Release dsROCrate 0.2.4 · FederatedMethods/dsROCrate

Bug fixes

Fixed safe_output() reading Opal log timestamps in the local time zone
instead of UTC. Opal returns UTC timestamps in ISO 8601 format (e.g.,
2026-10-13T04:26:14.076Z); they are now parsed as UTC, including fractional
seconds and Z/+hh:mm offsets. Previously, on machines whose time zone was
not UTC, the logs_from/logs_to window could drop recent log entries (or
include old ones).
Fixed safe_project() overwriting the user attribute stored in the returned
RO-Crate: a loop variable shadowed the user argument.
Fixed table lineage links (isBasedOn) between tables and resources being
written to rocrate$graph instead of rocrate$`@graph`, so they are now
recorded in the RO-Crate graph.
Fixed the symbol registry lookup so it always returns a single row when several
symbols share the same created_at timestamp (dplyr::slice_max() now uses
with_ties = FALSE).
report() (path method) now forwards max_line_length and ... to the
RO-Crate method; previously max_line_length was silently ignored.
The error shown when the report directory does not exist now suggests
mkdir -p (was mkdir -r).
audit() and extract_safe_project() (opal method) now read project names
with $name, so they work whether backend_projects() returns a data frame
or a tibble.

Timestamps written by safe_output() (the audit log tibble, the
_mappings.csv file, and as.data.frame() of safe_call objects) are now
ISO 8601 in UTC with a trailing Z (e.g., 2026-07-01T10:00:00Z). Code that
compares these values as strings will need to be updated.
safe_output(): logs_from and logs_to accept POSIXct values or
date-time strings, with or without a Z/UTC offset. Strings without an offset
are interpreted as UTC, and Inf/-Inf still mean "no limit".
report() for a list of RO-Crates no longer has the unused study_name
argument.

Split the getting-started vignette into three. getting-started now covers
connecting, check_permissions(), audit() and report(); the new
building-crates vignette shows the step-by-step workflow with init() and
the safe_*() functions (including saving the RO-Crate); and the new
auditing-studies vignette shows how to audit several servers as one study.
audit-permissions vignette: explains how the permission check works, lists
the common error messages with their likely causes, and gives the minimum
Opal version (5.7.2).
deploy-local-datashield-server-with-opal vignette: corrected the clone
directory, added the demo accounts, the Opal version requirement, an audit
example and instructions to stop the server, and removed unused code.
Vignettes now only run their examples when the public Opal demo server can be
reached; otherwise the code is shown but not evaluated.
README: added the supported-backend and requirements table, a guide on which
function to use, check_permissions() in the quick start, and a list of all
vignettes.
Reference documentation: the description of ... is now defined once
(shared_params) and inherited by the functions, the documented default of
user_id_suffix was corrected ("#person:"), the Opal-specific wording was
removed from the profile argument, and stray formatting in the audit()
documentation was fixed.
Updated spell-check WORDLIST.

Added parse_utc(), parse_utc_limit(), format_utc() and fmt_limit()
(utils-date.R) so that all timestamps are parsed and formatted the same way.
They replace is_valid_posixct().
backend_logs() (opal method) now returns @timestamp as POSIXct (UTC) and
suppresses the progress messages printed by opalr. Other backends are
expected to return POSIXct timestamps.
Added tests for parse_utc(), run under a non-UTC time zone.
safe_output() tests covering RESOLVE/ASSIGN operations now set logs_from
and logs_to explicitly, so they no longer depend on the time they are run.
Test mocks now use type = "group" for group permissions, matching the values
returned by Opal, and the report() tests no longer pass study_name.
Rebuilt the vignettes against the current Opal demo server (6.0.1).