@eagleoutice/flowr 1.4.1 → 1.4.2

package/r-bridge/shell.js

@@ -26,16 +26,16 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.RShell = exports.DEFAULT_R_SHELL_OPTIONS = exports.DEFAULT_R_SHELL_EXEC_OPTIONS = exports.DEFAULT_OUTPUT_COLLECTOR_CONFIGURATION = void 0;
+exports.RShell = exports.DEFAULT_R_SHELL_OPTIONS = exports.DEFAULT_R_SHELL_EXEC_OPTIONS = exports.DEFAULT_R_PATH = exports.DEFAULT_OUTPUT_COLLECTOR_CONFIGURATION = void 0;
 const child_process_1 = require("child_process");
 const objects_1 = require("../util/objects");
-const readline = __importStar(require("node:readline"));
+const readline = __importStar(require("readline"));
 const lang_4_x_1 = require("./lang-4.x");
 const log_1 = require("../util/log");
 const preload_1 = __importDefault(require("semver/preload"));
 const os_1 = require("../util/os");
 const fs_1 = __importDefault(require("fs"));
-const retriever_1 = require("./retriever");
+const config_1 = require("../config");
 exports.DEFAULT_OUTPUT_COLLECTOR_CONFIGURATION = {
     from: 'stdout',
     postamble: `🐧${'-'.repeat(5)}🐧`,
@@ -47,13 +47,14 @@ exports.DEFAULT_OUTPUT_COLLECTOR_CONFIGURATION = {
     automaticallyTrimOutput: true,
     errorStopsWaiting: true
 };
+exports.DEFAULT_R_PATH = (0, os_1.getPlatform)() === 'windows' ? 'R.exe' : 'R';
 exports.DEFAULT_R_SHELL_EXEC_OPTIONS = {
-    pathToRExecutable: (0, os_1.getPlatform)() === 'windows' ? 'R.exe' : 'R',
+    pathToRExecutable: (0, config_1.getConfig)().rPath ?? exports.DEFAULT_R_PATH,
     commandLineOptions: ['--vanilla', '--quiet', '--no-echo', '--no-save'],
     cwd: process.cwd(),
     env: process.env,
     eol: '\n',
-    homeLibPath: (0, os_1.getPlatform)() === 'windows' ? undefined : '~/.r-libs',
+    homeLibPath: (0, os_1.getPlatform)() === 'windows' ? undefined : '~/.r-libs'
 };
 exports.DEFAULT_R_SHELL_OPTIONS = {
     ...exports.DEFAULT_R_SHELL_EXEC_OPTIONS,
@@ -74,7 +75,6 @@ class RShell {
     session;
     log;
     versionCache = null;
-    tokenMapCache = null;
     // should never be more than one, but let's be sure
     tempDirs = new Set();
     constructor(options) {
@@ -116,30 +116,28 @@ class RShell {
         this.versionCache = preload_1.default.coerce(result[0]);
         return result.length === 1 ? this.versionCache : null;
     }
-    /**
-     * Retrieve the token map of the xmlparsedata package.
-     *
-     * @note For multiple calls, this makes use of caching
-     */
-    async tokenMap() {
-        if (this.tokenMapCache === null) {
-            this.tokenMapCache = await this.retrieveTokenMap();
-        }
-        return this.tokenMapCache;
+    injectLibPaths(...paths) {
+        this.log.debug(`injecting lib paths ${JSON.stringify(paths)}`);
+        this._sendCommand(`.libPaths(c(.libPaths(), ${paths.map(lang_4_x_1.ts2r).join(',')}))`);
     }
-    async retrieveTokenMap() {
-        await this.ensurePackageInstalled('xmlparsedata', true /* use some kind of environment in the future */);
-        // we invert the token map to get a mapping back from the replacement
-        const parsed = (0, lang_4_x_1.parseCSV)(await this.sendCommandWithOutput('write.table(xmlparsedata::xml_parse_token_map,sep=",",col.names=FALSE)'));
-        if (parsed.some(s => s.length !== 2)) {
-            throw new Error(`Expected two columns in token map, but got ${JSON.stringify(parsed)}`);
+    tryToInjectHomeLibPath() {
+        // ensure the path exists first
+        if (this.options.homeLibPath === undefined) {
+            this.log.debug('ensuring home lib path exists (automatic inject)');
+            this.sendCommand('if(!dir.exists(Sys.getenv("R_LIBS_USER"))) { dir.create(path=Sys.getenv("R_LIBS_USER"),showWarnings=FALSE,recursive=TRUE) }');
+            this.sendCommand('.libPaths(c(.libPaths(), Sys.getenv("R_LIBS_USER")))');
         }
-        // we swap key and value to get the other direction, furthermore we remove quotes from keys if they are quoted
-        const cache = {};
-        for (const [key, value] of parsed) {
-            cache[value] = (0, retriever_1.removeTokenMapQuotationMarks)(key);
+        else {
+            this.injectLibPaths(this.options.homeLibPath);
         }
-        return cache;
+    }
+    /**
+     * checks if a given package is already installed on the system!
+     */
+    async isPackageInstalled(packageName) {
