@eagleoutice/flowr 2.9.4 → 2.9.6

package/README.md

@@ -24,7 +24,7 @@ It offers a wide variety of features, for example:
     
     ```shell
     $ docker run -it --rm eagleoutice/flowr # or npm run flowr 
-    flowR repl using flowR v2.9.3, R grammar v14 (tree-sitter engine)
+    flowR repl using flowR v2.9.5, R grammar v14 (tree-sitter engine)
     R> :query @linter "read.csv(\"/root/x.txt\")"
     ```
     
@@ -33,15 +33,15 @@ It offers a wide variety of features, for example:
     
     
     ```text
-    Query: linter (2 ms)
+    Query: linter (3 ms)
        ╰ Deprecated Functions (deprecated-functions):
-           ╰ Metadata: totalCalls: 0, totalFunctionDefinitions: 0, searchTimeMs: 0, processTimeMs: 0
+           ╰ Metadata: totalCalls: 0, totalFunctionDefinitions: 0, searchTimeMs: 1, processTimeMs: 0
        ╰ File Path Validity (file-path-validity):
            ╰ certain:
                ╰ Path `/root/x.txt` at 1.1-23
-           ╰ Metadata: totalReads: 1, totalUnknown: 0, totalWritesBeforeAlways: 0, totalValid: 0, searchTimeMs: 0, processTimeMs: 1
+           ╰ Metadata: totalReads: 1, totalUnknown: 0, totalWritesBeforeAlways: 0, totalValid: 0, searchTimeMs: 0, processTimeMs: 0
        ╰ Seeded Randomness (seeded-randomness):
-           ╰ Metadata: consumerCalls: 0, callsWithFunctionProducers: 0, callsWithAssignmentProducers: 0, callsWithNonConstantProducers: 0, callsWithOtherBranchProducers: 0, searchTimeMs: 0, processTimeMs: 0
+           ╰ Metadata: consumerCalls: 0, callsWithFunctionProducers: 0, callsWithAssignmentProducers: 0, callsWithNonConstantProducers: 0, callsWithOtherBranchProducers: 0, searchTimeMs: 1, processTimeMs: 0
        ╰ Absolute Paths (absolute-file-paths):
            ╰ certain:
                ╰ Path `/root/x.txt` at 1.1-23
@@ -53,12 +53,12 @@ It offers a wide variety of features, for example:
        ╰ Network Functions (network-functions):
            ╰ Metadata: totalCalls: 0, totalFunctionDefinitions: 0, searchTimeMs: 0, processTimeMs: 0
        ╰ Dataframe Access Validation (dataframe-access-validation):
-           ╰ Metadata: numOperations: 0, numAccesses: 0, totalAccessed: 0, searchTimeMs: 0, processTimeMs: 0
+           ╰ Metadata: numOperations: 0, numAccesses: 0, totalAccessed: 0, searchTimeMs: 0, processTimeMs: 1
        ╰ Dead Code (dead-code):
-           ╰ Metadata: consideredNodes: 5, searchTimeMs: 1, processTimeMs: 0
+           ╰ Metadata: consideredNodes: 5, searchTimeMs: 0, processTimeMs: 0
        ╰ Useless Loops (useless-loop):
            ╰ Metadata: numOfUselessLoops: 0, searchTimeMs: 0, processTimeMs: 0
-    All queries together required ≈2 ms (1ms accuracy, total 3 ms)
+    All queries together required ≈3 ms (1ms accuracy, total 3 ms)
     ```
     
     
@@ -82,13 +82,13 @@ It offers a wide variety of features, for example:
     
     Query: **linter** (3 ms)\
        ╰ **Deprecated Functions** (deprecated-functions):\
-    &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;╰ _Metadata_: <code>totalCalls: 0, totalFunctionDefinitions: 0, searchTimeMs: 1, processTimeMs: 0</code>\
+    &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;╰ _Metadata_: <code>totalCalls: 0, totalFunctionDefinitions: 0, searchTimeMs: 0, processTimeMs: 0</code>\
     &nbsp;&nbsp;&nbsp;╰ **File Path Validity** (file-path-validity):\
     &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;╰ certain:\
     &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;╰ Path `/root/x.txt` at 1.1-23\
-    &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;╰ _Metadata_: <code>totalReads: 1, totalUnknown: 0, totalWritesBeforeAlways: 0, totalValid: 0, searchTimeMs: 0, processTimeMs: 0</code>\
+    &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;╰ _Metadata_: <code>totalReads: 1, totalUnknown: 0, totalWritesBeforeAlways: 0, totalValid: 0, searchTimeMs: 1, processTimeMs: 0</code>\
     &nbsp;&nbsp;&nbsp;╰ **Seeded Randomness** (seeded-randomness):\
-    &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;╰ _Metadata_: <code>consumerCalls: 0, callsWithFunctionProducers: 0, callsWithAssignmentProducers: 0, callsWithNonConstantProducers: 0, callsWithOtherBranchProducers: 0, searchTimeMs: 0, processTimeMs: 1</code>\
+    &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;╰ _Metadata_: <code>consumerCalls: 0, callsWithFunctionProducers: 0, callsWithAssignmentProducers: 0, callsWithNonConstantProducers: 0, callsWithOtherBranchProducers: 0, searchTimeMs: 0, processTimeMs: 0</code>\
     &nbsp;&nbsp;&nbsp;╰ **Absolute Paths** (absolute-file-paths):\
     &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;╰ certain:\
     &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;╰ Path `/root/x.txt` at 1.1-23\
@@ -109,7 +109,7 @@ It offers a wide variety of features, for example:
     
     <details> <summary style="color:gray">Show Detailed Results as Json</summary>
     
-    The analysis required _2.6 ms_ (including parsing and normalization and the query) within the generation environment.
+    The analysis required _3.2 ms_ (including parsing and normalization and the query) within the generation environment.
     
     In general, the JSON contains the Ids of the nodes in question as they are present in the normalized AST or the dataflow graph of flowR.
     Please consult the [Interface](https://github.com/flowr-analysis/flowr/wiki/Interface) wiki page for more information on how to get those.
@@ -126,7 +126,7 @@ It offers a wide variety of features, for example:
             ".meta": {
               "totalCalls": 0,
               "totalFunctionDefinitions": 0,
-              "searchTimeMs": 1,
+              "searchTimeMs": 0,
               "processTimeMs": 0
             }
           },
@@ -149,7 +149,7 @@ It offers a wide variety of features, for example:
               "totalUnknown": 0,
               "totalWritesBeforeAlways": 0,
               "totalValid": 0,
-              "searchTimeMs": 0,
+              "searchTimeMs": 1,
               "processTimeMs": 0
             }
           },
@@ -162,7 +162,7 @@ It offers a wide variety of features, for example:
               "callsWithNonConstantProducers": 0,
               "callsWithOtherBranchProducers": 0,
               "searchTimeMs": 0,
-              "processTimeMs": 1
+              "processTimeMs": 0
             }
           },
           "absolute-file-paths": {
@@ -308,7 +308,7 @@ It offers a wide variety of features, for example:
     
     ```shell
     $ docker run -it --rm eagleoutice/flowr # or npm run flowr 
-    flowR repl using flowR v2.9.3, R grammar v14 (tree-sitter engine)
+    flowR repl using flowR v2.9.5, R grammar v14 (tree-sitter engine)
     R> :query @static-slice (11@sum) file://test/testfiles/example.R
     ```
     
@@ -322,7 +322,7 @@ It offers a wide variety of features, for example:
     N <- 10
     for(i in 1:(N-1)) sum <- sum + i + w
     sum
-    All queries together required ≈4 ms (1ms accuracy, total 4 ms)
+    All queries together required ≈3 ms (1ms accuracy, total 3 ms)
     ```
     
     
@@ -356,7 +356,7 @@ It offers a wide variety of features, for example:
          
 
 * 🚀 **fast call-graph, data-, and control-flow graphs**\
-  Within just [<i><span title="This measurement is automatically fetched from the latest benchmark!">121.6 ms</span></i> (as of Feb 4, 2026)](https://flowr-analysis.github.io/flowr/wiki/stats/benchmark), 
+  Within just [<i><span title="This measurement is automatically fetched from the latest benchmark!">99.6 ms</span></i> (as of Feb 5, 2026)](https://flowr-analysis.github.io/flowr/wiki/stats/benchmark), 
   _flowR_ can analyze the data- and control-flow of the average real-world R script. See the [benchmarks](https://flowr-analysis.github.io/flowr/wiki/stats/benchmark) for more information,
   and consult the [wiki pages](https://github.com/flowr-analysis/flowr/wiki/wiki/dataflow-graph) for more details on the dataflow graphs as well as call graphs.
 
