Your message dated Thu, 08 Jul 2021 22:03:29 +0000 with message-id <e1m1c7f-000cub...@fasolo.debian.org> and subject line Bug#990741: fixed in ncbi-entrez-direct 14.6.20210224+dfsg-4 has caused the Debian Bug report #990741, regarding ncbi-entrez-direct: efetch and einfo wrappers warn about some supported options 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.) -- 990741: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=990741 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Package: ncbi-entrez-direct Version: 14.6.20210224+dfsg-3+b2 Severity: serious Justification: maintainer prerogative In the course of checking whether https://bugs.launchpad.net/ubuntu/+source/ncbi-blast+/+bug/1934402 affects ncbi-blast+ in testing and unstable, I observed -- *only* -- a different issue: the efetch wrapper Debian deploys to avoid needing a formal conflict with acedb-other doesn't account for NCBI efetch's undocumented -docsum shorthand, which get_species_taxids uses. The wrapper's heuristics conclude that the NCBI implementation is probably in order, but it's a close call, and somewhat noisy: $ get_species_taxids -n 'Homo sapiens' Launching NCBI efetch rather than AceDB efetch despite misgivings, due to more severe misgivings about AceDB syntax compatibility. If you meant to run AceDB efetch, please explicitly run it via efetch.acedb. AceDB misgivings (1 major, 2 minor): -mode (major) -db (minor) taxonomy json (minor) NCBI misgivings (1 major, 0 minor): -docsum (major) WARNING: Redundant -db 'taxonomy' argument Taxid : 9606 rank : species division : primates scientific name : Homo sapiens common name : human 1 matche(s) found. I could certainly patch get_species_taxids, but would prefer to adjust ncbi-entrez-direct's efetch wrapper, since -docsum is legitimate, just undocumented. A full sweep revealed some other gaps in both this wrapper and the analogous einfo wrapper, mostly around other undocumented options. AFAICT, these arguments are all at *best* unlikely for these commands' homonyms; for instance, -docsum could only correspond to -d <dbfile> Specify database file (avoid this) with an inline value "ocsum"(!) -- System Information: Debian Release: 11.0 APT prefers testing-security APT policy: (500, 'testing-security'), (500, 'testing-debug'), (500, 'testing'), (500, 'stable'), (300, 'unstable-debug'), (300, 'unstable') Architecture: amd64 (x86_64) Foreign Architectures: i386, x32 Kernel: Linux 5.10.0-7-amd64 (SMP w/8 CPU threads) Kernel taint flags: TAINT_PROPRIETARY_MODULE, TAINT_OOT_MODULE, TAINT_UNSIGNED_MODULE Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8), LANGUAGE not set Shell: /bin/sh linked to /bin/dash Init: systemd (via /run/systemd/system) LSM: AppArmor: enabled Versions of packages ncbi-entrez-direct depends on: ii curl 7.74.0-1.3 ii libc6 2.31-12 ii libwww-perl 6.52-1 ii libxml-simple-perl 2.25-1 ii perl 5.32.1-4 ii wget 1.21-1+b1 ncbi-entrez-direct recommends no packages. Versions of packages ncbi-entrez-direct suggests: ii curl 7.74.0-1.3 ii libxml2-utils 2.9.10+dfsg-6.7 ii python3 3.9.2-3 -- no debconf information
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--- Begin Message ---Source: ncbi-entrez-direct Source-Version: 14.6.20210224+dfsg-4 Done: Aaron M. Ucko <u...@debian.org> We believe that the bug you reported is fixed in the latest version of ncbi-entrez-direct, 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 990...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Aaron M. Ucko <u...@debian.org> (supplier of updated ncbi-entrez-direct 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: SHA512 Format: 1.8 Date: Thu, 08 Jul 2021 17:36:20 -0400 Source: ncbi-entrez-direct Architecture: source Version: 14.6.20210224+dfsg-4 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Aaron M. Ucko <u...@debian.org> Closes: 990741 Changes: ncbi-entrez-direct (14.6.20210224+dfsg-4) unstable; urgency=medium . * debian/{efetch,einfo}: Refresh %ncbi_supported, taking care to include undocumented options. (In particular, ncbi-blast+'s get_species_taxids uses efetch's undocumented -docsum shorthand.) (Closes: #990741.) Checksums-Sha1: 52c7edd03f8304f4a91c5b9fb58f3acc204503ba 2597 ncbi-entrez-direct_14.6.20210224+dfsg-4.dsc dc162955ed851785398138622fb6c4d5c534ef8e 40992 ncbi-entrez-direct_14.6.20210224+dfsg-4.debian.tar.xz Checksums-Sha256: 52c3e8a352f69e501869d68f281efd3163267c751c1fea4e4c13ac0a2b0b8e02 2597 ncbi-entrez-direct_14.6.20210224+dfsg-4.dsc ab7bd55f1c032eb9d7ffef34b11e560b5a9bc850978048f0d5c857f4a18f0de1 40992 ncbi-entrez-direct_14.6.20210224+dfsg-4.debian.tar.xz Files: 41114366c49a071e6e2d45face81c9a2 2597 science optional ncbi-entrez-direct_14.6.20210224+dfsg-4.dsc 92554d03442ec8562ecc0de5e1183f97 40992 science optional ncbi-entrez-direct_14.6.20210224+dfsg-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEfDq5z9IwvTDdAJxZHnCRsfFKZKIFAmDncOoACgkQHnCRsfFK ZKKoEw//WT3211coaS7RwAcBrrnyjQ/OsgCWaJZKESfiAorHtHx+0nIQKpW1HJHh nNjzJgm1qHr9KDlnrIqNwyrLde7vnW1MNQYcDPoHH9TDpAbC9WUN/zfo1PdBe/s+ biBqYsHHi6g0AUFORWG3hlibA66L8T+Vvu8eV93ueJkW4/+5kNLMPa1p8gbWZ9+a g/wPdaz0YkdEGePQtvF1p2iy9nZqy8geaZ+29D6Z7JLnRJGItC0SvZLIv12cfk38 R3leglJTeMA0w1+bb440Rh74Dax1KjwzR6W5IYkND5nCEmexyrDRP4hoBlSNqOpg TR9ld9ZFoEr49WA8kBsCObSAAx1vjvXF7fHEw2K+SVZGgVujhJvX3ED7wlUv4R/J ObBi2fZn8U20RsVCq6M0edhLlGxmHYUskkU6+7jOPkPIeJ8+/Tnp3sDpNDwHUzsW 52zNDKx2ugBbrTqvdk0NzHGDm40vo2Ysn/jORsG+6WKFEGAVHZXtk3wVxl4ZrJVe QLFEj0oiutO7UNCRWDMWALwnzcJ2Ks1mjYXp/jT/QfUpcDa8e1AAzTdT12J6o7ke +FLwJiOy5zL8XISWOB2MvqglNmDkPBhL8qr2Z9gkyr8ffjfLcpz/rVrvXgKzyTma tXfB+JnWNhw0Ig6TJzxjevFySZBKjIw+fdNUWGNmSrBCc8XmydQ= =9Nb1 -----END PGP SIGNATURE-----
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