+        this.log.debug(`checking if package "${packageName}" is installed`);
+        const result = await this.sendCommandWithOutput(`cat(system.file(package="${packageName}")!="","${this.options.eol}")`);
+        return result.length === 1 && result[0] === 'TRUE';
     }
     /**
    * Send a command and collect the output
@@ -197,69 +195,6 @@ class RShell {
         this.log.info('continue in case of Errors');
         this._sendCommand('options(error=function() {})');
     }
-    injectLibPaths(...paths) {
-        this.log.debug(`injecting lib paths ${JSON.stringify(paths)}`);
-        this._sendCommand(`.libPaths(c(.libPaths(), ${paths.map(lang_4_x_1.ts2r).join(',')}))`);
-    }
-    tryToInjectHomeLibPath() {
-        // ensure the path exists first
-        if (this.options.homeLibPath === undefined) {
-            this.log.debug('ensuring home lib path exists (automatic inject)');
-            this.sendCommand('if(!dir.exists(Sys.getenv("R_LIBS_USER"))) { dir.create(path=Sys.getenv("R_LIBS_USER"),showWarnings=FALSE,recursive=TRUE) }');
-            this.sendCommand('.libPaths(c(.libPaths(), Sys.getenv("R_LIBS_USER")))');
-        }
-        else {
-            this.injectLibPaths(this.options.homeLibPath);
-        }
-    }
-    /**
-   * checks if a given package is already installed on the system!
-   */
-    async isPackageInstalled(packageName) {
-        this.log.debug(`checking if package "${packageName}" is installed`);
-        const result = await this.sendCommandWithOutput(`cat(system.file(package="${packageName}")!="","${this.options.eol}")`);
-        return result.length === 1 && result[0] === 'TRUE';
-    }
-    async allInstalledPackages() {
-        this.log.debug('getting all installed packages');
-        const [packages] = await this.sendCommandWithOutput(`cat(paste0(installed.packages()[,1], collapse=","),"${this.options.eol}")`);
-        return packages.split(',');
-    }
-    /**
-   * Installs the package using a temporary location
-   *
-   * @param packageName - The package to install
-   * @param autoload    - If true, the package will be loaded after installation
-   * @param force       - If true, the package will be installed no if it is already on the system and ready to be loaded
-   */
-    async ensurePackageInstalled(packageName, autoload = false, force = false) {
-        const packageExistedAlready = await this.isPackageInstalled(packageName);
-        if (!force && packageExistedAlready) {
-            this.log.info(`package "${packageName}" is already installed`);
-            if (autoload) {
-                this.sendCommand(`library(${(0, lang_4_x_1.ts2r)(packageName)})`);
-            }
-            return {
-                packageName,
-                packageExistedAlready: true
-            };
-        }
-        // obtain a temporary directory
-        const tempdir = await this.obtainTmpDir();
-        this.log.debug(`using temporary directory: "${tempdir}" to install package "${packageName}"`);
-        await this.sendCommandWithOutput(`install.packages(${(0, lang_4_x_1.ts2r)(packageName)},repos="https://cloud.r-project.org/",quiet=FALSE,lib=temp)`, {
-            ms: 750_000,
-            resetOnNewData: true
-        });
-        if (autoload) {
-            this.sendCommand(`library(${(0, lang_4_x_1.ts2r)(packageName)},lib.loc=temp)`);
-        }
-        return {
-            packageName,
-            libraryLocation: tempdir,
-            packageExistedAlready
-        };
-    }
     /**
      * Obtain the temporary directory used by R.
      * Additionally, this marks the directory for removal when the shell exits.
@@ -307,7 +242,9 @@ class RShellSession {
             input: this.bareSession.stderr,
             terminal: false
         });
-        this.onExit(() => { this.end(); });
+        this.onExit(() => {
+            this.end();
+        });
         this.options = options;
         this.log = log;
         this.setupRSessionLoggers();
@@ -351,7 +288,9 @@ class RShellSession {
                     this.collectionTimeout = makeTimer();
                 }
             };
-            error = () => { resolve(result); };
+            error = () => {
+                resolve(result);
+            };
             this.onExit(error);
             this.on(from, 'line', handler);
             action?.();