@@ -392,7 +392,7 @@ It offers a wide variety of features, for example:
     
     ```shell
     $ docker run -it --rm eagleoutice/flowr # or npm run flowr 
-    flowR repl using flowR v2.9.3, R grammar v14 (tree-sitter engine)
+    flowR repl using flowR v2.9.5, R grammar v14 (tree-sitter engine)
     R> :dataflow* test/testfiles/example.R
     ```
     
@@ -697,7 +697,7 @@ It offers a wide variety of features, for example:
     ```
     
     	
-    (The analysis required _2.3 ms_ (including parse and normalize, using the [tree-sitter](https://github.com/flowr-analysis/flowr/wiki/Engines) engine) within the generation environment.)
+    (The analysis required _4.3 ms_ (including parse and normalize, using the [tree-sitter](https://github.com/flowr-analysis/flowr/wiki/Engines) engine) within the generation environment.)
     
     
     

package/control-flow/cfg-dead-code.js

@@ -41,16 +41,17 @@ class CfgConditionalDeadCodeRemoval extends semantic_cfg_guided_visitor_1.Semant
         this.cachedConditions.set(id, value ? logic_1.Ternary.Always : logic_1.Ternary.Never);
     }
     startVisitor() {
-        this.invertedCfg = (0, invert_cfg_1.invertCfg)(this.config.controlFlow.graph);
-        for (const [from, targets] of this.config.controlFlow.graph.edges()) {
+        const cfg = this.config.controlFlow.graph;
+        this.invertedCfg = (0, invert_cfg_1.invertCfg)(cfg);
+        for (const [from, targets] of cfg.edges()) {
             for (const [target, edge] of targets) {
                 if (edge.label === 1 /* CfgEdgeType.Cd */) {
                     const og = this.getValue(edge.caused);
                     if (og === logic_1.Ternary.Always && edge.when === 'FALSE') {
-                        this.config.controlFlow.graph.removeEdge(from, target);
+                        cfg.removeEdge(from, target);
                     }
                     else if (og === logic_1.Ternary.Never && edge.when === 'TRUE') {
-                        this.config.controlFlow.graph.removeEdge(from, target);
+                        cfg.removeEdge(from, target);
                     }
                 }
                 else if (edge.label === 0 /* CfgEdgeType.Fd */ && this.isUnconditionalJump(target)) {
@@ -58,7 +59,7 @@ class CfgConditionalDeadCodeRemoval extends semantic_cfg_guided_visitor_1.Semant
                     for (const end of this.getCfgVertex(target)?.end ?? []) {
                         for (const [target, edge] of this.invertedCfg.outgoingEdges(end) ?? []) {
                             if (edge.label === 0 /* CfgEdgeType.Fd */) {
-                                this.config.controlFlow.graph.removeEdge(target, end);
+                                cfg.removeEdge(target, end);
                             }
                         }
                     }
@@ -67,6 +68,9 @@ class CfgConditionalDeadCodeRemoval extends semantic_cfg_guided_visitor_1.Semant
         }
     }
     handleValuesFor(id, valueId) {
+        if (this.cachedConditions.has(id)) {
+            return;
+        }
         const values = (0, general_1.valueSetGuard)((0, alias_tracking_1.resolveIdToValue)(valueId, {
             graph: this.config.dfg,
             full: true,
@@ -114,6 +118,9 @@ class CfgConditionalDeadCodeRemoval extends semantic_cfg_guided_visitor_1.Semant
         this.cachedStatements.set(data.call.id, true);
     }
     onStopIfNotCall(data) {
+        if (this.cachedStatements.has(data.call.id)) {
+            return;
+        }
         const arg = this.getBoolArgValue(data);
         if (arg !== undefined) {
             this.cachedStatements.set(data.call.id, !arg);

package/dataflow/environments/append.js

@@ -2,7 +2,7 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.uniqueMergeValuesInDefinitions = uniqueMergeValuesInDefinitions;
 exports.appendEnvironment = appendEnvironment;
-const assert_1 = require("../../util/assert");
+const scoping_1 = require("./scoping");
 /**
  * Merges two arrays of identifier definitions, ensuring uniqueness based on `nodeId` and `definedAt`.
  */
@@ -23,7 +23,14 @@ function appendEnvironment(base, next) {
     else if (next === undefined) {
         return base;
     }
-    (0, assert_1.guard)(base.level === next.level, 'environments must have the same level to be handled, it is up to the caller to ensure that');
+    if (base.level !== next.level) {
+        while (next.level < base.level) {
+            next = (0, scoping_1.pushLocalEnvironment)(next);
+        }
+        while (next.level > base.level) {
+            base = (0, scoping_1.pushLocalEnvironment)(base);
+        }
+    }
     return {
         current: base.current.append(next.current),
         level: base.level,

package/dataflow/environments/environment.js

@@ -164,7 +164,7 @@ class Environment {
      * This always recurses parents.
      */
     overwrite(other, applyCds) {
-        if (this.builtInEnv || this === other || !other) {
+        if (this.builtInEnv || this === other || !other || this.n !== other.n) {
             return this;
         }
         const map = new Map(this.memory);
@@ -211,7 +211,7 @@ class Environment {
      * This always recurses parents.
      */
     append(other) {
-        if (!other || this.builtInEnv) {
+        if (!other || this.builtInEnv || this === other || this.n !== other.n) {
             return this;
         }
         const map = new Map(this.memory);

package/dataflow/environments/overwrite.js

@@ -1,7 +1,7 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.overwriteEnvironment = overwriteEnvironment;
-const assert_1 = require("../../util/assert");
+const scoping_1 = require("./scoping");
 /**
  * Assumes, that all definitions within next replace those within base (given the same name).
  * <b>But</b> if all definitions within next are maybe, then they are appended to the base definitions (updating them to be `maybe` from now on as well), similar to {@link appendEnvironment}.
@@ -14,7 +14,14 @@ function overwriteEnvironment(base, next, applyCds) {
     else if (next === undefined) {
         return base;
     }
-    (0, assert_1.guard)(next.level === base.level, `cannot overwrite environments with differently nested local scopes, base ${base.level} vs. next ${next.level}. This should not happen.`);
+    if (base.level !== next.level) {
+        while (next.level < base.level) {
+            next = (0, scoping_1.pushLocalEnvironment)(next);
+        }
+        while (next.level > base.level) {
+            base = (0, scoping_1.pushLocalEnvironment)(base);
+        }
+    }
     return {
         current: base.current.overwrite(next.current, applyCds),
         level: base.level

package/dataflow/fn/recursive-function.js

@@ -7,7 +7,7 @@ const vertex_1 = require("../graph/vertex");
  */
 function isFunctionRecursive(id, graph) {
     const vert = graph.getVertex(id);
-    if (!vert || !(0, vertex_1.isFunctionDefinitionVertex)(vert)) {
+    if (!(0, vertex_1.isFunctionDefinitionVertex)(vert)) {
         return false;
     }
     const seen = new Set();

