@eagleoutice/flowr 1.4.1 → 1.4.2

package/r-bridge/lang-4.x/ast/parser/xml/internal/structure/elements.js

@@ -2,7 +2,6 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.parseNodesWithUnknownType = exports.normalizeBasedOnType = exports.splitComments = void 0;
 const arrays_1 = require("../../../../../../../util/arrays");
-const parser_1 = require("../../parser");
 const meta_1 = require("../meta");
 const single_element_1 = require("./single-element");
 const values_1 = require("../values");
@@ -11,6 +10,7 @@ const loops_1 = require("../loops");
 const control_1 = require("../control");
 const log_1 = require("../../../../../../../util/log");
 const other_1 = require("../other");
+const parser_1 = require("../../../json/parser");
 function normalizeMappedWithoutSemicolonBasedOnType(mappedWithName, data) {
     if (mappedWithName.length === 1) {
         return [(0, single_element_1.tryNormalizeSingleNode)(data, mappedWithName[0])];
@@ -103,14 +103,14 @@ function normalizeBasedOnType(data, obj) {
         mappedWithName = obj;
     }
     else {
-        mappedWithName = (0, meta_1.getWithTokenType)(data.config.tokenMap, obj);
+        mappedWithName = (0, meta_1.getWithTokenType)(obj);
     }
     log_1.log.trace(`[parseBasedOnType] names: [${mappedWithName.map(({ name }) => name).join(', ')}]`);
     const semiColons = [];
     const splitOnSemicolon = (0, arrays_1.splitArrayOn)(mappedWithName, node => {
         const res = node.name === ";" /* RawRType.Semicolon */;
         if (res) {
-            const { location, content } = (0, meta_1.retrieveMetaStructure)(data.config, node.content);
+            const { location, content } = (0, meta_1.retrieveMetaStructure)(node.content);
             semiColons.push({
                 type: "RDelimiter" /* RType.Delimiter */,
                 subtype: ";" /* RawRType.Semicolon */,

package/r-bridge/lang-4.x/ast/parser/xml/internal/structure/root.js

@@ -7,12 +7,11 @@ const elements_1 = require("./elements");
 const log_1 = require("../../../../../../../util/log");
 const arrays_1 = require("../../../../../../../util/arrays");
 function parseRootObjToAst(data, obj) {
-    const config = data.config;
     const exprContent = (0, input_format_1.getKeysGuarded)(obj, "exprlist" /* RawRType.ExpressionList */);
-    (0, meta_1.assureTokenType)(config.tokenMap, exprContent, "exprlist" /* RawRType.ExpressionList */);
+    (0, meta_1.assureTokenType)(exprContent, "exprlist" /* RawRType.ExpressionList */);
     let parsedChildren = [];
-    if (config.childrenName in exprContent) {
-        const children = (0, input_format_1.getKeysGuarded)(exprContent, config.childrenName);
+    if (input_format_1.childrenKey in exprContent) {
+        const children = (0, input_format_1.getKeysGuarded)(exprContent, input_format_1.childrenKey);
         parsedChildren = (0, elements_1.normalizeBasedOnType)(data, children);
     }
     else {

package/r-bridge/lang-4.x/ast/parser/xml/internal/structure/single-element.js

@@ -10,7 +10,7 @@ const other_1 = require("../other");
 const loops_1 = require("../loops");
 const line_directive_1 = require("../other/line-directive");
 function normalizeDelimiter(data, elem) {
-    const { location, content } = (0, meta_1.retrieveMetaStructure)(data.config, elem.content);
+    const { location, content } = (0, meta_1.retrieveMetaStructure)(elem.content);
     return {
         type: "RDelimiter" /* RType.Delimiter */,
         location,
@@ -52,7 +52,7 @@ function tryNormalizeSingleNode(data, elem) {
         case "SYMBOL" /* RawRType.Symbol */:
         case "SLOT" /* RawRType.Slot */:
         case "NULL_CONST" /* RawRType.NullConst */: {
-            const symbol = (0, values_1.tryNormalizeSymbol)(data, (0, meta_1.getWithTokenType)(data.config.tokenMap, [elem.content]));
+            const symbol = (0, values_1.tryNormalizeSymbol)(data, (0, meta_1.getWithTokenType)([elem.content]));
             (0, assert_1.guard)(symbol !== undefined, () => `should have been parsed to a symbol but was ${JSON.stringify(symbol)}`);
             return symbol;
         }