package/statistics/features/supported/assignments/post-process.js

@@ -6,7 +6,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.postProcess = void 0;
 const common_syntax_probability_1 = require("../../common-syntax-probability");
 const numbers_1 = require("../../../../util/numbers");
-const node_fs_1 = __importDefault(require("node:fs"));
+const fs_1 = __importDefault(require("fs"));
 const path_1 = __importDefault(require("path"));
 const data_1 = require("../../../../util/summarizer/benchmark/data");
 const process_1 = require("../../../../util/summarizer/benchmark/first-phase/process");
@@ -35,7 +35,7 @@ function retrieveUsageCombinationCounts(collected) {
         return new Map();
     }
     const allCombinations = [...(0, arrays_1.getUniqueCombinationsOfSize)(ops, 1)];
-    const store = new Map;
+    const store = new Map();
     for (const combs of allCombinations) {
         if (combs.length === 1) {
             // we can just copy the information
@@ -61,7 +61,7 @@ function retrieveUsageCombinationCounts(collected) {
 function writeOperatorCombinationsUsageToCsv(collected, outputPath) {
     // now to get all projects exhausted with _only_ a given subset (e.g., all projects only using '=')
     const operators = retrieveUsageCombinationCounts(collected);
-    const out = node_fs_1.default.createWriteStream(path_1.default.join(outputPath, 'assignments-assigned-combinations.csv'));
+    const out = fs_1.default.createWriteStream(path_1.default.join(outputPath, 'assignments-assigned-combinations.csv'));
     out.write('assignment,unique-projects,unique-files\n');
     for (const [key, val] of operators.entries()) {
         out.write(`${JSON.stringify(key)},${val.uniqueProjects},${val.uniqueFiles}\n`);
@@ -69,7 +69,7 @@ function writeOperatorCombinationsUsageToCsv(collected, outputPath) {
     out.close();
 }
 function writeAssignmentMetadataToCsv(outputPath, collected) {
-    const out = node_fs_1.default.createWriteStream(path_1.default.join(outputPath, 'assignments-meta.csv'));
+    const out = fs_1.default.createWriteStream(path_1.default.join(outputPath, 'assignments-meta.csv'));
     out.write(`kind,${(0, data_1.summarizedMeasurement2CsvHeader)()}\n`);
     const summarizedDeepestNesting = (0, process_1.summarizeMeasurement)(collected.deepestNesting.flat());
     out.write(`deepest-nesting,${(0, data_1.summarizedMeasurement2Csv)(summarizedDeepestNesting)}\n`);
@@ -78,7 +78,7 @@ function writeAssignmentMetadataToCsv(outputPath, collected) {
     out.close();
 }
 function writeAssignedTypesToCsv(outputPath, collected) {
-    const out = node_fs_1.default.createWriteStream(path_1.default.join(outputPath, 'assignments-assigned.csv'));
+    const out = fs_1.default.createWriteStream(path_1.default.join(outputPath, 'assignments-assigned.csv'));
     out.write(`kind,name,${(0, data_1.summarizedMeasurement2CsvHeader)()}\n`);
     for (const [entryName, values] of Object.entries(collected.assigned)) {
         if (Array.isArray(values)) {
@@ -93,7 +93,7 @@ function writeAssignedTypesToCsv(outputPath, collected) {
     out.close();
 }
 function writeAssignmentOperatorsToCsv(outputPath, collected) {
-    const fnOutStream = node_fs_1.default.createWriteStream(path_1.default.join(outputPath, 'assignments-assignment-operators.csv'));
+    const fnOutStream = fs_1.default.createWriteStream(path_1.default.join(outputPath, 'assignments-assignment-operators.csv'));
     fnOutStream.write(`assignment,unique-projects,unique-files,${(0, data_1.summarizedMeasurement2CsvHeader)()}\n`);
     for (const [key, val] of Object.entries(collected.assignmentOperator)) {
         const { uniqueProjects, uniqueFiles, counts } = val;

package/statistics/features/supported/comments/post-process.js

@@ -7,7 +7,7 @@ exports.postProcess = void 0;
 const data_1 = require("../../../../util/summarizer/benchmark/data");
 const comments_1 = require("./comments");
 const assert_1 = require("../../../../util/assert");
-const node_fs_1 = __importDefault(require("node:fs"));
+const fs_1 = __importDefault(require("fs"));
 const path_1 = __importDefault(require("path"));
 const process_1 = require("../../../../util/summarizer/benchmark/first-phase/process");
 // monoids would be helpful :c
@@ -37,7 +37,7 @@ function postProcess(featureRoot, info, outputPath, config) {
     for (const [filepath, feature] of info.entries()) {
         appendCommentsPostProcessing(collected, feature.comments, feature.stats.lines[0].length, filepath, config.projectSkip);
     }
-    const fnOutStream = node_fs_1.default.createWriteStream(path_1.default.join(outputPath, 'comments.csv'));
+    const fnOutStream = fs_1.default.createWriteStream(path_1.default.join(outputPath, 'comments.csv'));
     fnOutStream.write(`kind,unique-projects,unique-files,${(0, data_1.summarizedMeasurement2CsvHeader)('count')},${(0, data_1.summarizedMeasurement2CsvHeader)('frac-of-lines')}\n`);
     for (const [key, val] of Object.entries(collected)) {
         const { count, uniqueProjects, uniqueFiles, fracOfLines } = val;

