import z from "zod"import { Tool } from "./tool"import { spawn, type ChildProcess } from "child_process"import path from "path"import os from "os"import { unlinkSync } from "fs"import { Instance } from "@/project/instance"import { OpenScience } from "@/openscience"import type { Kernel, KernelManager, KernelLanguage, KernelStartOptions, ExecuteOptions, ExecuteResult, KernelOutput,} from "@/science/kernel/types" /** * Persistent R kernel, following the same pattern as the Python kernel in * `tool/notebook.ts` and the biology kernel it generalizes. * * One long-lived `Rscript` process per sessionID evaluates cells into the global * environment, so objects/attached packages persist across `execute` calls. * stdout (print output) is captured; warnings/messages/errors are surfaced; and * base-graphics or ggplot2 plots left on the device are captured as `image/png` * where the platform's png device is available. * * Host requirement: `Rscript` on PATH (base R only — grDevices/utils are default * packages; no CRAN packages required). If Rscript is missing the tool degrades * gracefully with an install hint instead of throwing. */ // The driver runs a REPL over blocking stdin. Real newlines here are real// newlines in the R source; `\\n` sequences are escaped newlines inside R string// literals. Results are framed by section markers (no JSON dependency in base R):// a header (OK / IMG path), then the captured stdout section, then the// warnings/messages/error section. The PNG is passed back by file path and read +// base64-encoded on the TS side, avoiding any base64 package requirement.const KERNEL_SCRIPT = `run_cell <- function(code) { imgfile <- tempfile(fileext = ".png") dev_ok <- tryCatch({ grDevices::png(filename = imgfile, width = 900, height = 650, res = 110, type = "cairo") TRUE }, error = function(e) tryCatch({ grDevices::png(filename = imgfile, width = 900, height = 650, res = 110) TRUE }, error = function(e2) FALSE)) msgs <- character(0) add_msg <- function(x) msgs[[length(msgs) + 1L]] <<- x ok <- TRUE errmsg <- NULL out <- tryCatch( utils::capture.output( withCallingHandlers( { exprs <- parse(text = code) for (i in seq_along(exprs)) { wv <- withVisible(eval(exprs[[i]], envir = globalenv())) if (isTRUE(wv$visible)) print(wv$value) } }, warning = function(w) { add_msg(paste0("Warning: ", conditionMessage(w))); invokeRestart("muffleWarning") }, message = function(m) { add_msg(sub("\\n$", "", conditionMessage(m))); invokeRestart("muffleMessage") } ) ), error = function(e) { ok <<- FALSE; errmsg <<- conditionMessage(e); character(0) } ) plotted <- FALSE if (isTRUE(dev_ok)) { plotted <- tryCatch(length(grDevices::recordPlot()[[1]]) > 0L, error = function(e) FALSE) tryCatch(grDevices::dev.off(), error = function(e) NULL) } imgpath <- "" if (isTRUE(plotted) && file.exists(imgfile) && file.info(imgfile)$size > 0) { imgpath <- imgfile } else { try(unlink(imgfile), silent = TRUE) } msg_text <- paste(msgs, collapse = "\\n") if (!is.null(errmsg)) { if (nchar(msg_text) > 0L) msg_text <- paste0(msg_text, "\\n") msg_text <- paste0(msg_text, "Error: ", errmsg) } out_text <- paste(out, collapse = "\\n") cat("__OPENSCIENCE_R_RESULT_START__\\n") cat("OK:", if (ok) "1" else "0", "\\n", sep = "") cat("IMG:", imgpath, "\\n", sep = "") cat("__OPENSCIENCE_R_OUT__\\n") cat(out_text) cat("\\n__OPENSCIENCE_R_MSG__\\n") cat(msg_text) cat("\\n__OPENSCIENCE_R_END__\\n") flush(stdout())} con <- file("stdin")open(con, blocking = TRUE)cat("__OPENSCIENCE_KERNEL_READY__\\n")flush(stdout()) repeat { lines <- character(0) got_end <- FALSE repeat { l <- readLines(con, n = 1L) if (length(l) == 0L) break if (identical(l, "__OPENSCIENCE_CODE_END__")) { got_end <- TRUE; break } lines <- c(lines, l) } if (!isTRUE(got_end)) break code <- paste(lines, collapse = "\\n") tryCatch(run_cell(code), error = function(e) { cat("__OPENSCIENCE_R_RESULT_START__\\nOK:0\\nIMG:\\n__OPENSCIENCE_R_OUT__\\n\\n__OPENSCIENCE_R_MSG__\\nError: ", conditionMessage(e), "\\n__OPENSCIENCE_R_END__\\n", sep = "") flush(stdout()) })}`.trim() const READY = "__OPENSCIENCE_KERNEL_READY__"const START = "__OPENSCIENCE_R_RESULT_START__\n"const END = "\n__OPENSCIENCE_R_END__"const IDLE_MS = 30 * 60 * 1000 async function findRscript(override?: string): Promise<string | null> { const candidates = override ? [override] : ["Rscript"] for (const bin of candidates) { try { const proc = Bun.spawn([bin, "--version"], { stdout: "pipe", stderr: "pipe" }) await proc.exited if (proc.exitCode === 0) return bin } catch {} } return null} interface RawResult { ok: boolean stdout: string messages: string imgPath: string} function parseFrame(block: string): RawResult { const outMarker = "__OPENSCIENCE_R_OUT__\n" const msgMarker = "\n__OPENSCIENCE_R_MSG__\n" const outIdx = block.indexOf(outMarker) const header = outIdx === -1 ? block : block.slice(0, outIdx) const rest = outIdx === -1 ? "" : block.slice(outIdx + outMarker.length) const msgIdx = rest.indexOf(msgMarker) const stdout = msgIdx === -1 ? rest : rest.slice(0, msgIdx) const messages = msgIdx === -1 ? "" : rest.slice(msgIdx + msgMarker.length) const ok = /OK:1/.test(header) const imgMatch = header.match(/IMG:(.*)/) const imgPath = imgMatch?.[1]?.trim() ?? "" return { ok, stdout, messages, imgPath }} async function frameToResult(raw: RawResult): Promise<ExecuteResult> { const outputs: KernelOutput[] = [] if (raw.stdout) outputs.push({ type: "stream", name: "stdout", data: { "text/plain": raw.stdout } }) if (raw.imgPath) { try { const bytes = await Bun.file(raw.imgPath).arrayBuffer() const b64 = Buffer.from(bytes).toString("base64") if (b64) outputs.push({ type: "display", data: { "image/png": b64 } }) } catch {} try { unlinkSync(raw.imgPath) } catch {} } if (raw.ok && raw.messages) { outputs.push({ type: "stream", name: "stderr", data: { "text/plain": raw.messages } }) } if (!raw.ok) { outputs.push({ type: "error", error: { name: "RError", message: raw.messages || "R evaluation error" } }) } return { ok: raw.ok, outputs, stdout: raw.stdout, stderr: raw.messages, }} class RKernel implements Kernel { readonly id: string readonly language: KernelLanguage = "r" proc?: ChildProcess scriptPath?: string lastUsed = Date.now() private stderrTail = "" constructor(id: string) { this.id = id } get ready(): boolean { return !!this.proc && !this.proc.killed && this.proc.exitCode === null } async start(opts?: KernelStartOptions): Promise<void> { if (this.ready) return const bin = await findRscript(opts?.binary) if (!bin) { throw new Error( "Rscript not found. Install R (https://www.r-project.org) so `Rscript` is on PATH to use the R kernel.", ) } const scriptPath = path.join(os.tmpdir(), `openscience-rkernel-${this.id.slice(0, 8)}-${Date.now()}.R`) await Bun.write(scriptPath, KERNEL_SCRIPT) this.scriptPath = scriptPath const proc = spawn(bin, ["--vanilla", scriptPath], { cwd: opts?.cwd ?? Instance.directory, env: { ...(await OpenScience.subprocessEnv(process.env)), ...