@eagleoutice/flowr 2.0.11 → 2.0.12

package/README.md

@@ -1,23 +1,56 @@
-[![flowR logo](https://raw.githubusercontent.com/wiki/Code-Inspect/flowr/img/flowR.png)](https://github.com/Code-Inspect/flowr/wiki)\
-[![QA (and potentially deploy)](https://github.com/Code-Inspect/flowr/actions/workflows/qa.yaml/badge.svg)](https://github.com/Code-Inspect/flowr/actions/workflows/qa.yaml) [![codecov](https://codecov.io/gh/Code-Inspect/flowr/graph/badge.svg)](https://codecov.io/gh/Code-Inspect/flowr) [![Docker Image Version (latest semver)](https://img.shields.io/docker/v/eagleoutice/flowr?logo=docker&logoColor=white&label=dockerhub)](https://hub.docker.com/r/eagleoutice/flowr) [![latest tag](https://badgen.net/github/tag/Code-Inspect/flowr?label=latest&color=purple)](https://github.com/Code-Inspect/flowr/releases/latest) [![Marketplace](https://badgen.net/vs-marketplace/v/code-inspect.vscode-flowr)](https://marketplace.visualstudio.com/items?itemName=code-inspect.vscode-flowr)
+[![flowR logo](https://raw.githubusercontent.com/wiki/flowr-analysis/flowr/img/flowR.png)](https://github.com/flowr-analysis/flowr/wiki)\
+[![QA (and potentially deploy)](https://github.com/flowr-analysis/flowr/actions/workflows/qa.yaml/badge.svg)](https://github.com/flowr-analysis/flowr/actions/workflows/qa.yaml) [![codecov](https://codecov.io/gh/flowr-analysis/flowr/graph/badge.svg)](https://codecov.io/gh/flowr-analysis/flowr) [![Docker Image Version (latest semver)](https://img.shields.io/docker/v/eagleoutice/flowr?logo=docker&logoColor=white&label=dockerhub)](https://hub.docker.com/r/eagleoutice/flowr) [![latest tag](https://badgen.net/github/tag/flowr-analysis/flowr?label=latest&color=purple)](https://github.com/flowr-analysis/flowr/releases/latest) [![Marketplace](https://badgen.net/vs-marketplace/v/code-inspect.vscode-flowr)](https://marketplace.visualstudio.com/items?itemName=code-inspect.vscode-flowr) [![All Contributors](https://img.shields.io/github/all-contributors/flowr-analysis/flowr)](#contributors)
 
 
-*flowR* is a static [dataflow analyzer](https://en.wikipedia.org/wiki/Data-flow_analysis) and [program slicer](https://github.com/Code-Inspect/flowr/wiki/Terminology#program-slice) for the [*R*](https://www.r-project.org/) programming language (currently tested for versions `4.x` and `3.6.x`). It is available as a [Visual Studio Code extension](https://marketplace.visualstudio.com/items?itemName=code-inspect.vscode-flowr) and as a [docker image](https://hub.docker.com/r/eagleoutice/flowr).
+*flowR* is a static [dataflow analyzer](https://en.wikipedia.org/wiki/Data-flow_analysis) and [program slicer](https://github.com/flowr-analysis/flowr/wiki/Terminology#program-slice) for the [*R*](https://www.r-project.org/) programming language (currently tested for versions `4.x` and `3.6.x`). It is available as a [Visual Studio Code extension](https://marketplace.visualstudio.com/items?itemName=code-inspect.vscode-flowr) and as a [docker image](https://hub.docker.com/r/eagleoutice/flowr).
 
 ## ⭐ Getting Started
 
-To get started with _flowR_, please check out the [Overview](https://github.com/Code-Inspect/flowr/wiki/Overview). The [Setup](https://github.com/Code-Inspect/flowr/wiki/Setup) wiki page explains how you can download and setup _flowR_ on your system. For Visual Studio Code, please see the [marketplace entry](https://marketplace.visualstudio.com/items?itemName=code-inspect.vscode-flowr). With docker 🐳️, the following line should be enough (and drop you directly into the REPL):
+To get started with _flowR_, please check out the [Overview](https://github.com/flowr-analysis/flowr/wiki/Overview). The [Setup](https://github.com/flowr-analysis/flowr/wiki/Setup) wiki page explains how you can download and setup _flowR_ on your system. For Visual Studio Code, please see the [marketplace entry](https://marketplace.visualstudio.com/items?itemName=code-inspect.vscode-flowr). With docker 🐳️, the following line should be enough (and drop you directly into the REPL):
 
 ```shell
 docker run -it --rm eagleoutice/flowr
  ```
 
