Control: tag -1 upstream Control: forwarded -1 https://github.com/bioperl/Bio-DB-NCBIHelper/issues/6
Hi Aaron, I have been looking in the issue below in the package libbio-db-ncbihelper-perl. If I understood correctly, the main point of the package is to rely on resources made available on the Internet. On Sun, 21 Feb 2021 14:05:39 +0100 gregor herrmann <gre...@debian.org> wrote: > not ok 44 > > # Failed test at t/Taxonomy.t line 102. > # got: 'Actinomycetia' > # expected: 'Actinobacteria' For reference, I see along those lines: 101 ok $n = $db->get_Taxonomy_Node('1760'); 102 is $n->scientific_name, 'Actinobacteria'; I would think the test 44 in t/Taxonomy.t is fooled following an update in the resource the package fetches on the Internet (https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi if I trust the package description). Hence I would be tempted to think the kind of bacteria is not necessarily that important, but that a character string could be fetched. But I'm not at all a specialist of the field so prefer referring to your expert view. (and I am also concerned that the previous tests rely on a perhaps magic index to refer to human genome, but maybe it is a "well known index".) In any case, I though upstream would be interested, so I took the liberty to open an issue in their VCS[0]. [0] https://github.com/bioperl/Bio-DB-NCBIHelper/issues/6 Gregor, Many Thanks for having spotted this in the first place! As the purpose of the package is to fetch resources on the web, I did something better described by the following commit[1]. [1] https://salsa.debian.org/med-team/libbio-db-ncbihelper-perl/-/commit/bde35697e319417ae17367d51aaa868c43e1715d It looked to me like the most sensible thing to do, since the entire set of tests part of smoke are otherwise skipped. I am not sure if there were more simple ways to approach that. I am concerned that all test are skipped and considered valid. Here is what I see if I smoke-env NO_NETWORK_TESTING=1: autopkgtest [18:43:55]: test autodep8-perl-build-deps: /usr/share/pkg-perl-autopkgtest/runner build-deps autopkgtest [18:43:55]: test autodep8-perl-build-deps: [----------------------- t/EntrezGene.t ..... skipped: NO_NETWORK_TESTING t/GenBank.t ........ skipped: NO_NETWORK_TESTING t/GenPept.t ........ skipped: NO_NETWORK_TESTING t/Query-Genbank.t .. skipped: NO_NETWORK_TESTING t/RefSeq.t ......... skipped: NO_NETWORK_TESTING t/Taxonomy.t ....... skipped: NO_NETWORK_TESTING Files=6, Tests=0, 0 wallclock secs ( 0.02 usr 0.00 sys + 0.07 cusr 0.00 csys = 0.09 CPU) Result: NOTESTS autopkgtest [18:43:55]: test autodep8-perl-build-deps: -----------------------] autopkgtest [18:43:55]: test autodep8-perl-build-deps: - - - - - - - - - - results - - - - - - - - - - autodep8-perl-build-deps PASS I'm sorry, I'm not sure that was that much of a Low Hanging Fruit, but that might do for this month's session hopefully. :) Thanks for your thoughts, -- Étienne Mollier <etienne.moll...@mailoo.org> Fingerprint: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da Sent from /dev/pts/8, please excuse my verbosity.
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