package/r-bridge/lang-4.x/ast/parser/xml/internal/values/number.js

@@ -2,9 +2,9 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.normalizeNumber = void 0;
 const values_1 = require("../../../../../values");
-const parser_1 = require("../../parser");
 const meta_1 = require("../meta");
 const hooks_1 = require("../../hooks");
+const parser_1 = require("../../../json/parser");
 /**
  * Normalize the given object as a R number (see {@link number2ts}), supporting booleans (see {@link boolean2ts}),
  * and special values.
@@ -16,7 +16,7 @@ const hooks_1 = require("../../hooks");
 function normalizeNumber(data, obj) {
     parser_1.parseLog.debug('[number]');
     obj = (0, hooks_1.executeHook)(data.hooks.values.onNumber.before, data, obj);
-    const { location, content } = (0, meta_1.retrieveMetaStructure)(data.config, obj);
+    const { location, content } = (0, meta_1.retrieveMetaStructure)(obj);
     const common = {
         location,
         lexeme: content,

package/r-bridge/lang-4.x/ast/parser/xml/internal/values/string.js

@@ -3,9 +3,9 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.normalizeString = void 0;
 const meta_1 = require("../meta");
 const values_1 = require("../../../../../values");
-const parser_1 = require("../../parser");
 const hooks_1 = require("../../hooks");
 const assert_1 = require("../../../../../../../util/assert");
+const parser_1 = require("../../../json/parser");
 /**
  * Normalize the given object as a R string (see {@link string2ts}).
  * This requires you to check the corresponding name beforehand.
@@ -16,7 +16,7 @@ const assert_1 = require("../../../../../../../util/assert");
 function normalizeString(data, obj) {
     parser_1.parseLog.debug('[string]');
     obj = (0, hooks_1.executeHook)(data.hooks.values.onString.before, data, obj);
-    const { location, content } = (0, meta_1.retrieveMetaStructure)(data.config, obj);
+    const { location, content } = (0, meta_1.retrieveMetaStructure)(obj);
     // based on https://www.rdocumentation.org/packages/utils/versions/3.6.2/topics/getParseData we do not get strings with 1000 characters or more within the text field.
     // therefore, we recover the full string from the surrounding expr lexeme field
     let stringContent = content;

package/r-bridge/lang-4.x/ast/parser/xml/internal/values/symbol.js

@@ -3,10 +3,10 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.tryNormalizeSymbol = void 0;
 const assert_1 = require("../../../../../../../util/assert");
 const meta_1 = require("../meta");
-const parser_1 = require("../../parser");
 const model_1 = require("../../../../model");
 const hooks_1 = require("../../hooks");
 const strings_1 = require("../../../../../../../util/strings");
+const parser_1 = require("../../../json/parser");
 /**
  * Normalize the given object as an R symbol (incorporating namespace information).
  * <p>
@@ -23,16 +23,16 @@ function tryNormalizeSymbol(data, objs) {
     objs = (0, hooks_1.executeHook)(data.hooks.values.onSymbol.before, data, objs);
     let location, content, namespace;
     if (objs.length === 1 && (0, model_1.isSymbol)(objs[0].name)) {
-        const meta = (0, meta_1.retrieveMetaStructure)(data.config, objs[0].content);
+        const meta = (0, meta_1.retrieveMetaStructure)(objs[0].content);
         location = meta.location;
         content = meta.content;
         namespace = undefined;
     }
     else if (objs.length === 3 && (0, model_1.isSymbol)(objs[2].name)) {
-        const meta = (0, meta_1.retrieveMetaStructure)(data.config, objs[2].content);
+        const meta = (0, meta_1.retrieveMetaStructure)(objs[2].content);
         location = meta.location;
         content = meta.content;
-        namespace = (0, meta_1.retrieveMetaStructure)(data.config, objs[0].content).content;
+        namespace = (0, meta_1.retrieveMetaStructure)(objs[0].content).content;
     }
     else {
         return (0, hooks_1.executeUnknownHook)(data.hooks.values.onSymbol.unknown, data, objs);