-
 ## 📜 More Information
 
-For more details, see the [wiki pages](https://github.com/Code-Inspect/flowr/wiki) and the deployed [code documentation](https://code-inspect.github.io/flowr/doc/).
-
-We welcome every contribution! Please check out the [contributing guidelines](https://github.com/Code-Inspect/flowr/tree/main/.github/CONTRIBUTING.md) for more information.
+For more details, see the [wiki pages](https://github.com/flowr-analysis/flowr/wiki) and the deployed [code documentation](https://flowr-analysis.github.io/flowr/doc/).
+
+## 🚀 Contributing
+
+We welcome every contribution! Please check out the [contributing guidelines](https://github.com/flowr-analysis/flowr/tree/main/.github/CONTRIBUTING.md) for more information.
+
+### Contributors
+
+<!-- ALL-CONTRIBUTORS-LIST:START - Do not remove or modify this section -->
+<!--suppress ALL -->
+<!-- prettier-ignore-start -->
+<!-- markdownlint-disable -->
+<table>
+  <tbody>
+    <tr>
+      <td align="center" valign="top" width="14.28%"><a href="https://github.com/EagleoutIce"><img src="https://avatars.githubusercontent.com/u/9303573?v=4?s=100" width="100px;" alt="Florian Sihler"/><br /><sub><b>Florian Sihler</b></sub></a><br /><a href="https://github.com/flowr-analysis/flowr/commits?author=EagleoutIce" title="Code">💻</a> <a href="#ideas-EagleoutIce" title="Ideas, Planning, & Feedback">🤔</a> <a href="#maintenance-EagleoutIce" title="Maintenance">🚧</a> <a href="#projectManagement-EagleoutIce" title="Project Management">📆</a> <a href="#research-EagleoutIce" title="Research">🔬</a> <a href="https://github.com/flowr-analysis/flowr/commits?author=EagleoutIce" title="Tests">⚠️</a> <a href="#talk-EagleoutIce" title="Talks">📢</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://ellpeck.de/"><img src="https://avatars.githubusercontent.com/u/5741138?v=4?s=100" width="100px;" alt="Ell"/><br /><sub><b>Ell</b></sub></a><br /><a href="https://github.com/flowr-analysis/flowr/commits?author=Ellpeck" title="Code">💻</a> <a href="#maintenance-Ellpeck" title="Maintenance">🚧</a> <a href="https://github.com/flowr-analysis/flowr/commits?author=Ellpeck" title="Tests">⚠️</a> <a href="#plugin-Ellpeck" title="Plugin/utility libraries">🔌</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://lukas.pietzschmann.org/"><img src="https://avatars.githubusercontent.com/u/49213919?v=4?s=100" width="100px;" alt="Lukas Pietzschmann"/><br /><sub><b>Lukas Pietzschmann</b></sub></a><br /><a href="https://github.com/flowr-analysis/flowr/commits?author=LukasPietzschmann" title="Code">💻</a> <a href="https://github.com/flowr-analysis/flowr/commits?author=LukasPietzschmann" title="Tests">⚠️</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://github.com/bjthehun"><img src="https://avatars.githubusercontent.com/u/38729215?v=4?s=100" width="100px;" alt="Benedikt Jutz"/><br /><sub><b>Benedikt Jutz</b></sub></a><br /><a href="https://github.com/flowr-analysis/flowr/commits?author=bjthehun" title="Code">💻</a> <a href="https://github.com/flowr-analysis/flowr/commits?author=bjthehun" title="Tests">⚠️</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://github.com/Core5563"><img src="https://avatars.githubusercontent.com/u/140061253?v=4?s=100" width="100px;" alt="Core5563"/><br /><sub><b>Core5563</b></sub></a><br /><a href="https://github.com/flowr-analysis/flowr/commits?author=Core5563" title="Code">💻</a> <a href="https://github.com/flowr-analysis/flowr/commits?author=Core5563" title="Tests">⚠️</a></td>
+      <td align="center" valign="top" width="14.28%"><a href="https://github.com/Ehcsan"><img src="https://avatars.githubusercontent.com/u/68707578?v=4?s=100" width="100px;" alt="Ehcsan"/><br /><sub><b>Ehcsan</b></sub></a><br /><a href="https://github.com/flowr-analysis/flowr/commits?author=Ehcsan" title="Code">💻</a> <a href="https://github.com/flowr-analysis/flowr/commits?author=Ehcsan" title="Tests">⚠️</a></td>
+    </tr>
+  </tbody>
+  <tfoot>
+    <tr>
+      <td align="center" size="13px" colspan="7">
+        <img src="https://raw.githubusercontent.com/all-contributors/all-contributors-cli/1b8533af435da9854653492b1327a23a4dbd0a10/assets/logo-small.svg">
+          <a href="https://all-contributors.js.org/docs/en/bot/usage">Add your contributions</a>
+        </img>
+      </td>
+    </tr>
+  </tfoot>
+</table>
+
+<!-- markdownlint-restore -->
+<!-- prettier-ignore-end -->
+<!-- ALL-CONTRIBUTORS-LIST:END -->
 