(opts?.env ?? {}) }, stdio: ["pipe", "pipe", "pipe"], }) this.proc = proc proc.stderr?.on("data", (d: Buffer) => { this.stderrTail += d.toString() if (this.stderrTail.length > 10_000) this.stderrTail = this.stderrTail.slice(-5000) }) await new Promise<void>((resolve, reject) => { const timer = setTimeout(() => { try { proc.kill() } catch {} reject(new Error(`R kernel startup timed out. stderr: ${this.stderrTail}`)) }, 20_000) let buf = "" const onData = (d: Buffer) => { buf += d.toString() if (buf.includes(READY)) { clearTimeout(timer) proc.stdout?.off("data", onData) resolve() } } proc.stdout?.on("data", onData) proc.once("error", (err) => { clearTimeout(timer) reject(err) }) proc.once("exit", (code) => { clearTimeout(timer) reject(new Error(`R kernel exited during startup (code ${code}). stderr: ${this.stderrTail}`)) }) }) } async execute(code: string, opts?: ExecuteOptions): Promise<ExecuteResult> { if (!this.ready) await this.start() const proc = this.proc! this.lastUsed = Date.now() const timeout = Math.min(Math.max(opts?.timeout ?? 120_000, 5_000), 600_000) const raw = await new Promise<RawResult>((resolve, reject) => { const timer = setTimeout(() => { cleanup() try { proc.kill() } catch {} reject(new Error(`Cell execution timed out after ${Math.round(timeout / 1000)}s`)) }, timeout) const onAbort = () => { cleanup() try { proc.kill() } catch {} reject(new Error("Execution aborted")) } let buffer = "" const onData = (d: Buffer) => { buffer += d.toString() const s = buffer.indexOf(START) const e = buffer.indexOf(END) if (s !== -1 && e !== -1 && e > s) { cleanup() resolve(parseFrame(buffer.slice(s + START.length, e))) } } const onExit = (code: number | null) => { cleanup() reject(new Error(`R kernel died during execution (exit code ${code}). stderr: ${this.stderrTail}`)) } function cleanup() { clearTimeout(timer) proc.stdout?.off("data", onData) proc.off("exit", onExit) opts?.signal?.removeEventListener("abort", onAbort) } opts?.signal?.addEventListener("abort", onAbort, { once: true }) proc.stdout?.on("data", onData) proc.once("exit", onExit) proc.stdin?.write(code + "\n__OPENSCIENCE_CODE_END__\n") }) return frameToResult(raw) } async shutdown(): Promise<void> { try { this.proc?.kill() } catch {} if (this.scriptPath) { try { unlinkSync(this.scriptPath) } catch {} this.scriptPath = undefined } }} class RKernelManager implements KernelManager { readonly language: KernelLanguage = "r" private kernels = new Map<string, RKernel>() private reapIdle() { const now = Date.now() for (const [id, k] of this.kernels) { if (now - k.lastUsed > IDLE_MS || !k.ready) { k.shutdown() this.kernels.delete(id) } } } async get(sessionID: string, opts?: KernelStartOptions): Promise<RKernel> { this.reapIdle() const existing = this.kernels.get(sessionID) if (existing && existing.ready) { existing.lastUsed = Date.now() return existing } if (existing) { await existing.shutdown() this.kernels.delete(sessionID) } const kernel = new RKernel(sessionID) await kernel.start(opts) this.kernels.set(sessionID, kernel) return kernel } async release(sessionID: string): Promise<void> { const k = this.kernels.get(sessionID) if (!k) return await k.shutdown() this.kernels.delete(sessionID) } async shutdownAll(): Promise<void> { for (const [id, k] of this.kernels) { await k.shutdown() this.kernels.delete(id) } }} /** Process-wide singleton manager. */export const rKernels = new RKernelManager() let exitHooked = falsefunction hookExit() { if (exitHooked) return exitHooked = true const cleanup = () => void rKernels.shutdownAll() process.on("exit", cleanup) process.on("SIGTERM", cleanup) process.on("SIGINT", cleanup)}hookExit() function clip(s: string, max = 30_000): string { return s.length > max ? s.slice(0, max) + "\n\n... (truncated)" : s} export const RKernelTool = Tool.define("rkernel", { description: [ "Execute R code in a persistent kernel. Objects, attached packages, and state persist across calls.", "Use instead of `bash Rscript` for