package/r-bridge/lang-4.x/values.d.ts

@@ -36,4 +36,3 @@ export declare function string2ts(value: string): RStringValue;
 export declare const RNa = "NA";
 export declare const RNull = "NULL";
 export declare function isNA(value: string): value is (typeof RNa);
-export declare function parseCSV(lines: string[]): string[][];

package/r-bridge/lang-4.x/values.js

@@ -1,7 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.parseCSV = exports.isNA = exports.RNull = exports.RNa = exports.string2ts = exports.number2ts = exports.RInf = exports.RIntegerMarker = exports.RImaginaryMarker = exports.RNumHexFloatRegex = exports.boolean2ts = exports.isBoolean = exports.RFalse = exports.RTrue = exports.ts2r = void 0;
-const sync_1 = require("csv-parse/sync");
+exports.isNA = exports.RNull = exports.RNa = exports.string2ts = exports.number2ts = exports.RInf = exports.RIntegerMarker = exports.RImaginaryMarker = exports.RNumHexFloatRegex = exports.boolean2ts = exports.isBoolean = exports.RFalse = exports.RTrue = exports.ts2r = void 0;
 class ValueConversionError extends Error {
     constructor(message) {
         super(message);
@@ -19,6 +18,12 @@ function ts2r(value) {
         return JSON.stringify(value);
     }
     else if (typeof value === 'number') {
+        if (isNaN(value)) {
+            return exports.RNa;
+        }
+        else if (!isFinite(value)) {
+            return exports.RInf;
+        }
         return value.toString();
     }
     else if (typeof value === 'boolean') {
@@ -81,6 +86,13 @@ function number2ts(value) {
             markedAsInt
         };
     }
+    if (value === exports.RNa) {
+        return {
+            num: NaN,
+            complexNumber,
+            markedAsInt
+        };
+    }
     const floatHex = lcValue.match(exports.RNumHexFloatRegex);
     if (floatHex == null) {
         return {
@@ -142,8 +154,4 @@ function isNA(value) {
     return value === exports.RNa;
 }
 exports.isNA = isNA;
-function parseCSV(lines) {
-    return (0, sync_1.parse)(lines.join('\n'), { skipEmptyLines: true });
-}
-exports.parseCSV = parseCSV;
 //# sourceMappingURL=values.js.map