 ----
 

package/abstract-interpretation/domain.d.ts

@@ -5,23 +5,53 @@ interface IntervalBound {
 export declare class Interval {
     readonly min: IntervalBound;
     readonly max: IntervalBound;
+    /**
+     * Build a new interval from the given bounds.
+     * If the interval represents a scalar, the min and max bounds should be equal, as well as their inclusivity.
+     * @param min - The minimum bound of the interval.
+     * @param max - The maximum bound of the interval.
+     */
     constructor(min: IntervalBound, max: IntervalBound);
     toString(): string;
 }
+/**
+ * A domain represents a set of intervals describing a range of possible values a variable may hold.
+ * In the future we may want to extend this to support more complex types.
+ */
 export declare class Domain {
+    /** set of intervals to hold */
     private readonly _intervals;
     private constructor();
     static bottom(): Domain;
-    static fromIntervals(intervals: Interval[] | Set<Interval>): Domain;
+    static fromIntervals(intervals: readonly Interval[] | ReadonlySet<Interval>): Domain;
     static fromScalar(n: number): Domain;
     get intervals(): Set<Interval>;
     private set intervals(value);
     addInterval(interval: Interval): void;
     toString(): string;
 }
+/**
+ * Returns true if the given intervals overlap, checking for inclusivity.
+ */
 export declare function doIntervalsOverlap(interval1: Interval, interval2: Interval): boolean;
-export declare function unifyDomains(domains: Domain[]): Domain;
-export declare function unifyOverlappingIntervals(intervals: Interval[]): Interval[];
+/**
+ * Unifies the given domains by creating a new domain that contains all values from all given domains.
+ */
+export declare function unifyDomains(domains: readonly Domain[]): Domain;
+/**
+ * Unify all intervals which overlap with each other to one.
+ */
+export declare function unifyOverlappingIntervals(intervals: readonly Interval[]): Interval[];
+/**
+ * Returns domain1 + domain2, mapping the inclusivity.
+ *
+ * @see subtractDomains
+ */
 export declare function addDomains(domain1: Domain, domain2: Domain): Domain;
+/**
+ * Returns domain1 - domain2, mapping the inclusivity.
+ *
+ * @see addDomains
+ */
 export declare function subtractDomains(domain1: Domain, domain2: Domain): Domain;
 export {};

