[Debian-med-packaging] Bug#1005476: gubbins: FTBFS: SystemExit: No usable version of IQTree could be found.

Lucas Nussbaum lucas at debian.org
Sun Feb 13 07:18:10 GMT 2022 

Source: gubbins
Version: 2.4.1-4
Severity: serious
Justification: FTBFS
Tags: bookworm sid ftbfs
User: lucas at debian.org
Usertags: ftbfs-20220212 ftbfs-bookworm

Hi,

During a rebuild of all packages in sid, your package failed to build
on amd64.


Relevant part (hopefully):
> make[3]: Entering directory '/<<PKGBUILDDIR>>'
> make[3]: Nothing to be done for 'check-am'.
> make[3]: Leaving directory '/<<PKGBUILDDIR>>'
> make[2]: Leaving directory '/<<PKGBUILDDIR>>'
> cd python && \
> PATH="$PATH:../src" python3 setup.py test
> running test
> WARNING: Testing via this command is deprecated and will be removed in a future version. Users looking for a generic test entry point independent of test runner are encouraged to use tox.
> running egg_info
> creating gubbins.egg-info
> writing gubbins.egg-info/PKG-INFO
> writing dependency_links to gubbins.egg-info/dependency_links.txt
> writing entry points to gubbins.egg-info/entry_points.txt
> writing requirements to gubbins.egg-info/requires.txt
> writing top-level names to gubbins.egg-info/top_level.txt
> writing manifest file 'gubbins.egg-info/SOURCES.txt'
> reading manifest file 'gubbins.egg-info/SOURCES.txt'
> adding license file 'LICENSE.txt'
> writing manifest file 'gubbins.egg-info/SOURCES.txt'
> running build_ext
> /<<PKGBUILDDIR>>/python/gubbins/common.py:538: DeprecationWarning: invalid escape sequence \d
>   elif re.match('^\d', vcf_line) is not None:
> /<<PKGBUILDDIR>>/python/gubbins/common.py:613: DeprecationWarning: invalid escape sequence \d
>   search_obj = re.search('misc_feature    ([\d]+)..([\d]+)$', line)
> /<<PKGBUILDDIR>>/python/gubbins/common.py:620: DeprecationWarning: invalid escape sequence \=
>   search_taxa = re.search('taxa\=\"([^"]+)\"', line)
> test_concatenate_fasta_files (gubbins.tests.test_alignment_python_methods.TestAlignmentMethods) ... ok
> test_get_sequence_names_from_alignment (gubbins.tests.test_alignment_python_methods.TestAlignmentMethods) ... ok
> test_number_of_sequences_in_alignment (gubbins.tests.test_alignment_python_methods.TestAlignmentMethods) ... ok
> test_reconvert_fasta_file (gubbins.tests.test_alignment_python_methods.TestAlignmentMethods) ... ok
> test_reinsert_gaps_into_fasta_file (gubbins.tests.test_alignment_python_methods.TestAlignmentMethods) ... ok
> test_get_recombination_files (gubbins.tests.test_converging_recombinations.TestConvergingRecombinations) ... ok
> test_multiple_files_have_one_match (gubbins.tests.test_converging_recombinations.TestConvergingRecombinations) ... ok
> test_reading_embl_file (gubbins.tests.test_converging_recombinations.TestConvergingRecombinations) ... ok
> test_two_files_are_different (gubbins.tests.test_converging_recombinations.TestConvergingRecombinations) ... ok
> test_two_files_are_same (gubbins.tests.test_converging_recombinations.TestConvergingRecombinations) ... ok
> test_cleanup (gubbins.tests.test_dependencies.TestExternalDependencies) ... ok
> test_fasttree (gubbins.tests.test_dependencies.TestExternalDependencies) ... ok
> test_hybrid (gubbins.tests.test_dependencies.TestExternalDependencies) ... ok
> test_iqtree (gubbins.tests.test_dependencies.TestExternalDependencies) ... ERROR
> test_raxml (gubbins.tests.test_dependencies.TestExternalDependencies) ... ok
> test_rename_final_output (gubbins.tests.test_dependencies.TestExternalDependencies) ... ok
> test_dont_filter_input_file_with_multiple_duplicate_sequences (gubbins.tests.test_pre_process_fasta.TestPreProcessFasta) ... ok
> test_filter_out_alignments_with_too_much_missing_data (gubbins.tests.test_pre_process_fasta.TestPreProcessFasta) ... ok
> test_input_file_with_all_duplicate_sequences (gubbins.tests.test_pre_process_fasta.TestPreProcessFasta) ... ok
> test_input_file_with_multiple_duplicate_sequences (gubbins.tests.test_pre_process_fasta.TestPreProcessFasta) ... ok
> test_input_file_with_no_duplicate_sequences (gubbins.tests.test_pre_process_fasta.TestPreProcessFasta) ... ok
> test_input_file_with_one_duplicate_sequences (gubbins.tests.test_pre_process_fasta.TestPreProcessFasta) ... ok
> test_filter_out_removed_taxa_from_tree (gubbins.tests.test_tree_methods.TestTreeMethods) ... ok
> test_has_tree_been_seen_before (gubbins.tests.test_tree_methods.TestTreeMethods) ... ok