package/statistics/features/supported/data-access/post-process.js

@@ -8,7 +8,7 @@ const data_1 = require("../../../../util/summarizer/benchmark/data");
 const common_syntax_probability_1 = require("../../common-syntax-probability");
 const post_processing_1 = require("../../post-processing");
 const numbers_1 = require("../../../../util/numbers");
-const node_fs_1 = __importDefault(require("node:fs"));
+const fs_1 = __importDefault(require("fs"));
 const path_1 = __importDefault(require("path"));
 const process_1 = require("../../../../util/summarizer/benchmark/first-phase/process");
 function addToList(data, dataAccess, filepath, config) {
@@ -37,7 +37,7 @@ function summarizeForBracket(dataAccess, data, filepath, config) {
     }
 }
 function writeSingleOrDoubleEmpty(outputPath, key, name, vals) {
-    const out = node_fs_1.default.createWriteStream(path_1.default.join(outputPath, `data-access-type-${key}-${name}.csv`));
+    const out = fs_1.default.createWriteStream(path_1.default.join(outputPath, `data-access-type-${key}-${name}.csv`));
     // name is for fields like number etc. to allow to group multiple entries
     out.write(`kind,unique-projects,unique-files,${(0, data_1.summarizedMeasurement2CsvHeader)()}\n`);
     out.write(`"0",${vals.uniqueProjects.size},${vals.uniqueFiles.size},${(0, data_1.summarizedMeasurement2Csv)((0, process_1.summarizeMeasurement)(vals.count))}\n`);
@@ -51,7 +51,7 @@ function writeSingleOrDoubleBrackets(data, outputPath, key) {
         }
         else {
             // non-0-column
-            const out = node_fs_1.default.createWriteStream(path_1.default.join(outputPath, `data-access-type-${key}-${name}.csv`));
+            const out = fs_1.default.createWriteStream(path_1.default.join(outputPath, `data-access-type-${key}-${name}.csv`));
             // name is for fields like number etc. to allow to group multiple entries
             out.write(`kind,name,${(0, data_1.summarizedMeasurement2CsvHeader)()}\n`);
             for (const [entryName, values] of Object.entries(vals)) {
@@ -91,7 +91,7 @@ function postProcess(featureRoot, info, outputPath, config) {
         summarizeForBracket(dataAccess.singleBracket, summarize.singleBracket, filepath, config);
         summarizeForBracket(dataAccess.doubleBracket, summarize.doubleBracket, filepath, config);
     }
-    const metaOut = node_fs_1.default.createWriteStream(path_1.default.join(outputPath, 'data-access-meta.csv'));
+    const metaOut = fs_1.default.createWriteStream(path_1.default.join(outputPath, 'data-access-meta.csv'));
     metaOut.write(`kind,unique-projects,unique-files,${(0, data_1.summarizedMeasurement2CsvHeader)()}\n`);
     for (const [key, value] of Object.entries(summarize)) {
         const data = value;