package/abstract-interpretation/domain.js

@@ -5,6 +5,12 @@ const assert_1 = require("../util/assert");
 class Interval {
     min;
     max;
+    /**
+     * Build a new interval from the given bounds.
+     * If the interval represents a scalar, the min and max bounds should be equal, as well as their inclusivity.
+     * @param min - The minimum bound of the interval.
+     * @param max - The maximum bound of the interval.
+     */
     constructor(min, max) {
         this.min = min;
         this.max = max;
@@ -16,7 +22,12 @@ class Interval {
     }
 }
 exports.Interval = Interval;
+/**
+ * A domain represents a set of intervals describing a range of possible values a variable may hold.
+ * In the future we may want to extend this to support more complex types.
+ */
 class Domain {
+    /** set of intervals to hold */
     _intervals;
     constructor(intervals = []) {
         this._intervals = new Set(unifyOverlappingIntervals(intervals));
@@ -67,6 +78,9 @@ function compareIntervalsByTheirMinimum(interval1, interval2) {
 function compareIntervalsByTheirMaximum(interval1, interval2) {
     return compareIntervals(1 /* CompareType.Max */, interval1.max, interval2.max);
 }
+/**
+ * Returns true if the given intervals overlap, checking for inclusivity.
+ */
 function doIntervalsOverlap(interval1, interval2) {
     const diff1 = compareIntervals(2 /* CompareType.IgnoreInclusivity */, interval1.max, interval2.min);
     const diff2 = compareIntervals(2 /* CompareType.IgnoreInclusivity */, interval2.max, interval1.min);
@@ -84,16 +98,22 @@ function doIntervalsOverlap(interval1, interval2) {
     return true;
 }
 exports.doIntervalsOverlap = doIntervalsOverlap;
+/**
+ * Unifies the given domains by creating a new domain that contains all values from all given domains.
+ */
 function unifyDomains(domains) {
     const unifiedIntervals = unifyOverlappingIntervals(domains.flatMap(domain => Array.from(domain.intervals)));
     return Domain.fromIntervals(unifiedIntervals);
 }
 exports.unifyDomains = unifyDomains;
+/**
+ * Unify all intervals which overlap with each other to one.
+ */
 function unifyOverlappingIntervals(intervals) {
     if (intervals.length === 0) {
         return [];
     }
-    const sortedIntervals = intervals.sort(compareIntervalsByTheirMinimum);
+    const sortedIntervals = [...intervals].sort(compareIntervalsByTheirMinimum);
     const unifiedIntervals = [];
     let currentInterval = sortedIntervals[0];
     for (const nextInterval of sortedIntervals) {
@@ -111,6 +131,11 @@ function unifyOverlappingIntervals(intervals) {
     return unifiedIntervals;
 }
 exports.unifyOverlappingIntervals = unifyOverlappingIntervals;
+/**
+ * Returns domain1 + domain2, mapping the inclusivity.
+ *
+ * @see subtractDomains
+ */
 function addDomains(domain1, domain2) {
     const intervals = new Set();
     for (const interval1 of domain1.intervals) {
@@ -127,6 +152,11 @@ function addDomains(domain1, domain2) {
     return Domain.fromIntervals(intervals);
 }
 exports.addDomains = addDomains;
+/**
+ * Returns domain1 - domain2, mapping the inclusivity.
+ *
+ * @see addDomains
+ */
 function subtractDomains(domain1, domain2) {
     const intervals = new Set();
     for (const interval1 of domain1.intervals) {

package/benchmark/slicer.d.ts

@@ -11,6 +11,9 @@ import type { NormalizedAst } from '../r-bridge/lang-4.x/ast/model/processing/de
 import type { SlicingCriteria } from '../slicing/criterion/parse';
 import type { RParseRequestFromFile, RParseRequestFromText } from '../r-bridge/retriever';
 import type { SlicingCriteriaFilter } from '../slicing/criterion/collect-all';
+/**
+ * The logger to be used for benchmarking as a global object.
+ */
 export declare const benchmarkLogger: import("tslog").Logger<import("tslog").ILogObj>;
 /**
  * Returns the stats but also the result of all setup steps (parsing, normalization, and the dataflow analysis) during the slicing.

package/benchmark/slicer.js

@@ -20,6 +20,9 @@ const retriever_1 = require("../r-bridge/retriever");
 const collect_all_1 = require("../slicing/criterion/collect-all");
 const visitor_1 = require("../r-bridge/lang-4.x/ast/model/processing/visitor");
 const size_of_1 = require("./stats/size-of");
+/**
+ * The logger to be used for benchmarking as a global object.
+ */
 exports.benchmarkLogger = log_1.log.getSubLogger({ name: 'benchmark' });
 /**
  * A slicer that can be used to slice exactly one file (multiple times).