package/r-bridge/retriever.d.ts

@@ -1,28 +1,34 @@
 import { type RShell } from './shell';
 import type { XmlParserHooks, NormalizedAst } from './lang-4.x';
-import type { DeepPartial, DeepReadonly } from 'ts-essentials';
+import type { AsyncOrSync, DeepPartial } from 'ts-essentials';
+import { RShellExecutor } from './shell-executor';
+export declare const fileProtocol: "file://";
 export interface RParseRequestFromFile {
-    request: 'file';
+    readonly request: 'file';
     /** The path to the file (absolute paths are probably best here */
-    content: string;
+    readonly content: string;
 }
 export interface RParseRequestFromText {
-    request: 'text';
-    content: string;
+    readonly request: 'text';
+    readonly content: string;
 }
-interface RParseRequestBase {
-    /**
-   * Ensure that all required packages are present and if not install them?
-   * The only reason to set this to `false` is probably in a series of parse requests for the same session.
-   */
-    ensurePackageInstalled: boolean;
+/**
+ * A provider for an {@link RParseRequest} that can be used, for example, to override source file parsing behavior in tests
+ */
+export interface RParseRequestProvider {
+    createRequest(path: string): RParseRequest;
 }
 /**
- * A request that can be passed along to {@link retrieveXmlFromRCode}.
+ * A request that can be passed along to {@link retrieveParseDataFromRCode}.
  */
-export type RParseRequest = (RParseRequestFromFile | RParseRequestFromText) & RParseRequestBase;
-export declare function requestFromInput(input: `file://${string}`): RParseRequestFromFile & RParseRequestBase;
-export declare function requestFromInput(input: string): RParseRequestFromText & RParseRequestBase;
+export type RParseRequest = (RParseRequestFromFile | RParseRequestFromText);
+export declare function requestFromInput(input: `${typeof fileProtocol}${string}`): RParseRequestFromFile;
+export declare function requestFromInput(input: string): RParseRequestFromText;
+export declare function requestProviderFromFile(): RParseRequestProvider;
+export declare function requestProviderFromText(text: {
+    [path: string]: string;
+}): RParseRequestProvider;
+export declare function requestFingerprint(request: RParseRequest): string;
 /**
  * Provides the capability to parse R files/R code using the R parser.
  * Depends on {@link RShell} to provide a connection to R.
@@ -30,19 +36,17 @@ export declare function requestFromInput(input: string): RParseRequestFromText &
  * Throws if the file could not be parsed.
  * If successful, allows to further query the last result with {@link retrieveNumberOfRTokensOfLastParse}.
  */
-export declare function retrieveXmlFromRCode(request: RParseRequest, shell: RShell): Promise<string>;
+export declare function retrieveParseDataFromRCode(request: RParseRequest, shell: (RShell | RShellExecutor)): AsyncOrSync<string>;
 /**
- * Uses {@link retrieveXmlFromRCode} and returns the nicely formatted object-AST.
+ * Uses {@link retrieveParseDataFromRCode} and returns the nicely formatted object-AST.
  * If successful, allows to further query the last result with {@link retrieveNumberOfRTokensOfLastParse}.
  */
 export declare function retrieveNormalizedAstFromRCode(request: RParseRequest, shell: RShell, hooks?: DeepPartial<XmlParserHooks>): Promise<NormalizedAst>;
 /**
  * If the string has (R-)quotes around it, they will be removed, otherwise the string is returned unchanged.
  */
-export declare function removeTokenMapQuotationMarks(str: string): string;
-export type TokenMap = DeepReadonly<Record<string, string>>;
+export declare function removeRQuotes(str: string): string;
 /**
- * Needs to be called *after*  {@link retrieveXmlFromRCode} (or {@link retrieveNormalizedAstFromRCode})
+ * Needs to be called *after*  {@link retrieveParseDataFromRCode} (or {@link retrieveNormalizedAstFromRCode})
  */
 export declare function retrieveNumberOfRTokensOfLastParse(shell: RShell): Promise<number>;
-export {};