analysis — no need to re-source data or reload packages between cells.", "Print output is captured; base-graphics and ggplot2 plots are captured as inline PNG images where the platform supports it.", "Requires Rscript on PATH; if R is not installed the tool reports a clear install hint.", ].join("\n"), parameters: z.object({ code: z.string().describe("R code to execute in the persistent kernel"), timeout: z.number().default(120_000).describe("Execution timeout in ms (default: 120s, max: 600s)"), }), async execute(params, ctx) { // Executes arbitrary code — same permission gate as bash. await ctx.ask({ permission: "bash", patterns: ["R (rkernel)"], always: ["Rscript*"], metadata: {}, }) // Degrade gracefully when R is not installed. const bin = await findRscript() if (!bin) { const msg = "Rscript not found. Install R from https://www.r-project.org (or `brew install r`) so `Rscript` is on PATH." ctx.metadata({ metadata: { output: msg, ok: false } }) return { title: "R kernel unavailable", output: msg, metadata: { ok: false, available: false, output: msg } } } const kernel = await rKernels.get(ctx.sessionID) const result = await kernel.execute(params.code, { timeout: params.timeout, signal: ctx.abort }) const images = result.outputs.filter((o) => o.type === "display" && o.data?.["image/png"]) const dataUrls = images.map((o) => `data:image/png;base64,${o.data!["image/png"]}`) const parts: string[] = [] if (result.stdout) parts.push(result.stdout) if (result.stderr) parts.push(`${result.ok ? "[messages]" : "[ERROR]"}\n${result.stderr}`) if (images.length) parts.push(`[figure] captured ${images.length} inline image(s)`) if (!parts.length) parts.push("(no output)") const output = clip(parts.join("\n")) ctx.metadata({ metadata: { output, ok: result.ok } }) return { title: result.ok ? "R cell" : "R cell (error)", output, metadata: { ok: result.ok, available: true, output, hasImages: images.length, ...(images.length ? { artifact: { kind: "image", data: { images: dataUrls } } } : {}), }, } },})
import z from "zod"
import { Tool } from "./tool"
import { spawn, type ChildProcess } from "child_process"
import path from "path"
import os from "os"
import { unlinkSync } from "fs"
import { Instance } from "@/project/instance"
import { OpenScience } from "@/openscience"
import type {
Kernel,
KernelManager,
KernelLanguage,
KernelStartOptions,
ExecuteOptions,
ExecuteResult,
KernelOutput,
} from "@/science/kernel/types"
/**
* Persistent R kernel, following the same pattern as the Python kernel in
* `tool/notebook.ts` and the biology kernel it generalizes.
*
* One long-lived `Rscript` process per sessionID evaluates cells into the global
* environment, so objects/attached packages persist across `execute` calls.
* stdout (print output) is captured; warnings/messages/errors are surfaced; and
* base-graphics or ggplot2 plots left on the device are captured as `image/png`
* where the platform's png device is available.
*
* Host requirement: `Rscript` on PATH (base R only — grDevices/utils are default
* packages; no CRAN packages required). If Rscript is missing the tool degrades
* gracefully with an install hint instead of throwing.
*/
// The driver runs a REPL over blocking stdin. Real newlines here are real
// newlines in the R source; `\\n` sequences are escaped newlines inside R string
// literals. Results are framed by section markers (no JSON dependency in base R):
// a header (OK / IMG path), then the captured stdout section, then the
// warnings/messages/error section. The PNG is passed back by file path and read +
// base64-encoded on the TS side, avoiding any base64 package requirement.
