Your message dated Sun, 13 Feb 2022 14:48:56 +0000
with message-id <e1njgbm-0000ek...@fasolo.debian.org>
and subject line Bug#1005476: fixed in gubbins 2.4.1-5
has caused the Debian Bug report #1005476,
regarding gubbins: FTBFS: SystemExit: No usable version of IQTree could be
found.
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)
--
1005476: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1005476
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: gubbins
Version: 2.4.1-4
Severity: serious
Justification: FTBFS
Tags: bookworm sid ftbfs
User: lu...@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.
--- End Message ---
--- Begin Message ---
Source: gubbins
Source-Version: 2.4.1-5
Done: Andreas Tille <ti...@debian.org>
We believe that the bug you reported is fixed in the latest version of
gubbins, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 1005...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <ti...@debian.org> (supplier of updated gubbins package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Sun, 13 Feb 2022 15:17:59 +0100
Source: gubbins
Architecture: source
Version: 2.4.1-5
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Andreas Tille <ti...@debian.org>
Closes: 1005476
Changes:
gubbins (2.4.1-5) unstable; urgency=medium
.
* Team Upload.
[ Andreas Tille ]
* New upstream version
* Standards-Version: 4.6.0 (routine-update)
* Build-Depends: python3-scipy <!nocheck>, python3-multiprocess <!nocheck>,
python3-wheel <!nocheck>
* Remove trailing whitespace in debian/changelog (routine-update)
* Adapt test to iqtree2
Closes: #1005476
.
[ Étienne Mollier ]
* d/control: update uploader address
* d/watch: bump to uscan version 4 and fix broken link to github
.
[ Nilesh Patra ]
* Switch from nosetest -> pytest
Checksums-Sha1:
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89fcfa7af8f8f9969ced267c183a16ccc4b845f1 7744 gubbins_2.4.1-5.debian.tar.xz
d3c5d5c26b7eb4fdd48848cb4e4db4f7f17f0aae 9726 gubbins_2.4.1-5_amd64.buildinfo
Checksums-Sha256:
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gubbins_2.4.1-5.dsc
75930a6941347dbbff34c11efcb00d10f5afee3c7e549e5c39a6edeca4bfa45c 7744
gubbins_2.4.1-5.debian.tar.xz
91e5b8c0ec3a8cb806ba537ebfec36c05d015e29a30c466f65a07d53410ff89e 9726
gubbins_2.4.1-5_amd64.buildinfo
Files:
7bf608c86a4c32c74a3c3ed2926a7287 2269 science optional gubbins_2.4.1-5.dsc
e28ed05f8817dfe3746f39168d2fdd21 7744 science optional
gubbins_2.4.1-5.debian.tar.xz
0b63246a48c1ad9a5d303d3b14769168 9726 science optional
gubbins_2.4.1-5_amd64.buildinfo
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--- End Message ---