package/benchmark/stats/print.js

@@ -46,7 +46,6 @@ function asPercentage(num) {
     if (isNaN(num)) {
         return '??%';
     }
-    (0, assert_1.guard)(num >= 0 && num <= 1, `Percentage ${num} should be between 0 and 1`);
     return pad(`${roundTo(num * 100, 3)}%`);
 }
 function asFloat(num) {

package/benchmark/summarizer/second-phase/graph.js

@@ -49,10 +49,10 @@ function writeGraphOutput(ultimate, outputGraphPath) {
     });
     data.push({
         name: 'memory (df-graph)',
-        unit: 'Bytes',
-        value: Number(ultimate.dataflow.sizeOfObject.mean),
-        range: Number(ultimate.dataflow.sizeOfObject.std),
-        extra: `median: ${(ultimate.dataflow.sizeOfObject.median).toFixed(2)}`
+        unit: 'KiB',
+        value: ultimate.dataflow.sizeOfObject.mean / 1024,
+        range: ultimate.dataflow.sizeOfObject.std / 1024,
+        extra: `median: ${(ultimate.dataflow.sizeOfObject.median / 1024).toFixed(2)}`
     });
     // write the output file
     fs_1.default.writeFileSync(outputGraphPath, JSON.stringify(data, json_1.jsonReplacer));

package/cli/flowr.d.ts

@@ -2,17 +2,18 @@ import type { OptionDefinition } from 'command-line-usage';
 export declare const toolName = "flowr";
 export declare const optionDefinitions: OptionDefinition[];
 export interface FlowrCliOptions {
-    verbose: boolean;
-    version: boolean;
-    help: boolean;
-    server: boolean;
-    ws: boolean;
-    port: number;
+    'config-file': string;
     'no-ansi': boolean;
+    'r-path': string | undefined;
+    'r-session-access': boolean;
     execute: string | undefined;
+    help: boolean;
+    port: number;
     script: string | undefined;
-    'config-file': string;
-    'r-path': string | undefined;
+    server: boolean;
+    verbose: boolean;
+    version: boolean;
+    ws: boolean;
 }
 export declare const optionHelp: ({
     header: string;