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@eagleoutice/flowr",
-  "version": "2.9.4",
+  "version": "2.9.6",
   "description": "Static Dataflow Analyzer and Program Slicer for the R Programming Language",
   "types": "dist/src/index.d.ts",
   "repository": {

package/project/plugins/file-plugins/files/flowr-rmarkdown-file.d.ts

@@ -13,6 +13,9 @@ export declare class FlowrRMarkdownFile extends FlowrFile<string> {
      * @param file - the file to load as R Markdown
      */
     constructor(file: FlowrFileProvider<string>);
+    /**
+     * Gets the parsed R Markdown information
+     */
     get rmd(): RmdInfo;
     /**
      * Loads and parses the content of the wrapped file.

package/project/plugins/file-plugins/files/flowr-rmarkdown-file.js

@@ -27,6 +27,9 @@ class FlowrRMarkdownFile extends flowr_file_1.FlowrFile {
         super(file.path(), file.roles ? [...file.roles, flowr_file_1.FileRole.Source] : [flowr_file_1.FileRole.Source]);
         this.wrapped = file;
     }
+    /**
+     * Gets the parsed R Markdown information
+     */
     get rmd() {
         if (!this.data) {
             this.loadContent();

package/project/plugins/file-plugins/files/flowr-sweave-file.d.ts

@@ -0,0 +1,70 @@
+import type { FlowrFileProvider } from '../../../context/flowr-file';
+import { FlowrFile } from '../../../context/flowr-file';
+/**
+ * This decorates a text file and parses its contents as a Sweave (latex with R code) file.
+ * Finally, it provides access to the single cells, and all cells fused together as one R file.
+ * So far, this does *not* support `\Sexpr` calls.
+ */
+export declare class FlowrSweaveFile extends FlowrFile<string> {
+    private readonly wrapped;
+    private data?;
+    /**
+     * Prefer the static {@link FlowrSweaveFile.from} method
+     * @param file - the file to load as Sweave
+     */
+    constructor(file: FlowrFileProvider<string>);
+    /**
+     * The content of the Sweave file.
+     */
+    get rnw(): SweaveInfo;
+    /**
+     * Loads and parses the content of the wrapped file.
+     * @returns the content of the Sweave file, which is the R code without the latex code, no-eval blocks, ...
+     */
+    protected loadContent(): string;
+    static from(file: FlowrFileProvider<string> | FlowrSweaveFile): FlowrSweaveFile;
+}
+export interface SweaveInfo {
+    /**
+     * The R code without the latex code, no-eval blocks, ...
+     */
+    content: string;
+    /**
+     * All code blocks, including those that should not be evaluated and the latex code.
+     */
+    blocks: SweaveCodeBlock[];
+}
+interface SweaveBlockBasis {
+    type: 'content' | 'reuse';
+    startLine: number;
+}
+export interface SweaveCodeBlockContent extends SweaveBlockBasis {
+    type: 'content';
+    content: string;
+    options: SweaveBlockOptions;
+}
+export interface SweaveCodeBlockReuse extends SweaveBlockBasis {
+    type: 'reuse';
+    reuse: string;
+}
+type SweaveCodeBlock = SweaveCodeBlockContent | SweaveCodeBlockReuse;
+export interface SweaveBlockOptions {
+    name?: string;
+    eval?: boolean;
+}
+export interface SweaveReuseOptions {
+    reuse: string;
+}
+/**
+ * Parse a Sweave file into joined content and blocks
+ * @param raw - raw contents of file
+ * @returns Joined Content and Blocks
+ */
+export declare function parseSweave(raw: string): SweaveInfo;
+/**
+ * Parses a Sweave Code Block Start if it can find one
+ * @param line - the line to parse
+ * @returns info about options and name if code block start was found
+ */
+export declare function parseSweaveCodeblockStart(line: string): SweaveBlockOptions | SweaveReuseOptions | undefined;
+export {};

package/project/plugins/file-plugins/files/flowr-sweave-file.js

@@ -0,0 +1,163 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.FlowrSweaveFile = void 0;
+exports.parseSweave = parseSweave;
+exports.parseSweaveCodeblockStart = parseSweaveCodeblockStart;
+const flowr_file_1 = require("../../../context/flowr-file");
+const assert_1 = require("../../../../util/assert");
+/**
+ * This decorates a text file and parses its contents as a Sweave (latex with R code) file.
+ * Finally, it provides access to the single cells, and all cells fused together as one R file.
+ * So far, this does *not* support `\Sexpr` calls.
+ */
+class FlowrSweaveFile extends flowr_file_1.FlowrFile {
+    wrapped;
+    data;
+    /**
+     * Prefer the static {@link FlowrSweaveFile.from} method
+     * @param file - the file to load as Sweave
+     */
+    constructor(file) {
+        super(file.path(), file.roles ? [...file.roles, flowr_file_1.FileRole.Source] : [flowr_file_1.FileRole.Source]);
+        this.wrapped = file;
+    }
+    /**
+     * The content of the Sweave file.
+     */
+    get rnw() {
+        if (!this.data) {
+            this.loadContent();
+        }
+        (0, assert_1.guard)(this.data);
+        return this.data;
+    }
+    /**
+     * Loads and parses the content of the wrapped file.
+     * @returns the content of the Sweave file, which is the R code without the latex code, no-eval blocks, ...
+     */
+    loadContent() {
+        this.data = parseSweave(this.wrapped.content());
+        return this.data.content;
+    }
+    static from(file) {
+        return file instanceof FlowrSweaveFile ? file : new FlowrSweaveFile(file);
+    }
+}
+exports.FlowrSweaveFile = FlowrSweaveFile;
+const CodeBlockStartPattern = /^<<([^>]*)>>(?<reuse>=)?/;
+const ReusePattern = /^<<([^>]*)>>/;
+/**
+ * Parse a Sweave file into joined content and blocks
+ * @param raw - raw contents of file
+ * @returns Joined Content and Blocks
+ */
+function parseSweave(raw) {
+    const lines = raw.split(/\r?\n/);
+    const blocks = [];
+    let currentBlock = undefined;
+    let lineNum = 0;
+    for (const line of lines) {
+        lineNum++;
+        if (currentBlock) { // Inside Code Block
+            if (isEndOfCodeBlock(line)) {
+                // drop the last '\n' and push the block
+                if (currentBlock.content.endsWith('\n')) {
+                    currentBlock.content = currentBlock.content.slice(0, -1);
+                }
+                blocks.push(currentBlock);
+                currentBlock = undefined;
+                continue;
+            }
+            else {
+                const reuseMatch = line.match(ReusePattern);
+                if (reuseMatch) {
+                    // we found a reuse inside a code block, we inline the content!
+                    const reuseName = reuseMatch[1].trim();
+                    const reuseBlock = blocks.find(b => 'options' in b && b.options.name === reuseName);
+                    if (reuseBlock && 'options' in reuseBlock) {
+                        currentBlock.content += reuseBlock.content + '\n';
+                    }
+                    continue;
+                }
+            }
+            currentBlock.content += line + '\n';
+        }
+        else { // Latex Code / Outside Code Block
+            const result = parseSweaveCodeblockStart(line);
+            if (result) {
+                if ('reuse' in result) {
+                    blocks.push({ type: 'reuse', reuse: result.reuse, startLine: lineNum });
+                    continue;
+                }
+                currentBlock = {
+                    type: 'content',
+                    options: result,
+                    content: '',
+                    startLine: lineNum
+                };
+            }
+        }
+    }
+    const content = [];
+    for (const block of blocks) {
+        // add empty lines until startline is met; the start line is still exclusive!
+        while (content.length < block.startLine) {
+            content.push('');
+        }
+        if ('reuse' in block) {
+            const reuseBlock = blocks.find(b => 'options' in b && b.options.name === block.reuse);
+            if (reuseBlock && 'options' in reuseBlock) {
+                content.push(...reuseBlock.content.split('\n'));
+            }
+        }
+        else if (block.options.eval !== false) {
+            content.push(...block.content.split('\n'));
+        }
+    }
+    return {
+        content: content.join('\n'),
+        blocks: blocks
+    };
+}
+const evalWithFlagPattern = /eval\s*=\s*(TRUE|FALSE)/i;
+/**
+ * Parses a Sweave Code Block Start if it can find one
+ * @param line - the line to parse
+ * @returns info about options and name if code block start was found
+ */
+function parseSweaveCodeblockStart(line) {
+    const match = line.match(CodeBlockStartPattern);
+    if (match) {
+        // No options provided (i.e <<>>=)
+        if (match[1] === '') {
+            return {};
+        }
+        const options = match[1].split(',');
+        let name = undefined;
+        let evalOpt = undefined;
+        // The first option can have no key and is then interpreted as the label of the block
+        if (!options[0].includes('=')) {
+            name = options[0].trim();
+        }
+        if (match.groups?.reuse === undefined) {
+            // this reuses!
+            return name ? { reuse: name } : {};
+        }
+        // Search for eval option
+        for (let i = name ? 1 : 0; i < options.length; i++) {
+            const opt = options[i].trim();
+            const evalMatch = opt.match(evalWithFlagPattern);
+            if (evalMatch) {
+                evalOpt = evalMatch[1].toUpperCase() === 'TRUE';
+            }
+        }
+        return {
+            name, eval: evalOpt
+        };
+    }
+    return undefined;
+}
+function isEndOfCodeBlock(line) {
+    return line.startsWith('@');
+}
+//# sourceMappingURL=flowr-sweave-file.js.map