package/statistics/features/supported/defined-functions/post-process.js

@@ -8,7 +8,7 @@ const data_1 = require("../../../../util/summarizer/benchmark/data");
 const process_1 = require("../../../../util/summarizer/benchmark/first-phase/process");
 const files_1 = require("../../../../util/files");
 const path_1 = __importDefault(require("path"));
-const node_fs_1 = __importDefault(require("node:fs"));
+const fs_1 = __importDefault(require("fs"));
 const time_1 = require("../../../../util/time");
 const defined_functions_1 = require("./defined-functions");
 const post_processing_1 = require("../../post-processing");
@@ -42,7 +42,7 @@ function retrievePerFileDefinitionInformation(featureRoot, info, config, outputP
     // we collect only `all-calls`
     (0, files_1.readLineByLineSync)(path_1.default.join(featureRoot, `${defined_functions_1.AllDefinitionsFileBase}.txt`), (line, lineNumber) => processNextLine(definitionsPerFile, lineNumber, info, JSON.parse(String(line))));
     console.log(`    [${(0, time_1.date2string)(new Date())}] Defined functions process completed, start to write out function info`);
-    const fnOutStream = node_fs_1.default.createWriteStream(path_1.default.join(outputPath, 'function-definitions.csv'));
+    const fnOutStream = fs_1.default.createWriteStream(path_1.default.join(outputPath, 'function-definitions.csv'));
     const prefixes = ['total', 'params', 'length-lines', 'length-chars', 'length-non-ws-chars', 'return-explicit', 'return-implicit', 'return-only-explicit', 'return-only-implicit', 'exit-points-line-crac', 'def-line-frac'];
     const others = prefixes.flatMap(data_1.summarizedMeasurement2CsvHeader).join(',');
     fnOutStream.write(`counter,${others}\n`);
@@ -84,7 +84,7 @@ function retrieveMetaInformation(info, config, outputPath) {
         addToList(data.deepestNesting, us.deepestNesting, filepath, config);
     }
     console.log(`    [${(0, time_1.date2string)(new Date())}] Defined functions metadata reading completed, summarizing and writing to file`);
-    const out = node_fs_1.default.createWriteStream(path_1.default.join(outputPath, 'function-definitions-meta.csv'));
+    const out = fs_1.default.createWriteStream(path_1.default.join(outputPath, 'function-definitions-meta.csv'));
     out.write(`kind,unique-projects,unique-files,${(0, data_1.summarizedMeasurement2CsvHeader)()}\n`);
     for (const [key, val] of Object.entries(data)) {
         const data = val;
@@ -107,7 +107,7 @@ function retrieveAssignedFunctionNames(featureRoot, config, outputPath) {
             addToList(get, count, context ?? '', config);
         }
     });
-    const varNamesOut = node_fs_1.default.createWriteStream(path_1.default.join(outputPath, 'function-definitions-var-names.csv'));
+    const varNamesOut = fs_1.default.createWriteStream(path_1.default.join(outputPath, 'function-definitions-var-names.csv'));
     varNamesOut.write(`name,unique-projects,unique-files,${(0, data_1.summarizedMeasurement2CsvHeader)()}\n`);
     for (const [key, val] of varNames.entries()) {
         varNamesOut.write(`${JSON.stringify(key)},${val.uniqueProjects.size},${val.uniqueFiles.size},${(0, data_1.summarizedMeasurement2Csv)((0, process_1.summarizeMeasurement)(val.count))}\n`);

package/statistics/features/supported/expression-list/post-process.js

@@ -5,13 +5,13 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.postProcess = void 0;
 const post_processing_1 = require("../../post-processing");
-const node_fs_1 = __importDefault(require("node:fs"));
+const fs_1 = __importDefault(require("fs"));
 const path_1 = __importDefault(require("path"));
 const data_1 = require("../../../../util/summarizer/benchmark/data");
 const process_1 = require("../../../../util/summarizer/benchmark/first-phase/process");
 function postProcess(featureRoot, info, outputPath, config) {
     const collected = {};
-    const deepestNestingOut = node_fs_1.default.createWriteStream(path_1.default.join(outputPath, 'deepest-nesting-per-file.csv'));
+    const deepestNestingOut = fs_1.default.createWriteStream(path_1.default.join(outputPath, 'deepest-nesting-per-file.csv'));
     deepestNestingOut.write('file,deepest-nesting\n');
     for (const [filepath, data] of info.entries()) {
         const value = data.expressionList;
@@ -31,7 +31,7 @@ function postProcess(featureRoot, info, outputPath, config) {
         }
     }
     deepestNestingOut.close();
-    const variablesOutStream = node_fs_1.default.createWriteStream(path_1.default.join(outputPath, 'used-expression-lists.csv'));
+    const variablesOutStream = fs_1.default.createWriteStream(path_1.default.join(outputPath, 'used-expression-lists.csv'));
     variablesOutStream.write(`kind,unique-projects,unique-files,${(0, data_1.summarizedMeasurement2CsvHeader)()}\n`);
     for (const [key, val] of Object.entries(collected)) {
         const data = val;

package/statistics/features/supported/loops/post-process.js

@@ -8,7 +8,7 @@ const post_processing_1 = require("../../post-processing");
 const common_syntax_probability_1 = require("../../common-syntax-probability");
 const numbers_1 = require("../../../../util/numbers");
 const path_1 = __importDefault(require("path"));
-const node_fs_1 = __importDefault(require("node:fs"));
+const fs_1 = __importDefault(require("fs"));
 const data_1 = require("../../../../util/summarizer/benchmark/data");
 const process_1 = require("../../../../util/summarizer/benchmark/first-phase/process");
 function postProcess(featureRoot, info, outputPath, config) {
@@ -41,7 +41,7 @@ function postProcess(featureRoot, info, outputPath, config) {
             }
         }
     }
-    const metaOut = node_fs_1.default.createWriteStream(path_1.default.join(outputPath, 'loops-meta.csv'));
+    const metaOut = fs_1.default.createWriteStream(path_1.default.join(outputPath, 'loops-meta.csv'));
     metaOut.write(`kind,unique-projects,unique-files,${(0, data_1.summarizedMeasurement2CsvHeader)()}\n`);
     for (const [key, val] of Object.entries(collected)) {
         const data = val;
@@ -50,7 +50,7 @@ function postProcess(featureRoot, info, outputPath, config) {
         }
         else {
             // new file for each :D
-            const out = node_fs_1.default.createWriteStream(path_1.default.join(outputPath, `loops-type-${key}.csv`));
+            const out = fs_1.default.createWriteStream(path_1.default.join(outputPath, `loops-type-${key}.csv`));
             // name is for fields like number etc to allow to group multiple entries
             out.write(`kind,name,${(0, data_1.summarizedMeasurement2CsvHeader)()}\n`);
             for (const [name, vals] of Object.entries(data)) {