package/cli/flowr.js

@@ -20,20 +20,27 @@ const main_1 = require("./repl/commands/main");
 const core_1 = require("./repl/core");
 const version_2 = require("./repl/commands/version");
 const print_version_1 = require("./repl/print-version");
-const scriptsText = Array.from(Object.entries(scripts_info_1.scripts).filter(([, { type }]) => type === 'master script'), ([k,]) => k).join(', ');
+let _scriptsText;
+function getScriptsText() {
+    if (_scriptsText === undefined) {
+        _scriptsText = Array.from(Object.entries(scripts_info_1.scripts).filter(([, { type }]) => type === 'master script'), ([k,]) => k).join(', ');
+    }
+    return _scriptsText;
+}
 exports.toolName = 'flowr';
 exports.optionDefinitions = [
-    { name: 'verbose', alias: 'v', type: Boolean, description: 'Run with verbose logging (will be passed to the corresponding script)' },
-    { name: 'help', alias: 'h', type: Boolean, description: 'Print this usage guide (or the guide of the corresponding script)' },
-    { name: 'version', alias: 'V', type: Boolean, description: 'Provide information about the version of flowR as well as its underlying R system and exit.' },
-    { name: 'server', type: Boolean, description: 'Do not drop into a repl, but instead start a server on the given port (default: 1042) and listen for messages.' },
-    { name: 'ws', type: Boolean, description: 'If the server flag is set, use websocket for messaging' },
-    { name: 'port', type: Number, description: 'The port to listen on, if --server is given.', defaultValue: 1042, typeLabel: '{underline port}' },
+    { name: 'config-file', type: String, description: 'The name of the configuration file to use', multiple: false },
     { name: 'execute', alias: 'e', type: String, description: 'Execute the given command and exit. Use a semicolon ";" to separate multiple commands.', typeLabel: '{underline command}', multiple: false },
+    { name: 'help', alias: 'h', type: Boolean, description: 'Print this usage guide (or the guide of the corresponding script)' },
     { name: 'no-ansi', type: Boolean, description: 'Disable ansi-escape-sequences in the output. Useful, if you want to redirect the output to a file.' },
-    { name: 'script', alias: 's', type: String, description: `The sub-script to run (${scriptsText})`, multiple: false, defaultOption: true, typeLabel: '{underline files}', defaultValue: undefined },
-    { name: 'config-file', type: String, description: 'The name of the configuration file to use', multiple: false },
-    { name: 'r-path', type: String, description: 'The path to the R executable to use. Defaults to your PATH.', multiple: false }
+    { name: 'port', type: Number, description: 'The port to listen on, if --server is given.', defaultValue: 1042, typeLabel: '{underline port}' },
+    { name: 'r-path', type: String, description: 'The path to the R executable to use. Defaults to your PATH.', multiple: false },
+    { name: 'r-session-access', type: Boolean, description: 'Allow to access the underlying R session when using flowR (security warning: this allows the execution of arbitrary R code!)' },
+    { name: 'script', alias: 's', type: String, description: `The sub-script to run (${getScriptsText()})`, multiple: false, defaultOption: true, typeLabel: '{underline files}', defaultValue: undefined },
+    { name: 'server', type: Boolean, description: 'Do not drop into a repl, but instead start a server on the given port (default: 1042) and listen for messages.' },
+    { name: 'verbose', alias: 'v', type: Boolean, description: 'Run with verbose logging (will be passed to the corresponding script)' },
+    { name: 'version', alias: 'V', type: Boolean, description: 'Provide information about the version of flowR as well as its underlying R system and exit.' },
+    { name: 'ws', type: Boolean, description: 'If the server flag is set, use websocket for messaging' }
 ];
 exports.optionHelp = [
     {
@@ -81,7 +88,7 @@ function retrieveShell() {
 async function mainRepl() {
     if (options.script) {
         let target = scripts_info_1.scripts[options.script].target;
-        (0, assert_1.guard)(target !== undefined, `Unknown script ${options.script}, pick one of ${scriptsText}.`);
+        (0, assert_1.guard)(target !== undefined, `Unknown script ${options.script}, pick one of ${getScriptsText()}.`);
         console.log(`Running script '${ansi_1.formatter.format(options.script, { style: 1 /* FontStyles.Bold */ })}'`);
         target = `cli/${target}`;
         log_1.log.debug(`Script maps to "${target}"`);
@@ -109,12 +116,13 @@ async function mainRepl() {
     // hook some handlers
     process.on('SIGINT', end);
     process.on('SIGTERM', end);
+    const allowRSessionAccess = options['r-session-access'] ?? false;
     if (options.execute) {
-        await (0, core_1.replProcessAnswer)(main_1.standardReplOutput, options.execute, shell);
+        await (0, core_1.replProcessAnswer)(main_1.standardReplOutput, options.execute, shell, allowRSessionAccess);
     }
     else {
         await (0, print_version_1.printVersionRepl)(shell);
-        await (0, core_1.repl)(shell);
+        await (0, core_1.repl)({ shell, allowRSessionAccess });
     }
     process.exit(0);
 }
@@ -130,7 +138,7 @@ async function mainServer(backend = new net_1.NetServer()) {
     // hook some handlers
     process.on('SIGINT', end);
     process.on('SIGTERM', end);
-    await new server_1.FlowRServer(shell, backend).start(options.port);
+    await new server_1.FlowRServer(shell, options['r-session-access'], backend).start(options.port);
 }
 if (options.server) {
     void mainServer(options.ws ? new net_1.WebSocketServerWrapper() : new net_1.NetServer());