package/r-bridge/retriever.js

@@ -1,21 +1,53 @@
 "use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.retrieveNumberOfRTokensOfLastParse = exports.removeTokenMapQuotationMarks = exports.retrieveNormalizedAstFromRCode = exports.retrieveXmlFromRCode = exports.requestFromInput = void 0;
+exports.retrieveNumberOfRTokensOfLastParse = exports.removeRQuotes = exports.retrieveNormalizedAstFromRCode = exports.retrieveParseDataFromRCode = exports.requestFingerprint = exports.requestProviderFromText = exports.requestProviderFromFile = exports.requestFromInput = exports.fileProtocol = void 0;
 const lang_4_x_1 = require("./lang-4.x");
 const strings_1 = require("../util/strings");
 const assert_1 = require("../util/assert");
+const shell_executor_1 = require("./shell-executor");
+const object_hash_1 = __importDefault(require("object-hash"));
+const parser_1 = require("./lang-4.x/ast/parser/json/parser");
+exports.fileProtocol = 'file://';
 /**
  * Creates a {@link RParseRequest} from a given input.
  */
 function requestFromInput(input) {
-    const file = input.startsWith('file://');
+    const file = input.startsWith(exports.fileProtocol);
     return {
         request: file ? 'file' : 'text',
-        content: file ? input.slice(7) : input,
-        ensurePackageInstalled: false // should be called within describeSession for that!
+        content: file ? input.slice(7) : input
     };
 }
 exports.requestFromInput = requestFromInput;
+function requestProviderFromFile() {
+    return {
+        createRequest(path) {
+            return {
+                request: 'file',
+                content: path,
+            };
+        }
+    };
+}
+exports.requestProviderFromFile = requestProviderFromFile;
+function requestProviderFromText(text) {
+    return {
+        createRequest(path) {
+            return {
+                request: 'text',
+                content: text[path]
+            };
+        }
+    };
+}
+exports.requestProviderFromText = requestProviderFromText;
+function requestFingerprint(request) {
+    return (0, object_hash_1.default)(request);
+}
+exports.requestFingerprint = requestFingerprint;
 const ErrorMarker = 'err';
 /**
  * Provides the capability to parse R files/R code using the R parser.
@@ -24,33 +56,47 @@ const ErrorMarker = 'err';
  * Throws if the file could not be parsed.
  * If successful, allows to further query the last result with {@link retrieveNumberOfRTokensOfLastParse}.
  */
-async function retrieveXmlFromRCode(request, shell) {
-    if (request.ensurePackageInstalled) {
-        await shell.ensurePackageInstalled('xmlparsedata', true);
-    }
+function retrieveParseDataFromRCode(request, shell) {
     const suffix = request.request === 'file' ? ', encoding="utf-8"' : '';
-    shell.sendCommands(`flowr_output <- flowr_parsed <- "${ErrorMarker}"`, 
-    // now, try to retrieve the ast
-    `try(flowr_parsed<-parse(${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 xml = await shell.sendCommandWithOutput(`cat(flowr_output,${(0, lang_4_x_1.ts2r)(shell.options.eol)})`);
-    const output = xml.join(shell.options.eol);
-    (0, assert_1.guard)(output !== ErrorMarker, () => `unable to parse R code (see the log for more information) for request ${JSON.stringify(request)}}`);
-    return output;
+    const eol = (0, lang_4_x_1.ts2r)(shell.options.eol);
+    const command = 
+    /* first check if flowr_get is already part of the environment */
+    'if(!exists("flowr_get")){'
+        /* if not, define it complete wrapped in a try so that we can handle failures gracefully on stdout */
+        + 'flowr_get<-function(...){tryCatch({'
+        /* the actual code to parse the R code, ... allows us to keep the old 'file=path' and 'text=content' semantics. we define flowr_output using the super assignment to persist it in the env! */
+        + 'flowr_output<<-utils::getParseData(parse(...,keep.source=TRUE),includeText=TRUE);'
+        /* json conversion of the output, dataframe="values" allows us to receive a list of lists (which is more compact)!
+         * so we do not depend on jsonlite and friends, we do so manually (:sparkles:)
+         */
+        + `cat("[",paste0(apply(flowr_output,1,function(o)sprintf("[%s,%s,%s,%s,%s,%s,%s,%s,%s]",o[[1]],o[[2]],o[[3]],o[[4]],o[[5]],o[[6]],deparse(o[[7]]),if(o[[8]])"true"else"false",deparse(o[[9]]))),collapse=","),"]",${eol},sep="")`
+        /* error handling (just produce the marker) */
+        + `},error=function(e){cat("${ErrorMarker}",${eol})})};`
+        /* compile the function to improve perf. */
+        + 'flowr_get<-compiler::cmpfun(flowr_get)};'
+        /* call the function with the request */
+        + `flowr_get(${request.request}=${JSON.stringify(request.content)}${suffix})`;
+    if (shell instanceof shell_executor_1.RShellExecutor) {
+        return guardRetrievedOutput(shell.run(command), request);
+    }
+    else {
+        return shell.sendCommandWithOutput(command).then(result => guardRetrievedOutput(result.join(shell.options.eol), request));
+    }
 }
-exports.retrieveXmlFromRCode = retrieveXmlFromRCode;
+exports.retrieveParseDataFromRCode = retrieveParseDataFromRCode;
 /**
- * Uses {@link retrieveXmlFromRCode} and returns the nicely formatted object-AST.
+ * Uses {@link retrieveParseDataFromRCode} and returns the nicely formatted object-AST.
  * If successful, allows to further query the last result with {@link retrieveNumberOfRTokensOfLastParse}.
  */
 async function retrieveNormalizedAstFromRCode(request, shell, hooks) {
-    const xml = await retrieveXmlFromRCode(request, shell);
-    return await (0, lang_4_x_1.normalize)(xml, await shell.tokenMap(), hooks);
+    const data = await retrieveParseDataFromRCode(request, shell);
+    return (0, parser_1.normalize)(data, hooks);
 }
 exports.retrieveNormalizedAstFromRCode = retrieveNormalizedAstFromRCode;
 /**
  * If the string has (R-)quotes around it, they will be removed, otherwise the string is returned unchanged.
  */
-function removeTokenMapQuotationMarks(str) {
+function removeRQuotes(str) {
     if (str.length > 1 && ((0, strings_1.startAndEndsWith)(str, '\'') || (0, strings_1.startAndEndsWith)(str, '"'))) {
         return str.slice(1, -1);
     }
@@ -58,14 +104,18 @@ function removeTokenMapQuotationMarks(str) {
         return str;
     }
 }
-exports.removeTokenMapQuotationMarks = removeTokenMapQuotationMarks;
+exports.removeRQuotes = removeRQuotes;
 /**
- * Needs to be called *after*  {@link retrieveXmlFromRCode} (or {@link retrieveNormalizedAstFromRCode})
+ * Needs to be called *after*  {@link retrieveParseDataFromRCode} (or {@link retrieveNormalizedAstFromRCode})
  */
 async function retrieveNumberOfRTokensOfLastParse(shell) {
-    const result = await shell.sendCommandWithOutput(`cat(nrow(getParseData(flowr_parsed)),${(0, lang_4_x_1.ts2r)(shell.options.eol)})`);
+    const result = await shell.sendCommandWithOutput(`cat(nrow(flowr_output),${(0, lang_4_x_1.ts2r)(shell.options.eol)})`);
     (0, assert_1.guard)(result.length === 1, () => `expected exactly one line to obtain the number of R tokens, but got: ${JSON.stringify(result)}`);
     return Number(result[0]);
 }
 exports.retrieveNumberOfRTokensOfLastParse = retrieveNumberOfRTokensOfLastParse;
+function guardRetrievedOutput(output, request) {
+    (0, assert_1.guard)(output !== ErrorMarker, () => `unable to parse R code (see the log for more information) for request ${JSON.stringify(request)}}`);
+    return output;
+}
 //# sourceMappingURL=retriever.js.map

