cleanup for CRAN

[egenn]

No description provided.

[gemini-code-assist]

Code Review

This pull request updates the package to version 0.8.1, adds API documentation links, and introduces a verbosity parameter to the available_tools function. It also modifies the security logging logic to use getOption with a temporary file fallback to satisfy CRAN policies. A high-severity bug was identified in the Agent's generate method, where the removal of the default logfile fallback could result in a NULL value being passed to the logging function, causing a crash during security incident reporting.

[Copilot]

Pull request overview

Updates the rtemis.llm package for CRAN readiness by tightening documentation, metadata, and defaults (notably around tool listings and security/audit logging) while fixing minor example syntax issues.

Changes:

• Refresh package metadata (version/date/Description URLs) and add bug-report links.
• Make available_tools() support a verbosity argument and document it.
• Adjust security logging defaults to avoid writing into the working directory, and clean up examples/docs.

Reviewed changes

Copilot reviewed 12 out of 12 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
r/man/rtemis.llm-package.Rd	Adds GitHub issues link in “Useful links”.
r/man/responses.Rd	Fixes example call syntax (adds missing comma).
r/man/reasoning.Rd	Fixes example call syntax (adds missing comma).
r/man/llmapply.Rd	Fixes example call syntax (adds missing comma).
r/man/available_tools.Rd	Documents new verbosity parameter and updated return wording.
r/R/zzz.R	Cleans comments and changes startup message emoji.
r/R/utils_security.R	Moves incident log default to getOption(..., tempfile(...)) to satisfy CRAN expectations.
r/R/map.R	Fixes roxygen example call syntax (adds missing comma).
r/R/07_Agent.R	Updates logfile documentation and changes logfile resolution in generate.Agent.
r/R/00_init.R	Implements available_tools(verbosity = 1L) behavior (conditional printing).
r/DESCRIPTION	Bumps version/date and adds explicit endpoint URLs in Description.
Makefile	Ensures document-r runs formatting first.

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[Copilot]

Because generate.Agent passes logfile = logfile explicitly, this default only applies when the argument is omitted; if logfile is explicitly NULL, the fallback here won’t run and incident logging will write to stdout instead of a file. To make logging robust, defensively coerce NULL to the getOption/tempfile fallback inside the function body (or avoid passing NULL from the caller).

Suggested change

	) {
	) {
	if (is.null(logfile)) {
	logfile <- getOption(
	"rtemis_security_logfile",
	tempfile("rtemis_security_log_", fileext = ".jsonl")
	)
	}

[Copilot]

The docstring says the package defaults the agent logfile to getOption("rtemis_security_logfile", tempfile(...)) when logfile is NULL, but the Agent constructor currently stores logfile = NULL without resolving it. Either implement this default resolution (e.g., in the constructor or generate path) or adjust the documentation so it matches actual behavior.

Suggested change

	#' @field logfile Optional character: Path to the agent's security log. Important! If NULL, the package
	#' defaults to
	#' `getOption("rtemis_security_logfile", tempfile("rtemis_security_log_", fileext = ".jsonl"))` to
	#' satisfy CRAN policy. It is important to set it to a non-temporary location that will persist
	#' and you can access. Otherwise, security incidents may be missed. Can be overridden per call
	#' on [generate].
	#' @field logfile Optional character: Path to the agent's security log. If NULL, no agent-level
	#' logfile path is stored on the object. For persistent security logging, set this to a
	#' non-temporary location that will persist and you can access. Otherwise, security incidents
	#' may be missed. Can be overridden per call on [generate].