package/project/plugins/file-plugins/notebooks/flowr-analyzer-sweave-file-plugin.d.ts

@@ -0,0 +1,22 @@
+import type { PathLike } from 'fs';
+import { SemVer } from 'semver';
+import type { FlowrAnalyzerContext } from '../../../context/flowr-analyzer-context';
+import { type FlowrFileProvider } from '../../../context/flowr-file';
+import { FlowrAnalyzerFilePlugin } from '../flowr-analyzer-file-plugin';
+import { FlowrSweaveFile } from '../files/flowr-sweave-file';
+/**
+ * The plugin provides support for Sweave (`.Rnw`) files
+ */
+export declare class FlowrAnalyzerSweaveFilePlugin extends FlowrAnalyzerFilePlugin {
+    readonly name = "sweave-file-plugin";
+    readonly description = "Parses R Sweave files";
+    readonly version: SemVer;
+    private readonly pattern;
+    /**
+     * Creates a new instance of the Sweave file plugin.
+     * @param filePattern - The pattern to identify Sweave files, see {@link SweavePattern} for the default pattern.
+     */
+    constructor(filePattern?: RegExp);
+    applies(file: PathLike): boolean;
+    protected process(_ctx: FlowrAnalyzerContext, arg: FlowrFileProvider<string>): FlowrSweaveFile;
+}

package/project/plugins/file-plugins/notebooks/flowr-analyzer-sweave-file-plugin.js

@@ -0,0 +1,33 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.FlowrAnalyzerSweaveFilePlugin = void 0;
+const semver_1 = require("semver");
+const flowr_analyzer_file_plugin_1 = require("../flowr-analyzer-file-plugin");
+const built_in_source_1 = require("../../../../dataflow/internal/process/functions/call/built-in/built-in-source");
+const flowr_sweave_file_1 = require("../files/flowr-sweave-file");
+const SweavePattern = /\.Rnw$/i;
+/**
+ * The plugin provides support for Sweave (`.Rnw`) files
+ */
+class FlowrAnalyzerSweaveFilePlugin extends flowr_analyzer_file_plugin_1.FlowrAnalyzerFilePlugin {
+    name = 'sweave-file-plugin';
+    description = 'Parses R Sweave files';
+    version = new semver_1.SemVer('0.1.0');
+    pattern;
+    /**
+     * Creates a new instance of the Sweave file plugin.
+     * @param filePattern - The pattern to identify Sweave files, see {@link SweavePattern} for the default pattern.
+     */
+    constructor(filePattern = SweavePattern) {
+        super();
+        this.pattern = filePattern;
+    }
+    applies(file) {
+        return this.pattern.test((0, built_in_source_1.platformBasename)(file.toString()));
+    }
+    process(_ctx, arg) {
+        return flowr_sweave_file_1.FlowrSweaveFile.from(arg);
+    }
+}
+exports.FlowrAnalyzerSweaveFilePlugin = FlowrAnalyzerSweaveFilePlugin;
+//# sourceMappingURL=flowr-analyzer-sweave-file-plugin.js.map

package/project/plugins/flowr-analyzer-plugin-defaults.js

@@ -13,6 +13,7 @@ const flowr_analyzer_vignette_file_plugin_1 = require("./file-plugins/flowr-anal
 const flowr_analyzer_test_file_plugin_1 = require("./file-plugins/flowr-analyzer-test-file-plugin");
 const flowr_analyzer_license_file_plugin_1 = require("./file-plugins/flowr-analyzer-license-file-plugin");
 const flowr_analyzer_meta_description_file_plugin_1 = require("./package-version-plugins/flowr-analyzer-meta-description-file-plugin");
+const flowr_analyzer_sweave_file_plugin_1 = require("./file-plugins/notebooks/flowr-analyzer-sweave-file-plugin");
 /**
  * Provides the default set of Flowr Analyzer plugins.
  */
@@ -26,6 +27,7 @@ function FlowrAnalyzerPluginDefaults() {
         new flowr_analyzer_meta_description_file_plugin_1.FlowrAnalyzerMetaDescriptionFilePlugin(),
         new flowr_analyzer_rmd_file_plugin_1.FlowrAnalyzerRmdFilePlugin(),
         new flowr_analyzer_qmd_file_plugin_1.FlowrAnalyzerQmdFilePlugin(),
+        new flowr_analyzer_sweave_file_plugin_1.FlowrAnalyzerSweaveFilePlugin(),
         new flowr_analyzer_license_file_plugin_1.FlowrAnalyzerLicenseFilePlugin(),
         new flowr_analyzer_jupyter_file_plugin_1.FlowrAnalyzerJupyterFilePlugin(),
         new flowr_analyzer_namespace_files_plugin_1.FlowrAnalyzerNamespaceFilesPlugin(),