> test_internal_node_taxons_removed_when_used_as_starting_tree (gubbins.tests.test_tree_methods.TestTreeMethods) ... ok
> test_remove_internal_node_labels (gubbins.tests.test_tree_methods.TestTreeMethods) ... ok
> test_reroot_tree (gubbins.tests.test_tree_methods.TestTreeMethods) ... ok
> test_reroot_tree_at_midpoint (gubbins.tests.test_tree_methods.TestTreeMethods) ... ok
> test_reroot_tree_with_outgroup (gubbins.tests.test_tree_methods.TestTreeMethods) ... ok
> test_reroot_tree_with_outgroups (gubbins.tests.test_tree_methods.TestTreeMethods) ... ok
> test_reroot_tree_with_outgroups_all_in_different_clade (gubbins.tests.test_tree_methods.TestTreeMethods) ... ok
> test_reroot_tree_with_outgroups_all_in_one_clade (gubbins.tests.test_tree_methods.TestTreeMethods) ... ok
> test_reroot_tree_with_outgroups_all_in_one_clade_large (gubbins.tests.test_tree_methods.TestTreeMethods) ... ok
> test_reroot_tree_with_outgroups_with_two_mixed_clades (gubbins.tests.test_tree_methods.TestTreeMethods) ... ok
> test_robinson_foulds_distance (gubbins.tests.test_tree_methods.TestTreeMethods) ... ok
> test_root_tree (gubbins.tests.test_tree_methods.TestTreeMethods) ... ok
> test_split_all_non_bi_nodes (gubbins.tests.test_tree_methods.TestTreeMethods) ... ok
> test_transfer_internal_node_labels_to_tree (gubbins.tests.test_tree_methods.TestTreeMethods) ... ERROR
> test_fasttree_treebuilding_command (gubbins.tests.test_treebuilders.TestStringConstruction) ... ok
> test_iqtree_convert_raw_ancestral_states_to_fasta (gubbins.tests.test_treebuilders.TestStringConstruction) ... ERROR
> test_iqtree_replace_internal_node_label (gubbins.tests.test_treebuilders.TestStringConstruction) ... ERROR
> test_iqtree_sequence_reconstruction_command (gubbins.tests.test_treebuilders.TestStringConstruction) ... ERROR
> test_iqtree_treebuilding_command (gubbins.tests.test_treebuilders.TestStringConstruction) ... ERROR
> test_raxml_convert_raw_ancestral_states_to_fasta (gubbins.tests.test_treebuilders.TestStringConstruction) ... ok
> test_raxml_replace_internal_node_label (gubbins.tests.test_treebuilders.TestStringConstruction) ... ok
> test_raxml_select_executable_based_on_threads (gubbins.tests.test_treebuilders.TestStringConstruction) ... ok
> test_raxml_sequence_reconstruction_command (gubbins.tests.test_treebuilders.TestStringConstruction) ... ok
> test_raxml_treebuilding_command (gubbins.tests.test_treebuilders.TestStringConstruction) ... ok
> test_check_and_fix_window_size (gubbins.tests.test_utils.TestUtilities) ... ok
> test_delete_files (gubbins.tests.test_utils.TestUtilities) ... ok
> test_do_files_exist (gubbins.tests.test_utils.TestUtilities) ... ok
> test_gubbins_command (gubbins.tests.test_utils.TestUtilities) ... ok
> test_is_executable (gubbins.tests.test_utils.TestUtilities) ... ok
> test_rename_files (gubbins.tests.test_utils.TestUtilities) ... ok
> test_replace_executable (gubbins.tests.test_utils.TestUtilities) ... ok
> test_translation_of_filenames_to_final_filenames (gubbins.tests.test_utils.TestUtilities) ... ok
> test_verbose_printer (gubbins.tests.test_utils.TestUtilities) ... ok
> test_which (gubbins.tests.test_utils.TestUtilities) ... ok
> test_are_all_sequence_names_unique (gubbins.tests.test_validate_fasta_input.TestValidateInputFastaFile) ... ok
> test_are_all_sequences_the_same_length (gubbins.tests.test_validate_fasta_input.TestValidateInputFastaFile) ... ok
> test_are_there_enough_sequences_to_build_a_tree (gubbins.tests.test_validate_fasta_input.TestValidateInputFastaFile) ... ok
> test_does_each_sequence_have_a_name (gubbins.tests.test_validate_fasta_input.TestValidateInputFastaFile) ... ok
> test_does_the_sequence_have_sensible_characters (gubbins.tests.test_validate_fasta_input.TestValidateInputFastaFile) ... ok
> test_valid_fasta_file (gubbins.tests.test_validate_fasta_input.TestValidateInputFastaFile) ... ok
> test_are_all_names_unique (gubbins.tests.test_validate_starting_tree.TestValidationOfStartingTree) ... ok
> test_do_the_names_match_the_fasta_file (gubbins.tests.test_validate_starting_tree.TestValidationOfStartingTree) ... ok
> test_is_it_a_valid_newick_tree (gubbins.tests.test_validate_starting_tree.TestValidationOfStartingTree) ... ok
> 
> ======================================================================