package/cli/repl/core.d.ts

@@ -2,6 +2,7 @@
 import * as readline from 'readline';
 import type { ReplOutput } from './commands/main';
 import { RShell } from '../../r-bridge/shell';
+import type { MergeableRecord } from '../../util/objects';
 /**
  * Used by the repl to provide automatic completions for a given (partial) input line
  */
@@ -10,11 +11,31 @@ export declare const DEFAULT_REPL_READLINE_CONFIGURATION: readline.ReadLineOptio
 /**
  * This function interprets the given `expr` as a REPL command (see {@link repl} for more on the semantics).
  *
- * @param output   - Defines two methods that every function in the repl uses to output its data.
- * @param expr     - The expression to process.
- * @param shell    - The {@link RShell} to use (see {@link repl}).
+ * @param output              - Defines two methods that every function in the repl uses to output its data.
+ * @param expr                - The expression to process.
+ * @param shell               - The {@link RShell} to use (see {@link repl}).
+ * @param allowRSessionAccess - If true, allows the execution of arbitrary R code.
  */
-export declare function replProcessAnswer(output: ReplOutput, expr: string, shell: RShell): Promise<void>;
+export declare function replProcessAnswer(output: ReplOutput, expr: string, shell: RShell, allowRSessionAccess: boolean): Promise<void>;
+/**
+ * Options for the {@link repl} function.
+ */
+export interface FlowrReplOptions extends MergeableRecord {
+    /** The shell to use, if you do not pass one it will automatically create a new one with the `revive` option set to 'always'. */
+    readonly shell?: RShell;
+    /**
+     * A potentially customized readline interface to be used for the repl to *read* from the user, we write the output with the {@link ReplOutput | `output` } interface.
+    * If you want to provide a custom one but use the same `completer`, refer to {@link replCompleter}.
+    * For the default arguments, see {@link DEFAULT_REPL_READLINE_CONFIGURATION}.
+     */
+    readonly rl?: readline.Interface;
+    /** Defines two methods that every function in the repl uses to output its data. */
+    readonly output?: ReplOutput;
+    /** The file to use for persisting the repl's history. Passing undefined causes history not to be saved. */
+    readonly historyFile?: string;
+    /** If true, allows the execution of arbitrary R code. This is a security risk, as it allows the execution of arbitrary R code. */
+    readonly allowRSessionAccess?: boolean;
+}
 /**
  * Provides a never-ending repl (read-evaluate-print loop) processor that can be used to interact with a {@link RShell} as well as all flowR scripts.
  *
@@ -22,15 +43,10 @@ export declare function replProcessAnswer(output: ReplOutput, expr: string, shel
  * - Starting with a colon `:`, indicating a command (probe `:help`, and refer to {@link commands}) </li>
  * - Starting with anything else, indicating default R code to be directly executed. If you kill the underlying shell, that is on you! </li>
  *
- * @param shell     - The shell to use, if you do not pass one it will automatically create a new one with the `revive` option set to 'always'
- * @param rl        - A potentially customized readline interface to be used for the repl to *read* from the user, we write the output with the {@link ReplOutput | `output` } interface.
- *                    If you want to provide a custom one but use the same `completer`, refer to {@link replCompleter}.
- *                    For the default arguments, see {@link DEFAULT_REPL_READLINE_CONFIGURATION}.
- * @param output    - Defines two methods that every function in the repl uses to output its data.
- * @param historyFile - The file to use for persisting the repl's history. Passing undefined causes history not to be saved.
+ * @param options - The options for the repl. See {@link FlowrReplOptions} for more information.
  *
- * For the execution, this function makes use of {@link replProcessAnswer}
+ * For the execution, this function makes use of {@link replProcessAnswer}.
  *
  */
-export declare function repl(shell?: RShell, rl?: readline.Interface, output?: ReplOutput, historyFile?: string | undefined): Promise<void>;
+export declare function repl({ shell, rl, output, historyFile, allowRSessionAccess }: FlowrReplOptions): Promise<void>;
 export declare function loadReplHistory(historyFile: string): string[] | undefined;