package/project/plugins/plugin-registry.d.ts

@@ -11,10 +11,11 @@ import { FlowrAnalyzerMetaVignetteFilesPlugin } from './file-plugins/flowr-analy
 import { FlowrAnalyzerMetaTestFilesPlugin } from './file-plugins/flowr-analyzer-test-file-plugin';
 import { FlowrAnalyzerLicenseFilePlugin } from './file-plugins/flowr-analyzer-license-file-plugin';
 import { FlowrAnalyzerMetaDescriptionFilePlugin } from './package-version-plugins/flowr-analyzer-meta-description-file-plugin';
+import { FlowrAnalyzerSweaveFilePlugin } from './file-plugins/notebooks/flowr-analyzer-sweave-file-plugin';
 /**
  * The built-in Flowr Analyzer plugins that are always available.
  */
-export declare const BuiltInPlugins: [["file:description", typeof FlowrAnalyzerDescriptionFilePlugin], ["versions:description", typeof FlowrAnalyzerPackageVersionsDescriptionFilePlugin], ["loading-order:description", typeof FlowrAnalyzerLoadingOrderDescriptionFilePlugin], ["meta:description", typeof FlowrAnalyzerMetaDescriptionFilePlugin], ["files:vignette", typeof FlowrAnalyzerMetaVignetteFilesPlugin], ["files:test", typeof FlowrAnalyzerMetaTestFilesPlugin], ["file:rmd", typeof FlowrAnalyzerRmdFilePlugin], ["file:qmd", typeof FlowrAnalyzerQmdFilePlugin], ["file:ipynb", typeof FlowrAnalyzerJupyterFilePlugin], ["file:namespace", typeof FlowrAnalyzerNamespaceFilesPlugin], ["file:news", typeof FlowrAnalyzerNewsFilePlugin], ["file:license", typeof FlowrAnalyzerLicenseFilePlugin]];
+export declare const BuiltInPlugins: [["file:description", typeof FlowrAnalyzerDescriptionFilePlugin], ["versions:description", typeof FlowrAnalyzerPackageVersionsDescriptionFilePlugin], ["loading-order:description", typeof FlowrAnalyzerLoadingOrderDescriptionFilePlugin], ["meta:description", typeof FlowrAnalyzerMetaDescriptionFilePlugin], ["files:vignette", typeof FlowrAnalyzerMetaVignetteFilesPlugin], ["files:test", typeof FlowrAnalyzerMetaTestFilesPlugin], ["file:rmd", typeof FlowrAnalyzerRmdFilePlugin], ["file:qmd", typeof FlowrAnalyzerQmdFilePlugin], ["file:rnw", typeof FlowrAnalyzerSweaveFilePlugin], ["file:ipynb", typeof FlowrAnalyzerJupyterFilePlugin], ["file:namespace", typeof FlowrAnalyzerNamespaceFilesPlugin], ["file:news", typeof FlowrAnalyzerNewsFilePlugin], ["file:license", typeof FlowrAnalyzerLicenseFilePlugin]];
 export type BuiltInFlowrPluginName = typeof BuiltInPlugins[number][0];
 export type BuiltInFlowrPluginArgs<N extends BuiltInFlowrPluginName> = N extends typeof BuiltInPlugins[number][0] ? ConstructorParameters<Extract<typeof BuiltInPlugins[number], [N, PluginProducer]>[1]> : never;
 type PluginProducer = new (...args: never[]) => FlowrAnalyzerPlugin;

package/project/plugins/plugin-registry.js

@@ -17,6 +17,7 @@ const flowr_analyzer_vignette_file_plugin_1 = require("./file-plugins/flowr-anal
 const flowr_analyzer_test_file_plugin_1 = require("./file-plugins/flowr-analyzer-test-file-plugin");
 const flowr_analyzer_license_file_plugin_1 = require("./file-plugins/flowr-analyzer-license-file-plugin");
 const flowr_analyzer_meta_description_file_plugin_1 = require("./package-version-plugins/flowr-analyzer-meta-description-file-plugin");
+const flowr_analyzer_sweave_file_plugin_1 = require("./file-plugins/notebooks/flowr-analyzer-sweave-file-plugin");
 /**
  * The built-in Flowr Analyzer plugins that are always available.
  */
@@ -29,6 +30,7 @@ exports.BuiltInPlugins = [
     ['files:test', flowr_analyzer_test_file_plugin_1.FlowrAnalyzerMetaTestFilesPlugin],
     ['file:rmd', flowr_analyzer_rmd_file_plugin_1.FlowrAnalyzerRmdFilePlugin],
     ['file:qmd', flowr_analyzer_qmd_file_plugin_1.FlowrAnalyzerQmdFilePlugin],
+    ['file:rnw', flowr_analyzer_sweave_file_plugin_1.FlowrAnalyzerSweaveFilePlugin],
     ['file:ipynb', flowr_analyzer_jupyter_file_plugin_1.FlowrAnalyzerJupyterFilePlugin],
     ['file:namespace', flowr_analyzer_namespace_files_plugin_1.FlowrAnalyzerNamespaceFilesPlugin],
     ['file:news', flowr_analyzer_news_file_plugin_1.FlowrAnalyzerNewsFilePlugin],

package/project/plugins/project-discovery/flowr-analyzer-project-discovery-plugin.js

@@ -24,7 +24,7 @@ class FlowrAnalyzerProjectDiscoveryPlugin extends flowr_analyzer_plugin_1.FlowrA
     }
 }
 exports.FlowrAnalyzerProjectDiscoveryPlugin = FlowrAnalyzerProjectDiscoveryPlugin;
-const discoverRSourcesRegex = /\.(r|rmd|ipynb|qmd)$/i;
+const discoverRSourcesRegex = /\.(r|rmd|ipynb|qmd|rnw)$/i;
 const ignorePathsWith = /(\.git|\.svn|\.hg|renv|packrat|node_modules|__pycache__|\.Rproj\.user)/i;
 const excludeRequestsForPaths = /vignettes?|tests?|revdep|inst|data/i;
 /**

package/queries/catalog/call-context-query/call-context-query-executor.d.ts

@@ -1,11 +1,12 @@
 import type { CallContextQuery, CallContextQueryResult, CallNameTypes, LinkTo } from './call-context-query-format';
 import type { BasicQueryData } from '../../base-query-format';
+export type PromotedCallTest = (t: string) => boolean;
 /**
  *
  */
-export declare function promoteCallName(callName: CallNameTypes, exact?: boolean): RegExp | Set<string>;
+export declare function promoteCallName(callName: CallNameTypes, exact?: boolean): PromotedCallTest;
 export type PromotedLinkTo<LT = LinkTo> = Omit<LT, 'callName'> & {
-    callName: RegExp | Set<string>;
+    callName: PromotedCallTest;
 };
 /**
  * Multi-stage call context query resolve.