const KERNEL_SCRIPT = `
run_cell <- function(code) {
imgfile <- tempfile(fileext = ".png")
dev_ok <- tryCatch({
grDevices::png(filename = imgfile, width = 900, height = 650, res = 110, type = "cairo")
TRUE
}, error = function(e) tryCatch({
grDevices::png(filename = imgfile, width = 900, height = 650, res = 110)
TRUE
}, error = function(e2) FALSE))
msgs <- character(0)
add_msg <- function(x) msgs[[length(msgs) + 1L]] <<- x
ok <- TRUE
errmsg <- NULL
out <- tryCatch(
utils::capture.output(
withCallingHandlers(
{
exprs <- parse(text = code)
for (i in seq_along(exprs)) {
wv <- withVisible(eval(exprs[[i]], envir = globalenv()))
if (isTRUE(wv$visible)) print(wv$value)
}
},
warning = function(w) { add_msg(paste0("Warning: ", conditionMessage(w))); invokeRestart("muffleWarning") },
message = function(m) { add_msg(sub("\\n$", "", conditionMessage(m))); invokeRestart("muffleMessage") }
)
),
error = function(e) { ok <<- FALSE; errmsg <<- conditionMessage(e); character(0) }
)
plotted <- FALSE
if (isTRUE(dev_ok)) {
plotted <- tryCatch(length(grDevices::recordPlot()[[1]]) > 0L, error = function(e) FALSE)
tryCatch(grDevices::dev.off(), error = function(e) NULL)
}
imgpath <- ""
if (isTRUE(plotted) && file.exists(imgfile) && file.info(imgfile)$size > 0) {
imgpath <- imgfile
} else {
try(unlink(imgfile), silent = TRUE)
}
msg_text <- paste(msgs, collapse = "\\n")
if (!is.null(errmsg)) {
if (nchar(msg_text) > 0L) msg_text <- paste0(msg_text, "\\n")
msg_text <- paste0(msg_text, "Error: ", errmsg)
}
out_text <- paste(out, collapse = "\\n")
cat("__OPENSCIENCE_R_RESULT_START__\\n")
cat("OK:", if (ok) "1" else "0", "\\n", sep = "")
cat("IMG:", imgpath, "\\n", sep = "")
cat("__OPENSCIENCE_R_OUT__\\n")
cat(out_text)
cat("\\n__OPENSCIENCE_R_MSG__\\n")
cat(msg_text)
cat("\\n__OPENSCIENCE_R_END__\\n")
flush(stdout())
}
con <- file("stdin")
open(con, blocking = TRUE)
cat("__OPENSCIENCE_KERNEL_READY__\\n")
flush(stdout())
repeat {
lines <- character(0)
got_end <- FALSE
repeat {
l <- readLines(con, n = 1L)
if (length(l) == 0L) break
if (identical(l, "__OPENSCIENCE_CODE_END__")) { got_end <- TRUE; break }
lines <- c(lines, l)
}
if (!isTRUE(got_end)) break
code <- paste(lines, collapse = "\\n")
tryCatch(run_cell(code), error = function(e) {
cat("__OPENSCIENCE_R_RESULT_START__\\nOK:0\\nIMG:\\n__OPENSCIENCE_R_OUT__\\n\\n__OPENSCIENCE_R_MSG__\\nError: ", conditionMessage(e), "\\n__OPENSCIENCE_R_END__\\n", sep = "")
flush(stdout())
})
}
`.trim()
const READY = "__OPENSCIENCE_KERNEL_READY__"
const START = "__OPENSCIENCE_R_RESULT_START__\n"
const END = "\n__OPENSCIENCE_R_END__"
const IDLE_MS = 30 * 60 * 1000
async function findRscript(override?: string): Promise<string | null> {
const candidates = override ? [override] : ["Rscript"]
for (const bin of candidates) {
try {
const proc = Bun.spawn([bin, "--version"], { stdout: "pipe", stderr: "pipe" })
await proc.exited
if (proc.exitCode === 0) return bin
} catch {}
}
return null
}
interface RawResult {
ok: boolean
stdout: string
messages: string
imgPath: string
}
function parseFrame(block: string): RawResult {
const outMarker = "__OPENSCIENCE_R_OUT__\n"
const msgMarker = "\n__OPENSCIENCE_R_MSG__\n"
const outIdx = block.indexOf(outMarker)
const header = outIdx === -1 ? block : block.slice(0, outIdx)
const rest = outIdx === -1 ? "" : block.slice(outIdx + outMarker.length)
const msgIdx = rest.indexOf(msgMarker)
const stdout = msgIdx === -1 ? rest : rest.slice(0, msgIdx)
const messages = msgIdx === -1 ? "" : rest.slice(msgIdx + msgMarker.length)
const ok = /OK:1/.test(header)
const imgMatch = header.match(/IMG:(.*)/)
const imgPath = imgMatch?.[1]?.trim() ?? ""
return { ok, stdout, messages, imgPath }
}
async function frameToResult(raw: RawResult): Promise<ExecuteResult> {
const outputs: KernelOutput[] = []
