tree f3ba890b684e12eba03776fe47806facc8667312
parent ae4079aee782740315e3c8d7cb6f19dbe1f73df8
author Marc Kupietz <kupietz@ids-mannheim.de> 1788240283 +0200
committer Marc Kupietz <kupietz@ids-mannheim.de> 1788240283 +0200

Drop the PTXQC dependency and bump to 1.3.0.9000

PTXQC was imported for exactly two small string functions, lcpCount()
and lcsCount(), both used only by queryStringToLabel(). It brought
rmzqc, jsonvalidate, seqinr and V8 with it, and V8 was the only
dependency in the whole tree that required a libv8 installation, which
made it by far the most expensive part of installing RKorAPClient on
Linux. The recursive dependency closure shrinks from 128 to 90 packages.

Both functions are pure R in PTXQC, so reimplementing them costs no
compiled code. The replacements determine the length of the common
prefix and suffix by binary search over vectorized startsWith() and
endsWith() calls, instead of comparing character by character (and, for
the suffix, reversing every string with strsplit/rev/paste first). That
makes them 10 to 65 times faster, depending on the number and length of
the strings:

                                      PTXQC      here
  10 query strings, 37 chars   prefix   183 us    16 us
                               suffix   127 us    13 us
  121 vcs, 42 chars            prefix   413 us    29 us
                               suffix  1029 us    26 us
  50 strings, 563 chars        prefix  1405 us    64 us
                               suffix  4362 us    67 us

Results are unchanged: the two functions were compared against their
PTXQC counterparts over 3020 inputs, and queryStringToLabel() over 8044
input/argument combinations, without a single difference. Empty vectors,
empty strings and the single string case (where a string is its own
prefix and suffix) behave exactly as before. The only deviation is for
NA input, where PTXQC's lcsCount() silently treats NA as the literal
string "NA"; queryStringToLabel() never reaches it in that case, because
the prefix function errors on NA in both implementations.

Since V8 is gone, and keyring no longer needs sodium either, libv8-dev
and libsodium-dev can be dropped from the Linux installation
instructions in the Readme.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Change-Id: Icad4bc76b773b1586922dd05458b82409d112932