package/queries/catalog/call-context-query/call-context-query-executor.js

@@ -48,13 +48,16 @@ function isSubCallQuery(query) {
  */
 function promoteCallName(callName, exact = false) {
     if (Array.isArray(callName)) {
-        return new Set(callName);
+        const s = new Set(callName);
+        return (t) => s.has(t);
     }
     else if (exact) {
-        return new Set([typeof callName === 'string' ? callName : callName.source]);
+        const s = new Set([typeof callName === 'string' ? callName : callName.source]);
+        return (t) => s.has(t);
     }
     else {
-        return new RegExp(callName);
+        const r = new RegExp(callName);
+        return (t) => r.test(t);
     }
 }
 function promoteQueryCallNames(queries) {
@@ -98,7 +101,7 @@ function retrieveAllCallAliases(nodeId, graph) {
     const aliases = new Map();
     const visited = new Set();
     /* we store the current call name */
-    let queue = [[(0, node_id_1.recoverContent)(nodeId, graph) ?? '', nodeId]];
+    const queue = [[(0, node_id_1.recoverContent)(nodeId, graph) ?? '', nodeId]];
     while (queue.length > 0) {
         const [str, id] = queue.shift();
         if (visited.has(id)) {
@@ -120,12 +123,13 @@ function retrieveAllCallAliases(nodeId, graph) {
         }
         const [info, outgoing] = vertex;
         if (info.tag !== vertex_1.VertexType.FunctionCall) {
+            const wantedTypes = edge_1.EdgeType.Reads | edge_1.EdgeType.DefinedBy | edge_1.EdgeType.DefinedByOnCall;
             const x = outgoing.entries()
-                .filter(([, e]) => edge_1.DfEdge.includesType(e, edge_1.EdgeType.Reads | edge_1.EdgeType.DefinedBy | edge_1.EdgeType.DefinedByOnCall))
+                .filter(([, e]) => edge_1.DfEdge.includesType(e, wantedTypes))
                 .map(([t]) => [(0, node_id_1.recoverContent)(t, graph) ?? '', t])
                 .toArray();
             /** only follow defined-by and reads */
-            queue = queue.concat(x);
+            queue.push(...x);
             continue;
         }
         let track = edge_1.EdgeType.Calls | edge_1.EdgeType.Reads | edge_1.EdgeType.DefinedBy | edge_1.EdgeType.DefinedByOnCall;
@@ -164,7 +168,7 @@ function doesFilepathMatch(file, filter) {
     if (file === undefined) {
         return filter.includeUndefinedFiles ?? true;
     }
-    return filter.filter instanceof RegExp ? filter.filter.test(file) : filter.filter.has(file);
+    return filter.filter(file);
 }
 function isParameterDefaultValue(nodeId, ast) {
     let node = ast.idMap.get(nodeId);
@@ -172,7 +176,8 @@ function isParameterDefaultValue(nodeId, ast) {
         if (node.info.role === "param-value" /* RoleInParent.ParameterDefaultValue */) {
             return true;
         }
-        node = node.info.parent ? ast.idMap.get(node.info.parent) : undefined;
+        const nip = node.info.parent;
+        node = nip ? ast.idMap.get(nip) : undefined;
     }
     return false;
 }
@@ -196,7 +201,7 @@ async function executeCallContextQueries({ analyzer }, queries) {
     const { promotedQueries, requiresCfg } = promoteQueryCallNames(queries);
     let cfg = undefined;
     if (requiresCfg) {
-        cfg = await analyzer.controlflow([], cfg_kind_1.CfgKind.WithDataflow);
+        cfg = await analyzer.controlflow(undefined, cfg_kind_1.CfgKind.Quick);
     }
     const calls = cfg ? (0, extract_cfg_1.getCallsInCfg)(cfg, dataflow.graph) : undefined;
     const queriesWhichWantAliases = promotedQueries.filter(q => q.includeAliases);
@@ -211,14 +216,14 @@ async function executeCallContextQueries({ analyzer }, queries) {
             const targets = retrieveAllCallAliases(nodeId, dataflow.graph);
             for (const [l, ids] of targets.entries()) {
                 for (const query of queriesWhichWantAliases) {
-                    if (query.callName instanceof RegExp ? query.callName.test(l) : query.callName.has(l)) {
+                    if (query.callName(l)) {
                         initialIdCollector.add(query.kind ?? '.', query.subkind ?? '.', (0, objects_1.compactRecord)({ id: nodeId, name: info.name, aliasRoots: ids }));
                     }
                 }
             }
         }
         const n = identifier_1.Identifier.getName(info.name);
-        for (const query of promotedQueries.filter(q => !q.includeAliases && (q.callName instanceof RegExp ? q.callName.test(n) : q.callName.has(n)))) {
+        for (const query of promotedQueries.filter(q => !q.includeAliases && q.callName(n))) {
             const file = ast.idMap.get(nodeId)?.info.file;
             if (!doesFilepathMatch(file, query.fileFilter)) {
                 continue;

package/queries/catalog/call-context-query/identify-link-to-last-call-relation.js

@@ -135,7 +135,7 @@ function identifyLinkToLastCallRelationSync(from, cfg, graph, { callName, cascad
     }
     const found = [];
     const cNameCheck = callName instanceof RegExp ? ({ name }) => callName.test(identifier_1.Identifier.getName(name))
-        : ({ name }) => callName.has(identifier_1.Identifier.getName(name));
+        : ({ name }) => callName(identifier_1.Identifier.getName(name));
     const getVertex = knownCalls ?
         (node) => knownCalls.get(node) :
         (node) => {

package/queries/catalog/call-context-query/identify-link-to-nested-call-relation.js

@@ -2,6 +2,8 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.identifyLinkToNestedRelation = identifyLinkToNestedRelation;
 const call_graph_1 = require("../../../dataflow/graph/call-graph");
+const vertex_1 = require("../../../dataflow/graph/vertex");
+const identifier_1 = require("../../../dataflow/environments/identifier");
 /**
  * **Please refer to {@link identifyLinkToRelation}.**
  *
@@ -14,15 +16,16 @@ async function identifyLinkToNestedRelation(from, analyzer, { callName, ignoreIf
     if (ignoreIf?.(from, df.graph)) {
         return [];
     }
+    const test = callName instanceof RegExp ? (t) => callName.test(t) : callName;
     const found = [];
     const cg = await analyzer.callGraph();
     const subCg = (0, call_graph_1.getSubCallGraph)(cg, new Set([from]));
-    for (const [, { id, name }] of subCg.vertices(true)) {
-        if (typeof name !== 'string') {
+    for (const [, t] of subCg.vertices(true)) {
+        if (!(0, vertex_1.isFunctionCallVertex)(t)) {
             continue;
         }
-        if (callName instanceof RegExp ? callName.test(name) : callName.has(name)) {
-            found.push(id);
+        if (test(identifier_1.Identifier.toString(t.name))) {
+            found.push(t.id);
         }
     }
     return found;

