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