package/statistics/features/supported/used-functions/post-process.js

@@ -9,7 +9,7 @@ const common_syntax_probability_1 = require("../../common-syntax-probability");
 const process_1 = require("../../../../util/summarizer/benchmark/first-phase/process");
 const files_1 = require("../../../../util/files");
 const path_1 = __importDefault(require("path"));
-const node_fs_1 = __importDefault(require("node:fs"));
+const fs_1 = __importDefault(require("fs"));
 const time_1 = require("../../../../util/time");
 const used_functions_1 = require("./used-functions");
 const numbers_1 = require("../../../../util/numbers");
@@ -33,7 +33,7 @@ function retrieveFunctionCallInformation(featureRoot, info, config, outputPath)
         'assign',
         'get',
         'setGeneric',
-        'R6Class'].map(name => [name, node_fs_1.default.createWriteStream(path_1.default.join(outputPath, `${name}.csv`))]));
+        'R6Class'].map(name => [name, fs_1.default.createWriteStream(path_1.default.join(outputPath, `${name}.csv`))]));
     for (const [, value] of importantFunctions) {
         value.write('filepath,location,namespace,inspected by,classification,notes\n');
     }
@@ -44,7 +44,7 @@ function retrieveFunctionCallInformation(featureRoot, info, config, outputPath)
     }
     importantFunctions.clear();
     console.log(`    [${(0, time_1.date2string)(new Date())}] Used functions process completed, start to write out function info`);
-    const fnOutStream = node_fs_1.default.createWriteStream(path_1.default.join(outputPath, 'function-calls.csv'));
+    const fnOutStream = fs_1.default.createWriteStream(path_1.default.join(outputPath, 'function-calls.csv'));
     const prefixes = ['total', 'args', 'line-frac'];
     const others = prefixes.flatMap(data_1.summarizedMeasurement2CsvHeader).join(',');
     fnOutStream.write(`function,unique-projects,unique-files,${others}\n`);
@@ -58,7 +58,7 @@ function retrieveFunctionCallInformation(featureRoot, info, config, outputPath)
     fnOutStream.close();
 }
 function writeFunctionCallsMetaInformationToCsv(outputPath, data) {
-    const out = node_fs_1.default.createWriteStream(path_1.default.join(outputPath, 'function-calls-meta.csv'));
+    const out = fs_1.default.createWriteStream(path_1.default.join(outputPath, 'function-calls-meta.csv'));
     out.write(`kind,unique-projects,unique-files,${(0, data_1.summarizedMeasurement2CsvHeader)()}\n`);
     out.write(`average-call,${(0, data_1.summarizedMeasurement2Csv)((0, process_1.summarizeMeasurement)(data.averageCall.flat()))}\n`);
     out.write(`nested-calls,${(0, data_1.summarizedMeasurement2Csv)((0, process_1.summarizeMeasurement)(data.nestedCalls.flat()))}\n`);
@@ -102,7 +102,7 @@ function retrieveFunctionCallMetaInformation(info, outputPath) {
             // we treat the first/0-argument entry separate for legacy reasons
             continue;
         }
-        const out = node_fs_1.default.createWriteStream(path_1.default.join(outputPath, `function-calls-arg-${index}.csv`));
+        const out = fs_1.default.createWriteStream(path_1.default.join(outputPath, `function-calls-arg-${index}.csv`));
         out.write(`kind,name,${(0, data_1.summarizedMeasurement2CsvHeader)()}\n`);
         for (const [name, vals] of Object.entries(arg)) {
             if (Array.isArray(vals)) {