package/queries/catalog/dependencies-query/dependencies-query-executor.js

@@ -4,26 +4,39 @@ exports.executeDependenciesQuery = executeDependenciesQuery;
 const query_1 = require("../../query");
 const dependencies_query_format_1 = require("./dependencies-query-format");
 const vertex_1 = require("../../../dataflow/graph/vertex");
-const log_1 = require("../../../util/log");
 const type_1 = require("../../../r-bridge/lang-4.x/ast/model/type");
 const objects_1 = require("../../../util/objects");
 const function_info_1 = require("./function-info/function-info");
 const identify_link_to_last_call_relation_1 = require("../call-context-query/identify-link-to-last-call-relation");
 const resolve_argument_1 = require("../../../dataflow/eval/resolve/resolve-argument");
 const assert_1 = require("../../../util/assert");
+const log_1 = require("../../../util/log");
 /**
  * Executes a dependencies query.
  */
 async function executeDependenciesQuery({ analyzer, }, queries) {
+    let query = queries[0];
     if (queries.length !== 1) {
-        log_1.log.warn('Dependencies query expects only up to one query, but got ', queries.length, 'only using the first query');
+        // merge
+        for (let i = 1; i < queries.length; i++) {
+            const q = queries[i];
+            query = {
+                ...query,
+                enabledCategories: query.enabledCategories === undefined && q.enabledCategories === undefined ? undefined : [...(query.enabledCategories ?? []), ...(q.enabledCategories ?? [])],
+                ignoreDefaultFunctions: query.ignoreDefaultFunctions || q.ignoreDefaultFunctions,
+                additionalCategories: {
+                    ...query.additionalCategories,
+                    ...q.additionalCategories
+                }
+            };
+        }
+        log_1.log.info('Merged multiple dependencies queries into one:', query);
     }
     const data = { analyzer };
     const normalize = await analyzer.normalize();
     const dataflow = await analyzer.dataflow();
     const config = analyzer.flowrConfig;
     const now = Date.now();
-    const [query] = queries;
     const ignoreDefault = query.ignoreDefaultFunctions ?? false;
     const functions = new Map(Object.entries(dependencies_query_format_1.DefaultDependencyCategories).map(([c, v]) => {
         return [c, getFunctionsToCheck(query[`${c}Functions`], c, query.enabledCategories, ignoreDefault, v.functions)];
@@ -35,12 +48,12 @@ async function executeDependenciesQuery({ analyzer, }, queries) {
         }
     }
     const queryResults = functions.values().toArray().flat().length === 0 ? { kinds: {}, '.meta': { timing: 0 } } :
-        await (0, query_1.executeQueriesOfSameType)(data, functions.entries().map(([c, f]) => makeCallContextQuery(f, c)).toArray().flat());
+        await (0, query_1.executeQueriesOfSameType)(data, functions.entries().flatMap(makeCallContextQuery).toArray());
     const g = (0, dependencies_query_format_1.getAllCategories)(queries);
+    const enabled = query.enabledCategories;
     const results = Object.fromEntries(await Promise.all(functions.entries().map(async ([c, f]) => {
         const results = getResults(queries, { dataflow, config, normalize }, queryResults, c, f, data);
         // only default categories allow additional analyses, so we null-coalesce here!
-        const enabled = query.enabledCategories;
         if (enabled === undefined || (enabled?.length > 0 && enabled.includes(c))) {
             await g[c]?.additionalAnalysis?.(data, ignoreDefault, f, queryResults, results);
         }
@@ -53,7 +66,7 @@ async function executeDependenciesQuery({ analyzer, }, queries) {
         ...results,
     };
 }
-function makeCallContextQuery(functions, kind) {
+function makeCallContextQuery([kind, functions]) {
     return functions.map(f => ({
         type: 'call-context',
         callName: f.name,
@@ -75,90 +88,95 @@ const readOnlyModes = new Set(['r', 'rt', 'rb']);
 const writeOnlyModes = new Set(['w', 'wt', 'wb', 'a', 'at', 'ab']);
 function getResults(queries, { dataflow, config, normalize }, results, kind, functions, data) {
     const defaultValue = (0, dependencies_query_format_1.getAllCategories)(queries)[kind].defaultValue;
+    const vars = config.solver.variables;
     const functionMap = new Map(functions.map(f => [f.name, f]));
     const kindEntries = Object.entries(results?.kinds[kind]?.subkinds ?? {});
-    return kindEntries.flatMap(([name, results]) => results.flatMap(({ id, linkedIds }) => {
-        const vertex = dataflow.graph.getVertex(id);
-        const info = functionMap.get(name);
-        const args = (0, resolve_argument_1.getArgumentStringValue)(config.solver.variables, dataflow.graph, vertex, info.argIdx, info.argName, info.resolveValue, data.analyzer.inspectContext());
-        const linkedArgs = collectValuesFromLinks(args, { dataflow, config, ctx: data.analyzer.inspectContext() }, linkedIds);
-        const linked = dropInfoOnLinkedIds(linkedIds);
-        function ignoreOnArgVal() {
-            if (info.ignoreIf === 'arg-true' || info.ignoreIf === 'arg-false') {
-                const margs = info.additionalArgs?.val;
-                (0, assert_1.guard)(margs, 'Need additional argument val when checking for arg-true');
-                const valArgs = (0, resolve_argument_1.getArgumentStringValue)(config.solver.variables, dataflow.graph, vertex, margs.argIdx, margs.argName, margs.resolveValue, data?.analyzer.inspectContext());
-                const valValues = valArgs?.values().flatMap(v => Array.from(v)).toArray() ?? [];
-                if (valValues.length === 0) {
-                    return false;
+    const finalResults = [];
+    const ictx = data.analyzer.inspectContext();
+    const d = ictx.deps;
+    const dfg = dataflow.graph;
+    for (const [name, results] of kindEntries) {
+        for (const { id, linkedIds } of results) {
+            const vertex = dfg.getVertex(id);
+            const info = functionMap.get(name);
+            const args = (0, resolve_argument_1.getArgumentStringValue)(vars, dfg, vertex, info.argIdx, info.argName, info.resolveValue, ictx);
+            const linkedArgs = collectValuesFromLinks(args, { dataflow, config, ctx: ictx }, linkedIds);
+            const linked = dropInfoOnLinkedIds(linkedIds);
+            function ignoreOnArgVal() {
+                if (info.ignoreIf === 'arg-true' || info.ignoreIf === 'arg-false') {
+                    const margs = info.additionalArgs?.val;
+                    (0, assert_1.guard)(margs, 'Need additional argument val when checking for arg-true');
+                    const valArgs = (0, resolve_argument_1.getArgumentStringValue)(vars, dfg, vertex, margs.argIdx, margs.argName, margs.resolveValue, data?.analyzer.inspectContext());
+                    const valValues = valArgs?.values().flatMap(v => Array.from(v)).toArray() ?? [];
+                    if (valValues.length === 0) {
+                        return false;
+                    }
+                    if (info.ignoreIf === 'arg-true' && valValues.every(v => v === 'TRUE')) {
+                        // all values are TRUE, so we can ignore this
+                        return true;
+                    }
+                    else if (info.ignoreIf === 'arg-false' && valValues.every(v => v === 'FALSE')) {
+                        // all values are FALSE, so we can ignore this
+                        return true;
+                    }
                 }
-                if (info.ignoreIf === 'arg-true' && valValues.every(v => v === 'TRUE')) {
-                    // all values are TRUE, so we can ignore this
-                    return true;
+                return false;
+            }
+            const foundValues = linkedArgs ?? args;
+            if (!foundValues) {
+                if (info.ignoreIf === 'arg-missing') {
+                    continue;
                 }
-                else if (info.ignoreIf === 'arg-false' && valValues.every(v => v === 'FALSE')) {
-                    // all values are FALSE, so we can ignore this
-                    return true;
+                else if (ignoreOnArgVal()) {
+                    continue;
                 }
-            }
-            return false;
-        }
-        const foundValues = linkedArgs ?? args;
-        if (!foundValues) {
-            if (info.ignoreIf === 'arg-missing') {
-                return [];
-            }
-            else if (ignoreOnArgVal()) {
-                return [];
-            }
-            const record = (0, objects_1.compactRecord)({
-                nodeId: id,
-                functionName: vertex.name,
-                lexemeOfArgument: undefined,
-                linkedIds: linked?.length ? linked : undefined,
-                value: info.defaultValue ?? defaultValue
-            });
-            return record ? [record] : [];
-        }
-        else if (info.ignoreIf === 'mode-only-read' || info.ignoreIf === 'mode-only-write') {
-            (0, assert_1.guard)('mode' in (info.additionalArgs ?? {}), 'Need additional argument mode when checking for mode');
-            const margs = info.additionalArgs?.mode;
-            (0, assert_1.guard)(margs, 'Need additional argument mode when checking for mode');
-            const modeArgs = (0, resolve_argument_1.getArgumentStringValue)(config.solver.variables, dataflow.graph, vertex, margs.argIdx, margs.argName, margs.resolveValue, data?.analyzer.inspectContext());
-            const modeValues = modeArgs?.values().flatMap(v => Array.from(v)) ?? [];
-            if (info.ignoreIf === 'mode-only-read' && modeValues.every(m => m && readOnlyModes.has(m))) {
-                // all modes are read-only, so we can ignore this
-                return [];
-            }
-            else if (info.ignoreIf === 'mode-only-write' && modeValues.every(m => m && writeOnlyModes.has(m))) {
-                // all modes are write-only, so we can ignore this
-                return [];
-            }
-        }
-        else if (ignoreOnArgVal()) {
-            return [];
-        }
-        const results = [];
-        for (const [arg, values] of foundValues.entries()) {
-            for (const value of values) {
-                const dep = value ? data?.analyzer.inspectContext().deps.getDependency(value) ?? undefined : undefined;
-                const result = (0, objects_1.compactRecord)({
+                const record = (0, objects_1.compactRecord)({
                     nodeId: id,
                     functionName: vertex.name,
-                    lexemeOfArgument: getLexeme(value, arg),
+                    lexemeOfArgument: undefined,
                     linkedIds: linked?.length ? linked : undefined,
-                    value: value ?? info.defaultValue ?? defaultValue,
-                    versionConstraints: dep?.versionConstraints,
-                    derivedVersion: dep?.derivedVersion,
-                    namespaceInfo: dep?.namespaceInfo
+                    value: info.defaultValue ?? defaultValue
                 });
-                if (result) {
-                    results.push(result);
+                if (record) {
+                    finalResults.push(record);
+                }
+                continue;
+            }
+            else if (info.ignoreIf === 'mode-only-read' || info.ignoreIf === 'mode-only-write') {
+                const margs = info.additionalArgs?.mode;
+                (0, assert_1.guard)(margs, 'Need additional argument mode when checking for mode');
+                const modeArgs = (0, resolve_argument_1.getArgumentStringValue)(vars, dfg, vertex, margs.argIdx, margs.argName, margs.resolveValue, data?.analyzer.inspectContext());
+                const modeValues = modeArgs?.values().flatMap(v => Array.from(v)) ?? [];
+                if (info.ignoreIf === 'mode-only-read' && modeValues.every(m => m && readOnlyModes.has(m))) {
+                    // all modes are read-only, so we can ignore this
+                    continue;
+                }
+                else if (info.ignoreIf === 'mode-only-write' && modeValues.every(m => m && writeOnlyModes.has(m))) {
+                    // all modes are write-only, so we can ignore this
+                    continue;
+                }
+            }
+            else if (ignoreOnArgVal()) {
+                continue;
+            }
+            for (const [arg, values] of foundValues.entries()) {
+                for (const value of values) {
+                    const dep = value ? d.getDependency(value) ?? undefined : undefined;
+                    finalResults.push((0, objects_1.compactRecord)({
+                        nodeId: id,
+                        functionName: vertex.name,
+                        lexemeOfArgument: getLexeme(value, arg),
+                        linkedIds: linked?.length ? linked : undefined,
+                        value: value ?? info.defaultValue ?? defaultValue,
+                        versionConstraints: dep?.versionConstraints,
+                        derivedVersion: dep?.derivedVersion,
+                        namespaceInfo: dep?.namespaceInfo
+                    }));
                 }
             }
         }
-        return results;
-    })) ?? [];
+    }
+    return finalResults;
     function getLexeme(argument, id) {
         if ((argument && argument !== dependencies_query_format_1.Unknown) || !id) {
             return undefined;
@@ -174,7 +192,7 @@ function collectValuesFromLinks(args, data, linkedIds) {
     if (!linkedIds || linkedIds.length === 0) {
         return undefined;
     }
-    const hasAtLeastAValue = args !== undefined && [...args.values()].some(set => [...set].some(v => v !== dependencies_query_format_1.Unknown && v !== undefined));
+    const hasAtLeastAValue = args !== undefined && args.values().flatMap(x => Array.from(x)).toArray().some(v => v !== dependencies_query_format_1.Unknown && v !== undefined);
     const map = new Map();
     for (const linkedId of linkedIds) {
         if (typeof linkedId !== 'object' || !linkedId.info) {
@@ -187,7 +205,7 @@ function collectValuesFromLinks(args, data, linkedIds) {
         }
         // collect this one!
         const vertex = data.dataflow.graph.getVertex(linkedId.id);
-        if (vertex === undefined || vertex.tag !== vertex_1.VertexType.FunctionCall) {
+        if (vertex?.tag !== vertex_1.VertexType.FunctionCall) {
             continue;
         }
         const args = (0, resolve_argument_1.getArgumentStringValue)(data.config.solver.variables, data.dataflow.graph, vertex, info.argIdx, info.argName, info.resolveValue, data.ctx);
@@ -209,7 +227,7 @@ function getFunctionsToCheck(customFunctions, functionFlag, enabled, ignoreDefau
     if (enabled !== undefined && (enabled?.length === 0 || enabled.indexOf(functionFlag) < 0)) {
         return [];
     }
-    let functions = ignoreDefaultFunctions ? [] : [...defaultFunctions];
+    let functions = ignoreDefaultFunctions ? [] : defaultFunctions.slice();
     if (customFunctions) {
         functions = functions.concat(customFunctions);
     }

