_dependancies.py", line 90, in test_rename_final_output_fasttree
gubbins_runner.parse_and_run()
File "/build/gubbins-1.4.9/python/gubbins/common.py", line 143, in parse_and_run
if GubbinsCommon.which(FASTML_EXEC) is None:
File "/build/gubbins-1.4.9/python/gubbins/common.py", line 889, in which
executable = program.split(" ")
AttributeError: 'NoneType' object has no attribute 'split'
======================================================================
ERROR: test_rename_final_output_hybrid (test_external_dependancies.TestExternalDependancies)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/build/gubbins-1.4.9/python/gubbins/tests/test_external_dependancies.py", line 107, in test_rename_final_output_hybrid
gubbins_runner.parse_and_run()
File "/build/gubbins-1.4.9/python/gubbins/common.py", line 143, in parse_and_run
if GubbinsCommon.which(FASTML_EXEC) is None:
File "/build/gubbins-1.4.9/python/gubbins/common.py", line 889, in which
executable = program.split(" ")
AttributeError: 'NoneType' object has no attribute 'split'
======================================================================
ERROR: test_robinson_foulds_convergence (test_external_dependancies.TestExternalDependancies)
----------------------------------------------------------------------
Traceback (most recent call last):
File "/build/gubbins-1.4.9/python/gubbins/tests/test_external_dependancies.py", line 80, in test_robinson_foulds_convergence
gubbins_runner.parse_and_run()
File "/build/gubbins-1.4.9/python/gubbins/common.py", line 143, in parse_and_run
if GubbinsCommon.which(FASTML_EXEC) is None:
File "/build/gubbins-1.4.9/python/gubbins/common.py", line 889, in which
executable = program.split(" ")
AttributeError: 'NoneType' object has no attribute 'split'
----------------------------------------------------------------------
Ran 76 tests in 0.486s
FAILED (errors=10)
More information about the Debian-med-packaging
mailing list