> ERROR: test_iqtree (gubbins.tests.test_dependencies.TestExternalDependencies)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "/<<PKGBUILDDIR>>/python/gubbins/tests/test_dependencies.py", line 31, in test_iqtree
>     common.parse_and_run(parser.parse_args(["--tree_builder", "iqtree",
>   File "/<<PKGBUILDDIR>>/python/gubbins/common.py", line 82, in parse_and_run
>     tree_builder = IQTree(input_args.threads, internal_node_label_prefix, input_args.verbose)
>   File "/<<PKGBUILDDIR>>/python/gubbins/treebuilders.py", line 70, in __init__
>     sys.exit("No usable version of IQTree could be found.")
> SystemExit: No usable version of IQTree could be found.
> -------------------- >> begin captured stdout << ---------------------
> 
> --- Gubbins 2.4.1 ---
> 
> 
> 
> Checking dependencies...
> 
> --------------------- >> end captured stdout << ----------------------
> 
> ======================================================================
> ERROR: test_transfer_internal_node_labels_to_tree (gubbins.tests.test_tree_methods.TestTreeMethods)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "/<<PKGBUILDDIR>>/python/gubbins/tests/test_tree_methods.py", line 142, in test_transfer_internal_node_labels_to_tree
>     reconstructor = treebuilders.IQTree(1, "internal_")
>   File "/<<PKGBUILDDIR>>/python/gubbins/treebuilders.py", line 70, in __init__
>     sys.exit("No usable version of IQTree could be found.")
> SystemExit: No usable version of IQTree could be found.
> 
> ======================================================================
> ERROR: test_iqtree_convert_raw_ancestral_states_to_fasta (gubbins.tests.test_treebuilders.TestStringConstruction)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "/<<PKGBUILDDIR>>/python/gubbins/tests/test_treebuilders.py", line 44, in test_iqtree_convert_raw_ancestral_states_to_fasta
>     iqtree = treebuilders.IQTree(8)
>   File "/<<PKGBUILDDIR>>/python/gubbins/treebuilders.py", line 70, in __init__
>     sys.exit("No usable version of IQTree could be found.")
> SystemExit: No usable version of IQTree could be found.
> 
> ======================================================================
> ERROR: test_iqtree_replace_internal_node_label (gubbins.tests.test_treebuilders.TestStringConstruction)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "/<<PKGBUILDDIR>>/python/gubbins/tests/test_treebuilders.py", line 52, in test_iqtree_replace_internal_node_label
>     iqtree = treebuilders.IQTree(8, 'AAA')
>   File "/<<PKGBUILDDIR>>/python/gubbins/treebuilders.py", line 70, in __init__
>     sys.exit("No usable version of IQTree could be found.")
> SystemExit: No usable version of IQTree could be found.
> 
> ======================================================================
> ERROR: test_iqtree_sequence_reconstruction_command (gubbins.tests.test_treebuilders.TestStringConstruction)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "/<<PKGBUILDDIR>>/python/gubbins/tests/test_treebuilders.py", line 37, in test_iqtree_sequence_reconstruction_command
>     iqtree = treebuilders.IQTree(8)
>   File "/<<PKGBUILDDIR>>/python/gubbins/treebuilders.py", line 70, in __init__
>     sys.exit("No usable version of IQTree could be found.")
> SystemExit: No usable version of IQTree could be found.
> 
> ======================================================================
> ERROR: test_iqtree_treebuilding_command (gubbins.tests.test_treebuilders.TestStringConstruction)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "/<<PKGBUILDDIR>>/python/gubbins/tests/test_treebuilders.py", line 28, in test_iqtree_treebuilding_command
>     iqtree = treebuilders.IQTree(8)
>   File "/<<PKGBUILDDIR>>/python/gubbins/treebuilders.py", line 70, in __init__
>     sys.exit("No usable version of IQTree could be found.")
> SystemExit: No usable version of IQTree could be found.
> 
> ----------------------------------------------------------------------
> Ran 67 tests in 3.221s
> 
> FAILED (errors=6)
> Test failed: <unittest.runner.TextTestResult run=67 errors=6 failures=0>
> error: Test failed: <unittest.runner.TextTestResult run=67 errors=6 failures=0>
> make[1]: *** [debian/rules:25: override_dh_auto_test] Error 1


The full build log is available from:
http://qa-logs.debian.net/2022/02/12/gubbins_2.4.1-4_unstable.log

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 marking 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.

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