package/queries/query.js

@@ -73,10 +73,11 @@ exports.SupportedQueries = {
  */
 async function executeQueriesOfSameType(data, queries) {
     (0, assert_1.guard)(queries.length > 0, 'At least one query must be provided');
+    const qzt = queries[0].type;
     /* every query must have the same type */
-    (0, assert_1.guard)(queries.every(q => q.type === queries[0].type), 'All queries must have the same type');
-    const query = exports.SupportedQueries[queries[0].type];
-    (0, assert_1.guard)(query !== undefined, `Unsupported query type: ${queries[0].type}`);
+    (0, assert_1.guard)(queries.every(q => q.type === qzt), 'All queries must have the same type');
+    const query = exports.SupportedQueries[qzt];
+    (0, assert_1.guard)(query !== undefined, `Unsupported query type: ${qzt}`);
     return query.executor(data, queries);
 }
 function isVirtualQuery(query) {

package/r-bridge/data/data.d.ts

@@ -664,6 +664,26 @@ export declare const flowrCapabilities: {
             readonly id: "system-calls";
             readonly supported: "not";
             readonly description: "_Handle [`system`](https://www.rdocumentation.org/packages/base/versions/3.6.2/topics/system), `system.*`, ..._ We do not support system calls but treat them as unknown function calls.";
+        }, {
+            readonly name: "R-Markdown files";
+            readonly id: "file:rmd";
+            readonly supported: "fully";
+            readonly description: "Support R-Markdown files as R sources.";
+        }, {
+            readonly name: "Jupyter Notebook";
+            readonly id: "file:ipynb";
+            readonly supported: "partially";
+            readonly description: "Support Jupyter Notebooks as R sources.";
+        }, {
+            readonly name: "Quarto";
+            readonly id: "file:qmd";
+            readonly supported: "partially";
+            readonly description: "Support Quarto files as R sources.";
+        }, {
+            readonly name: "Sweave";
+            readonly id: "file:rnw";
+            readonly supported: "partially";
+            readonly description: "Support for Sweave files as R sources.";
         }];
     }, {
         readonly name: "Pre-Processors/external Tooling";

package/r-bridge/data/data.js

@@ -829,6 +829,30 @@ ${await (0, doc_dfg_1.printDfGraphForCode)(parser, code, { simplified: true })}
                     id: 'system-calls',
                     supported: 'not',
                     description: '_Handle [`system`](https://www.rdocumentation.org/packages/base/versions/3.6.2/topics/system), `system.*`, ..._ We do not support system calls but treat them as unknown function calls.'
+                },
+                {
+                    name: 'R-Markdown files',
+                    id: 'file:rmd',
+                    supported: 'fully',
+                    description: 'Support R-Markdown files as R sources.'
+                },
+                {
+                    name: 'Jupyter Notebook',
+                    id: 'file:ipynb',
+                    supported: 'partially',
+                    description: 'Support Jupyter Notebooks as R sources.'
+                },
+                {
+                    name: 'Quarto',
+                    id: 'file:qmd',
+                    supported: 'partially',
+                    description: 'Support Quarto files as R sources.'
+                },
+                {
+                    name: 'Sweave',
+                    id: 'file:rnw',
+                    supported: 'partially',
+                    description: 'Support for Sweave files as R sources.'
                 }
             ]
         },

package/util/version.js

@@ -6,7 +6,7 @@ exports.printVersionInformation = printVersionInformation;
 const semver_1 = require("semver");
 const assert_1 = require("./assert");
 // this is automatically replaced with the current version by release-it
-const version = '2.9.4';
+const version = '2.9.6';
 /**
  * Retrieves the current flowR version as a new {@link SemVer} object.
  */