package/r-bridge/shell-executor.d.ts

@@ -1,25 +1,11 @@
 import type { RShellExecutionOptions } from './shell';
 import type { SemVer } from 'semver';
-import type { TokenMap } from './retriever';
 export declare class RShellExecutor {
     readonly options: Readonly<RShellExecutionOptions>;
-    private readonly log;
     private readonly prerequisites;
     constructor(options?: Partial<RShellExecutionOptions>);
-    continueOnError(): RShellExecutor;
-    injectLibPaths(...paths: string[]): RShellExecutor;
-    tryToInjectHomeLibPath(): RShellExecutor;
-    addPrerequisites(commands: string | string[]): RShellExecutor;
+    continueOnError(): this;
+    addPrerequisites(commands: string | string[]): this;
     usedRVersion(): SemVer | null;
-    allInstalledPackages(): string[];
-    isPackageInstalled(packageName: string): boolean;
-    ensurePackageInstalled(packageName: string, autoload?: boolean, force?: boolean): {
-        packageName: string;
-        packageExistedAlready: boolean;
-        /** the temporary directory used for the installation, undefined if none was used */
-        libraryLocation?: string;
-    };
-    obtainTempDir(): string;
-    getTokenMap(): TokenMap;
-    run(commands: string | string[], returnErr?: boolean): string;
+    run(command: string, returnErr?: boolean): string;
 }

