NEWS
drugTargetInteractions 1.21.15 (2026-10-13)
- buildGtoPdbDb() now builds from the public GtoPdb bulk download files
(interactions.tsv and GtP_to_HGNC_mapping.tsv) instead of the
/services/interactions REST endpoint, which requires a registered API
key as of 2026 and returned HTTP 401 on any machine without one. No
key is needed for the default build.
- downloadGtoPdb() and buildGtoPdbDb() gained useServices and apiKey
arguments for building from GtoPdb's authenticated REST endpoint
instead; apiKey defaults to the GTOPDB_API_KEY environment variable. A
missing or rejected key is now reported as an authentication failure
rather than an opaque bfcadd() error.
- The gtp_interactions table and gtoPdbTargetAnnot() now report pubmedId,
the PubMed ID of each interaction's reference, in place of refIds,
GtoPdb's internal reference IDs. The REST route cannot supply pubmedId.
- buildGtoPdbDb() gained a paths argument for building from local copies
of the two bulk files. A small extract of both now ships in
inst/extdata, so the GtoPdb examples and vignette section run without
network access.
- A cached SQLite is reused only when its tables and columns are the
ones the installed version of the package writes. The upstream release
in the cache name is not a sufficient key on its own: BiocFileCache
persists between runs on the Bioconductor builders, so a database
built by an earlier package version survives an upgrade there and was
returned under the same name, after which the query functions failed
on columns they expect and cannot find. Renaming refIds to pubmedId is
exactly that case. A database with any other layout is now rebuilt.
Applies to the TTD, Repurposing Hub, GtoPdb and UniChem builds.
- buildGtoPdbDb() always returns an unnamed character(1), as documented;
the cached-reuse and fresh-build paths disagreed before.
- A field named through 'fields' that a source documents but a given
response does not carry is now returned as an NA column instead of
raising an error. Previously a transient outage at ChEMBL, PubChem,
DGIdb or Open Targets turned any fields = c(...) request into a hard
error, which could fail a vignette build. A name no source documents is
still rejected.
- Repurposing Hub downloads pass the supplemental CA bundle as a
per-request option rather than setting CURL_CA_BUNDLE in the session.
- getSymEnsUp() loads its EnsDb package namespace instead of attaching it
with require(), and reports a missing package.
- Added runnable examples throughout; most man pages now demonstrate
their function without network access.
drugTargetInteractions 0.99.0 (2021-01-11)
- Submitted to Bioconductor