package/cli/repl/core.js

@@ -94,37 +94,42 @@ exports.DEFAULT_REPL_READLINE_CONFIGURATION = {
     removeHistoryDuplicates: true,
     completer: replCompleter
 };
-async function replProcessStatement(output, statement, shell) {
+async function replProcessStatement(output, statement, shell, allowRSessionAccess) {
     if (statement.startsWith(':')) {
         const command = statement.slice(1).split(' ')[0].toLowerCase();
         const processor = (0, commands_1.getCommand)(command);
+        const bold = (s) => output.formatter.format(s, { style: 1 /* FontStyles.Bold */ });
         if (processor) {
             try {
                 await processor.fn(output, shell, statement.slice(command.length + 2).trim());
             }
             catch (e) {
-                console.log(`${(0, ansi_1.bold)(`Failed to execute command ${command}`)}: ${e?.message}. Using the ${(0, ansi_1.bold)('--verbose')} flag on startup may provide additional information.`);
+                output.stdout(`${bold(`Failed to execute command ${command}`)}: ${e?.message}. Using the ${bold('--verbose')} flag on startup may provide additional information.\n`);
             }
         }
         else {
-            console.log(`the command '${command}' is unknown, try ${(0, ansi_1.bold)(':help')} for more information`);
+            output.stdout(`the command '${command}' is unknown, try ${bold(':help')} for more information\n`);
         }
     }
-    else {
+    else if (allowRSessionAccess) {
         await (0, execute_1.executeRShellCommand)(output, shell, statement);
     }
+    else {
+        output.stderr(`${output.formatter.format('You are not allowed to execute arbitrary R code.', { style: 1 /* FontStyles.Bold */, color: 1 /* Colors.Red */, effect: ansi_1.ColorEffect.Foreground })}\nIf you want to do so, please restart flowR with the ${output.formatter.format('--r-session-access', { style: 1 /* FontStyles.Bold */ })}  flag. Please be careful of the security implications of this action.`);
+    }
 }
 /**
  * This function interprets the given `expr` as a REPL command (see {@link repl} for more on the semantics).
  *
- * @param output   - Defines two methods that every function in the repl uses to output its data.
- * @param expr     - The expression to process.
- * @param shell    - The {@link RShell} to use (see {@link repl}).
+ * @param output              - Defines two methods that every function in the repl uses to output its data.
+ * @param expr                - The expression to process.
+ * @param shell               - The {@link RShell} to use (see {@link repl}).
+ * @param allowRSessionAccess - If true, allows the execution of arbitrary R code.
  */
-async function replProcessAnswer(output, expr, shell) {
+async function replProcessAnswer(output, expr, shell, allowRSessionAccess) {
     const statements = (0, args_1.splitAtEscapeSensitive)(expr, false, ';');
     for (const statement of statements) {
-        await replProcessStatement(output, statement, shell);
+        await replProcessStatement(output, statement, shell, allowRSessionAccess);
     }
 }
 exports.replProcessAnswer = replProcessAnswer;
@@ -135,17 +140,12 @@ exports.replProcessAnswer = replProcessAnswer;
  * - Starting with a colon `:`, indicating a command (probe `:help`, and refer to {@link commands}) </li>
  * - Starting with anything else, indicating default R code to be directly executed. If you kill the underlying shell, that is on you! </li>
  *
- * @param shell     - The shell to use, if you do not pass one it will automatically create a new one with the `revive` option set to 'always'
- * @param rl        - A potentially customized readline interface to be used for the repl to *read* from the user, we write the output with the {@link ReplOutput | `output` } interface.
- *                    If you want to provide a custom one but use the same `completer`, refer to {@link replCompleter}.
- *                    For the default arguments, see {@link DEFAULT_REPL_READLINE_CONFIGURATION}.
- * @param output    - Defines two methods that every function in the repl uses to output its data.
- * @param historyFile - The file to use for persisting the repl's history. Passing undefined causes history not to be saved.
+ * @param options - The options for the repl. See {@link FlowrReplOptions} for more information.
  *
- * For the execution, this function makes use of {@link replProcessAnswer}
+ * For the execution, this function makes use of {@link replProcessAnswer}.
  *
  */
-async function repl(shell = new shell_1.RShell({ revive: 2 /* RShellReviveOptions.Always */ }), rl = readline.createInterface(exports.DEFAULT_REPL_READLINE_CONFIGURATION), output = main_1.standardReplOutput, historyFile = defaultHistoryFile) {
+async function repl({ shell = new shell_1.RShell({ revive: 2 /* RShellReviveOptions.Always */ }), rl = readline.createInterface(exports.DEFAULT_REPL_READLINE_CONFIGURATION), output = main_1.standardReplOutput, historyFile = defaultHistoryFile, allowRSessionAccess = false }) {
     if (historyFile) {
         rl.on('history', h => fs_1.default.writeFileSync(historyFile, h.join('\n'), { encoding: 'utf-8' }));
     }
@@ -155,7 +155,7 @@ async function repl(shell = new shell_1.RShell({ revive: 2 /* RShellReviveOption
         await new Promise((resolve, reject) => {
             rl.question((0, prompt_1.prompt)(), answer => {
                 rl.pause();
-                replProcessAnswer(output, answer, shell).then(() => {
+                replProcessAnswer(output, answer, shell, allowRSessionAccess).then(() => {
                     rl.resume();
                     resolve();
                 }).catch(reject);

package/cli/repl/server/connection.d.ts

@@ -12,8 +12,9 @@ export declare class FlowRServerConnection {
     private readonly shell;
     private readonly name;
     private readonly logger;
+    private readonly allowRSessionAccess;
     private readonly fileMap;
-    constructor(socket: Socket, name: string, shell: RShell);
+    constructor(socket: Socket, name: string, shell: RShell, allowRSessionAccess: boolean);
     private currentMessageBuffer;
     private handleData;
     private handleFileAnalysisRequest;