package/r-bridge/shell-executor.js

@@ -10,107 +10,38 @@ const child_process_1 = require("child_process");
 const lang_4_x_1 = require("./lang-4.x");
 const preload_1 = __importDefault(require("semver/preload"));
 const log_1 = require("../util/log");
-const fs_1 = __importDefault(require("fs"));
-const retriever_1 = require("./retriever");
+const executorLog = log_1.log.getSubLogger({ name: 'RShellExecutor' });
 class RShellExecutor {
     options;
-    log;
     prerequisites = [];
     constructor(options) {
         this.options = (0, objects_1.deepMergeObject)(shell_1.DEFAULT_R_SHELL_OPTIONS, options);
-        this.log = log_1.log.getSubLogger({ name: 'RShellExecutor' });
     }
     continueOnError() {
-        this.log.info('continue in case of Errors');
+        executorLog.info('continue in case of Errors');
         this.addPrerequisites('options(error=function() {})');
         return this;
     }
-    injectLibPaths(...paths) {
-        this.log.debug(`injecting lib paths ${JSON.stringify(paths)}`);
-        this.addPrerequisites(`.libPaths(c(.libPaths(), ${paths.map(lang_4_x_1.ts2r).join(',')}))`);
-        return this;
-    }
-    tryToInjectHomeLibPath() {
-        if (this.options.homeLibPath === undefined) {
-            this.log.debug('ensuring home lib path exists (automatic inject)');
-            this.addPrerequisites([
-                'if(!dir.exists(Sys.getenv("R_LIBS_USER"))) { dir.create(path=Sys.getenv("R_LIBS_USER"),showWarnings=FALSE,recursive=TRUE) }',
-                '.libPaths(c(.libPaths(), Sys.getenv("R_LIBS_USER")))'
-            ]);
-        }
-        else {
-            this.injectLibPaths(this.options.homeLibPath);
-        }
-        return this;
-    }
     addPrerequisites(commands) {
         this.prerequisites.push(...(typeof commands == 'string' ? [commands] : commands));
         return this;
     }
     usedRVersion() {
         const version = this.run(`cat(paste0(R.version$major,".",R.version$minor), ${(0, lang_4_x_1.ts2r)(this.options.eol)})`);
-        this.log.trace(`raw version: ${JSON.stringify(version)}`);
+        executorLog.trace(`raw version: ${JSON.stringify(version)}`);
         return preload_1.default.coerce(version);
     }
-    allInstalledPackages() {
-        this.log.debug('getting all installed packages');
-        const packages = this.run(`cat(paste0(installed.packages()[,1], collapse=","),"${this.options.eol}")`);
-        return packages.split(',');
-    }
-    isPackageInstalled(packageName) {
-        this.log.debug(`checking if package "${packageName}" is installed`);
-        return this.run(`cat(system.file(package="${packageName}")!="","${this.options.eol}")`) === 'TRUE';
-    }
-    ensurePackageInstalled(packageName, autoload = false, force = false) {
-        const packageExistedAlready = this.isPackageInstalled(packageName);
-        if (!force && packageExistedAlready) {
-            this.log.info(`package "${packageName}" is already installed`);
-            if (autoload)
-                this.addPrerequisites(`library(${(0, lang_4_x_1.ts2r)(packageName)})`);
-            return { packageName, packageExistedAlready };
+    run(command, returnErr = false) {
+        command += ';base::quit()';
+        if (executorLog.settings.minLevel >= 1 /* LogLevel.Trace */) {
+            executorLog.trace(`> ${JSON.stringify(command)}`);
         }
-        const tempDir = this.obtainTempDir();
-        this.log.debug(`using temporary directory: "${tempDir}" to install package "${packageName}"`);
-        this.run(`install.packages(${(0, lang_4_x_1.ts2r)(packageName)},repos="https://cloud.r-project.org/",quiet=FALSE,lib=temp)`);
-        if (autoload)
-            this.addPrerequisites(`library(${(0, lang_4_x_1.ts2r)(packageName)},lib.loc=temp)`);
-        return { packageName, packageExistedAlready, libraryLocation: tempDir };
-    }
-    obtainTempDir() {
-        const tempDir = this.run([
-            'temp <- tempdir()',
-            `cat(temp, ${(0, lang_4_x_1.ts2r)(this.options.eol)})`
-        ]);
-        log_1.log.info(`obtained temp dir ${tempDir}`);
-        const deleteOnExit = function () {
-            if (fs_1.default.existsSync(tempDir)) {
-                log_1.log.info(`deleting temp dir ${tempDir}`);
-                fs_1.default.rmSync(tempDir, { recursive: true, force: true });
-            }
-        };
-        process.on('SIGINT', deleteOnExit);
-        process.on('SIGTERM', deleteOnExit);
-        return tempDir;
-    }
-    getTokenMap() {
-        this.ensurePackageInstalled('xmlparsedata', true);
-        // we invert the token map to get a mapping back from the replacement
-        const parsed = (0, lang_4_x_1.parseCSV)(this.run('write.table(xmlparsedata::xml_parse_token_map,sep=",",col.names=FALSE)').split('\n'));
-        if (parsed.some(s => s.length !== 2))
-            throw new Error(`Expected two columns in token map, but got ${JSON.stringify(parsed)}`);
-        // we swap key and value to get the other direction, furthermore we remove quotes from keys if they are quoted
-        const ret = {};
-        for (const [key, value] of parsed)
-            ret[value] = (0, retriever_1.removeTokenMapQuotationMarks)(key);
-        return ret;
-    }
-    run(commands, returnErr = false) {
-        this.log.trace(`> ${JSON.stringify(commands)}`);
         const returns = (0, child_process_1.spawnSync)(this.options.pathToRExecutable, this.options.commandLineOptions, {
             env: this.options.env,
             cwd: this.options.cwd,
+            windowsHide: true,
             encoding: 'utf8',
-            input: [...this.prerequisites, commands].join(this.options.eol)
+            input: [...this.prerequisites, command].join(this.options.eol)
         });
         return (returnErr ? returns.stderr : returns.stdout).trim();
     }