if (raw.stdout) outputs.push({ type: "stream", name: "stdout", data: { "text/plain": raw.stdout } })
if (raw.imgPath) {
try {
const bytes = await Bun.file(raw.imgPath).arrayBuffer()
const b64 = Buffer.from(bytes).toString("base64")
if (b64) outputs.push({ type: "display", data: { "image/png": b64 } })
} catch {}
try {
unlinkSync(raw.imgPath)
} catch {}
}
if (raw.ok && raw.messages) {
outputs.push({ type: "stream", name: "stderr", data: { "text/plain": raw.messages } })
}
if (!raw.ok) {
outputs.push({ type: "error", error: { name: "RError", message: raw.messages || "R evaluation error" } })
}
return {
ok: raw.ok,
outputs,
stdout: raw.stdout,
stderr: raw.messages,
}
}
class RKernel implements Kernel {
readonly id: string
readonly language: KernelLanguage = "r"
proc?: ChildProcess
scriptPath?: string
lastUsed = Date.now()
private stderrTail = ""
constructor(id: string) {
this.id = id
}
get ready(): boolean {
return !!this.proc && !this.proc.killed && this.proc.exitCode === null
}
async start(opts?: KernelStartOptions): Promise<void> {
if (this.ready) return
const bin = await findRscript(opts?.binary)
if (!bin) {
throw new Error(
"Rscript not found. Install R (https://www.r-project.org) so `Rscript` is on PATH to use the R kernel.",
)
}
const scriptPath = path.join(os.tmpdir(), `openscience-rkernel-${this.id.slice(0, 8)}-${Date.now()}.R`)
await Bun.write(scriptPath, KERNEL_SCRIPT)
this.scriptPath = scriptPath
const proc = spawn(bin, ["--vanilla", scriptPath], {
cwd: opts?.cwd ?? Instance.directory,
env: { ...(await OpenScience.subprocessEnv(process.env)), ...(opts?.env ?? {}) },
stdio: ["pipe", "pipe", "pipe"],
})
this.proc = proc
proc.stderr?.on("data", (d: Buffer) => {
this.stderrTail += d.toString()
if (this.stderrTail.length > 10_000) this.stderrTail = this.stderrTail.slice(-5000)
})
await new Promise<void>((resolve, reject) => {
const timer = setTimeout(() => {
try {
proc.kill()
} catch {}
reject(new Error(`R kernel startup timed out. stderr: ${this.stderrTail}`))
}, 20_000)
let buf = ""
const onData = (d: Buffer) => {
buf += d.toString()
if (buf.includes(READY)) {
clearTimeout(timer)
proc.stdout?.off("data", onData)
resolve()
}
}
proc.stdout?.on("data", onData)
proc.once("error", (err) => {
clearTimeout(timer)
reject(err)
})
proc.once("exit", (code) => {
clearTimeout(timer)
reject(new Error(`R kernel exited during startup (code ${code}). stderr: ${this.stderrTail}`))
})
})
}
async execute(code: string, opts?: ExecuteOptions): Promise<ExecuteResult> {
if (!this.ready) await this.start()
const proc = this.proc!
this.lastUsed = Date.now()
const timeout = Math.min(Math.max(opts?.timeout ?? 120_000, 5_000), 600_000)
const raw = await new Promise<RawResult>((resolve, reject) => {
const timer = setTimeout(() => {
cleanup()
try {
proc.kill()
} catch {}
reject(new Error(`Cell execution timed out after ${Math.round(timeout / 1000)}s`))
}, timeout)
const onAbort = () => {
cleanup()
try {
proc.kill()
} catch {}
reject(new Error("Execution aborted"))
}
let buffer = ""
const onData = (d: Buffer) => {
buffer += d.toString()
const s = buffer.indexOf(START)
const e = buffer.indexOf(END)
if (s !== -1 && e !== -1 && e > s) {
cleanup()
resolve(parseFrame(buffer.slice(s + START.length, e)))
}
}
const onExit = (code: number | null) => {
cleanup()
reject(new Error(`R kernel died during execution (exit code ${code}). stderr: ${this.stderrTail}`))
}
function cleanup() {
clearTimeout(timer)
proc.stdout?.off("data", onData)
proc.off("exit", onExit)
opts?.signal?.removeEventListener("abort", onAbort)
}
opts?.signal?.addEventListener("abort", onAbort, { once: true })
proc.stdout?.on("data", onData)
proc.once("exit", onExit)
proc.stdin?.write(code + "\n__OPENSCIENCE_CODE_END__\n")
})
return frameToResult(raw)
}
async shutdown(): Promise<void> {
try {