package/statistics/features/supported/used-packages/post-process.js

@@ -6,7 +6,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.postProcess = void 0;
 const post_processing_1 = require("../../post-processing");
 const used_packages_1 = require("./used-packages");
-const node_fs_1 = __importDefault(require("node:fs"));
+const fs_1 = __importDefault(require("fs"));
 const path_1 = __importDefault(require("path"));
 const data_1 = require("../../../../util/summarizer/benchmark/data");
 const process_1 = require("../../../../util/summarizer/benchmark/first-phase/process");
@@ -29,7 +29,7 @@ function postProcess(featureRoot, info, outputPath, config) {
             }
         }
     }
-    const variablesOutStream = node_fs_1.default.createWriteStream(path_1.default.join(outputPath, 'loading-functions.csv'));
+    const variablesOutStream = fs_1.default.createWriteStream(path_1.default.join(outputPath, 'loading-functions.csv'));
     variablesOutStream.write(`kind,unique-projects,unique-files,${(0, data_1.summarizedMeasurement2CsvHeader)()}\n`);
     for (const [key, val] of Object.entries(collected)) {
         const data = val;
@@ -58,7 +58,7 @@ function postProcess(featureRoot, info, outputPath, config) {
         }
     }
     const output = path_1.default.join(outputPath, 'all-operators.csv');
-    const out = node_fs_1.default.createWriteStream(output);
+    const out = fs_1.default.createWriteStream(output);
     out.write(`kind,unique-projects,unique-files,${(0, data_1.summarizedMeasurement2CsvHeader)()}\n`);
     for (const [key, val] of loadedLibraries.entries()) {
         const { count, uniqueProjects, uniqueFiles } = val;
@@ -71,7 +71,7 @@ exports.postProcess = postProcess;
 // directly writes the results to the output path
 function retrieveDataForLoad(operator, readFromPath, outputPath, config) {
     const input = path_1.default.join(readFromPath, `${operator}.txt`);
-    if (!node_fs_1.default.existsSync(input)) {
+    if (!fs_1.default.existsSync(input)) {
         // if there is nothing with this, just return :)
         return new Map();
     }
@@ -108,7 +108,7 @@ function retrieveDataForLoad(operator, readFromPath, outputPath, config) {
         }
     });
     const output = path_1.default.join(outputPath, `${operator}.csv`);
-    const out = node_fs_1.default.createWriteStream(output);
+    const out = fs_1.default.createWriteStream(output);
     out.write(`kind,unique-projects,unique-files,${(0, data_1.summarizedMeasurement2CsvHeader)()}\n`);
     for (const [key, val] of collected.entries()) {
         const { count, uniqueProjects, uniqueFiles } = val;

package/statistics/features/supported/values/post-process.js

@@ -5,7 +5,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.postProcess = void 0;
 const data_1 = require("../../../../util/summarizer/benchmark/data");
-const node_fs_1 = __importDefault(require("node:fs"));
+const fs_1 = __importDefault(require("fs"));
 const path_1 = __importDefault(require("path"));
 const process_1 = require("../../../../util/summarizer/benchmark/first-phase/process");
 const files_1 = require("../../../../util/files");
@@ -28,7 +28,7 @@ function postProcess(featureRoot, info, outputPath, config) {
             }
         }
     }
-    const valuesOutStream = node_fs_1.default.createWriteStream(path_1.default.join(outputPath, 'values.csv'));
+    const valuesOutStream = fs_1.default.createWriteStream(path_1.default.join(outputPath, 'values.csv'));
     valuesOutStream.write(`kind,unique-projects,unique-files,${(0, data_1.summarizedMeasurement2CsvHeader)()}\n`);
     for (const [key, val] of Object.entries(collected)) {
         const data = val;
@@ -60,7 +60,7 @@ function postProcess(featureRoot, info, outputPath, config) {
             }
         }
     });
-    const magicNumbersOutStream = node_fs_1.default.createWriteStream(path_1.default.join(outputPath, 'magic-numbers.csv'));
+    const magicNumbersOutStream = fs_1.default.createWriteStream(path_1.default.join(outputPath, 'magic-numbers.csv'));
     magicNumbersOutStream.write(`num,unique-projects,unique-files,${(0, data_1.summarizedMeasurement2CsvHeader)()}\n`);
     for (const [key, val] of valueMap.entries()) {
         const sum = (0, process_1.summarizeMeasurement)(val.count);

package/statistics/features/supported/variables/post-process.js

@@ -5,7 +5,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.writeVariableInfoToCsv = exports.postProcess = void 0;
 const post_processing_1 = require("../../post-processing");
-const node_fs_1 = __importDefault(require("node:fs"));
+const fs_1 = __importDefault(require("fs"));
 const path_1 = __importDefault(require("path"));
 const data_1 = require("../../../../util/summarizer/benchmark/data");
 const process_1 = require("../../../../util/summarizer/benchmark/first-phase/process");
@@ -27,7 +27,7 @@ function collectRedefinedVariables(featureRoot, info, config, outputPath) {
     redefined.clear();
 }
 function writeVariableCountsToCsv(outputPath, collected) {
-    const variablesOutStream = node_fs_1.default.createWriteStream(path_1.default.join(outputPath, 'variable-counts.csv'));
+    const variablesOutStream = fs_1.default.createWriteStream(path_1.default.join(outputPath, 'variable-counts.csv'));
     variablesOutStream.write(`kind,unique-projects,unique-files,${(0, data_1.summarizedMeasurement2CsvHeader)()}\n`);
     for (const [key, val] of Object.entries(collected)) {
         if (key === 'unknownVariables') {
@@ -67,7 +67,7 @@ function postProcess(featureRoot, info, outputPath, config) {
 }
 exports.postProcess = postProcess;
 function writeVariableInfoToCsv(outputPath, filename, data) {
-    const out = node_fs_1.default.createWriteStream(path_1.default.join(outputPath, filename));
+    const out = fs_1.default.createWriteStream(path_1.default.join(outputPath, filename));
     out.write(`variable,unique-projects,unique-files,${(0, data_1.summarizedMeasurement2CsvHeader)('count')},${(0, data_1.summarizedMeasurement2CsvHeader)('line-frac')}\n`);
     for (const [key, val] of data.entries()) {
         const { count, uniqueProjects, uniqueFiles, linePercentageInFile } = val;