package/r-bridge/shell.d.ts

@@ -1,7 +1,6 @@
 /// <reference types="node" />
 import { type MergeableRecord } from '../util/objects';
 import type { SemVer } from 'semver';
-import type { TokenMap } from './retriever';
 export type OutputStreamSelector = 'stdout' | 'stderr' | 'both';
 export interface CollectorTimeout extends MergeableRecord {
     /**
@@ -60,6 +59,7 @@ export interface RShellSessionOptions extends RShellExecutionOptions {
 export interface RShellOptions extends RShellSessionOptions {
     readonly sessionName: string;
 }
+export declare const DEFAULT_R_PATH: string;
 export declare const DEFAULT_R_SHELL_EXEC_OPTIONS: RShellExecutionOptions;
 export declare const DEFAULT_R_SHELL_OPTIONS: RShellOptions;
 /**
@@ -75,7 +75,6 @@ export declare class RShell {
     private session;
     private readonly log;
     private versionCache;
-    private tokenMapCache;
     private tempDirs;
     constructor(options?: Partial<RShellOptions>);
     private revive;
@@ -85,13 +84,12 @@ export declare class RShell {
    */
     sendCommand(command: string): void;
     usedRVersion(): Promise<SemVer | null>;
+    injectLibPaths(...paths: string[]): void;
+    tryToInjectHomeLibPath(): void;
     /**
-     * Retrieve the token map of the xmlparsedata package.
-     *
-     * @note For multiple calls, this makes use of caching
+     * checks if a given package is already installed on the system!
      */
-    tokenMap(): Promise<TokenMap>;
-    private retrieveTokenMap;
+    isPackageInstalled(packageName: string): Promise<boolean>;
     /**
    * Send a command and collect the output
    *
@@ -115,26 +113,6 @@ export declare class RShell {
    * continue working!
    */
     continueOnError(): void;
-    injectLibPaths(...paths: string[]): void;
-    tryToInjectHomeLibPath(): void;
-    /**
-   * checks if a given package is already installed on the system!
-   */
-    isPackageInstalled(packageName: string): Promise<boolean>;
-    allInstalledPackages(): Promise<string[]>;
-    /**
-   * 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
-   */
-    ensurePackageInstalled(packageName: string, autoload?: boolean, force?: boolean): Promise<{
-        packageName: string;
-        packageExistedAlready: boolean;
-        /** the temporary directory used for the installation, undefined if none was used */
-        libraryLocation?: string;
-    }>;
     /**
      * Obtain the temporary directory used by R.
      * Additionally, this marks the directory for removal when the shell exits.