this.proc?.kill()
} catch {}
if (this.scriptPath) {
try {
unlinkSync(this.scriptPath)
} catch {}
this.scriptPath = undefined
}
}
}
class RKernelManager implements KernelManager {
readonly language: KernelLanguage = "r"
private kernels = new Map<string, RKernel>()
private reapIdle() {
const now = Date.now()
for (const [id, k] of this.kernels) {
if (now - k.lastUsed > IDLE_MS || !k.ready) {
k.shutdown()
this.kernels.delete(id)
}
}
}
async get(sessionID: string, opts?: KernelStartOptions): Promise<RKernel> {
this.reapIdle()
const existing = this.kernels.get(sessionID)
if (existing && existing.ready) {
existing.lastUsed = Date.now()
return existing
}
if (existing) {
await existing.shutdown()
this.kernels.delete(sessionID)
}
const kernel = new RKernel(sessionID)
await kernel.start(opts)
this.kernels.set(sessionID, kernel)
return kernel
}
async release(sessionID: string): Promise<void> {
const k = this.kernels.get(sessionID)
if (!k) return
await k.shutdown()
this.kernels.delete(sessionID)
}
async shutdownAll(): Promise<void> {
for (const [id, k] of this.kernels) {
await k.shutdown()
this.kernels.delete(id)
}
}
}
/** Process-wide singleton manager. */
export const rKernels = new RKernelManager()
let exitHooked = false
function hookExit() {
if (exitHooked) return
exitHooked = true
const cleanup = () => void rKernels.shutdownAll()
process.on("exit", cleanup)
process.on("SIGTERM", cleanup)
process.on("SIGINT", cleanup)
}
hookExit()
function clip(s: string, max = 30_000): string {
return s.length > max ? s.slice(0, max) + "\n\n... (truncated)" : s
}
export const RKernelTool = Tool.define("rkernel", {
description: [
"Execute R code in a persistent kernel. Objects, attached packages, and state persist across calls.",
"Use instead of `bash Rscript` for analysis — no need to re-source data or reload packages between cells.",
"Print output is captured; base-graphics and ggplot2 plots are captured as inline PNG images where the platform supports it.",
"Requires Rscript on PATH; if R is not installed the tool reports a clear install hint.",
].join("\n"),
parameters: z.object({
code: z.string().describe("R code to execute in the persistent kernel"),
timeout: z.number().default(120_000).describe("Execution timeout in ms (default: 120s, max: 600s)"),
}),
async execute(params, ctx) {
// Executes arbitrary code — same permission gate as bash.
await ctx.ask({
permission: "bash",
patterns: ["R (rkernel)"],
always: ["Rscript*"],
metadata: {},
})
// Degrade gracefully when R is not installed.
const bin = await findRscript()
if (!bin) {
const msg =
"Rscript not found. Install R from https://www.r-project.org (or `brew install r`) so `Rscript` is on PATH."
ctx.metadata({ metadata: { output: msg, ok: false } })
return { title: "R kernel unavailable", output: msg, metadata: { ok: false, available: false, output: msg } }
}
const kernel = await rKernels.get(ctx.sessionID)
const result = await kernel.execute(params.code, { timeout: params.timeout, signal: ctx.abort })
const images = result.outputs.filter((o) => o.type === "display" && o.data?.["image/png"])
const dataUrls = images.map((o) => `data:image/png;base64,${o.data!["image/png"]}`)
const parts: string[] = []
if (result.stdout) parts.push(result.stdout)
if (result.stderr) parts.push(`${result.ok ? "[messages]" : "[ERROR]"}\n${result.stderr}`)
if (images.length) parts.push(`[figure] captured ${images.length} inline image(s)`)
if (!parts.length) parts.push("(no output)")
const output = clip(parts.join("\n"))
ctx.metadata({ metadata: { output, ok: result.ok } })
return {
title: result.ok ? "R cell" : "R cell (error)",
output,
metadata: {
ok: result.ok,
available: true,
output,
hasImages: images.length,
...(images.length ? { artifact: { kind: "image", data: { images: dataUrls } } } : {}),
},
}
},
})