package/statistics/output/ansi.js

@@ -17,7 +17,7 @@ exports.voidFormatter = new class {
     reset() {
         return '';
     }
-};
+}();
 /**
  * This does not work if the {@link setFormatter | formatter} is void. Tries to format the text with a bold font weight.
  */

package/statistics/statistics.js

@@ -4,6 +4,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.extractUsageStatistics = exports.staticRequests = void 0;
+const r_bridge_1 = require("../r-bridge");
 const features_1 = require("./features");
 const xmldom_1 = require("@xmldom/xmldom");
 const fs_1 = __importDefault(require("fs"));
@@ -37,7 +38,6 @@ exports.staticRequests = staticRequests;
 async function extractUsageStatistics(shell, onRequest, features, requests, rootPath) {
     let result = initializeFeatureStatistics();
     const meta = (0, meta_statistics_1.initialMetaStatistics)();
-    let first = true;
     const outputs = new Map();
     for await (const request of requests) {
         onRequest(request);
@@ -45,14 +45,10 @@ async function extractUsageStatistics(shell, onRequest, features, requests, root
         const suffix = request.request === 'file' ? request.content.replace(new RegExp('^' + (rootPath ?? '')), '') : undefined;
         try {
             let output;
-            ({ stats: result, output } = await extractSingle(result, shell, {
-                ...request,
-                ensurePackageInstalled: first
-            }, features, suffix));
+            ({ stats: result, output } = await extractSingle(result, shell, request, features, suffix));
             outputs.set(request, output);
             processMetaOnSuccessful(meta, request);
             meta.numberOfNormalizedNodes.push(output.normalize.idMap.size);
-            first = false;
         }
         catch (e) {
             log_1.log.error('for request: ', request, e);
@@ -89,8 +85,11 @@ async function extractSingle(result, shell, request, features, suffixFilePath) {
         stepOfInterest: 'dataflow',
         request, shell
     }).allRemainingSteps();
-    // await retrieveXmlFromRCode(from, shell)
-    const doc = parser.parseFromString(slicerOutput.parse, 'text/xml');
+    // retrieve parsed xml through (legacy) xmlparsedata
+    const suffix = request.request === 'file' ? ', encoding="utf-8"' : '';
+    shell.sendCommands(`try(flowr_parsed<-parse(${request.request}=${JSON.stringify(request.content)},keep.source=TRUE${suffix}),silent=FALSE)`, 'try(flowr_output<-xmlparsedata::xml_parse_data(flowr_parsed,includeText=TRUE,pretty=FALSE),silent=FALSE)');
+    const parsed = (await shell.sendCommandWithOutput(`cat(flowr_output,${(0, r_bridge_1.ts2r)(shell.options.eol)})`)).join(shell.options.eol);
+    const doc = parser.parseFromString(parsed, 'text/xml');
     // eslint-disable-next-line @typescript-eslint/no-explicit-any
     for (const [key, feature] of Object.entries(features_1.ALL_FEATURES)) {
         if (features !== 'all' && !features.has(key)) {

package/util/args.d.ts

@@ -4,11 +4,15 @@
  * @module
  */
 /**
- * This splits an input string on the given split string (e.g., ` `) but checks if the string is quoted or escaped.
+ * This splits an input string on the given split string (e.g., ` `), but checks if the string is quoted or escaped.
  *
- * Given an input string like `a "b c" d` with a space character as split this splits the arguments similar to common shell interpreters (i.e., `a`, `b c`, and `d`).
+ * Given an input string like `a "b c" d`, with a space character as split, and escapeQuote set to true,
+ * this splits the arguments similar to common shell interpreters (i.e., `a`, `b c`, and `d`).
+ *
+ * When escapeQuote is set to false instead, we keep quotation marks in the result (i.e., `a`, `"b c"`, and `d`.).
  *
  * @param inputString - The string to split
- * @param split       - The **single** character to split on (can not be the backslash or quote)
+ * @param escapeQuote - Keep quotes in args
+ * @param split       - The **single** character to split on (can not be backslash or quote)
  */
-export declare function splitAtEscapeSensitive(inputString: string, split?: string): string[];
+export declare function splitAtEscapeSensitive(inputString: string, escapeQuote?: boolean, split?: string): string[];