@eagleoutice/flowr 2.2.11 → 2.2.12

package/documentation/print-core-wiki.js

@@ -390,10 +390,10 @@ ${await (0, doc_repl_1.documentReplSession)(shell, [{
 ### Getting flowR to Talk
 
 When using flowR from the CLI, you can use the ${(0, doc_cli_option_1.getCliLongOptionOf)('flowr', 'verbose')} option to get more information about what flowR is doing.
-While coding, however, you can use the ${log_1.setMinLevelOfAllLogs.name} function to set the minimum level of logs to be displayed (this works with the ${(0, doc_types_1.shortLink)(log_2.FlowrLogger.name, info)} abstraction).
+While coding, however, you can use the ${(0, doc_types_1.shortLink)(log_1.setMinLevelOfAllLogs.name, info)} function to set the minimum level of logs to be displayed (this works with the ${(0, doc_types_1.shortLink)(log_2.FlowrLogger.name, info)} abstraction).
 In general, you can configure the levels of individual logs, such as the general \`log\` (obtained with ${(0, doc_types_1.shortLink)('getActiveLog', info)}) or the ${(0, doc_types_1.shortLink)('parseLog', info)}.
 Please note that flowR makes no guarantees that log outputs are persistent across versions, and it is up to the implementors to provide sensible logging.
-If you are an implementor and want to add logging, please make sure that there are no larger runtime impliciations when logging is disabled. 
+If you are an implementor and want to add logging, please make sure there are no larger runtime impliciations when logging is disabled. 
 Have a look at the ${(0, doc_types_1.shortLink)(log_2.expensiveTrace.name, info)} function for example, which uses a function to generate the log message only when the log level is reached.
 
 `;

package/documentation/print-interface-wiki.js

@@ -203,6 +203,7 @@ ${(0, doc_code_1.codeBlock)('json', JSON.stringify({
         engines: [{ type: 'r-shell' }],
         solver: {
             variables: config_1.VariableResolve.Alias,
+            evalStrings: true,
             pointerTracking: true,
             resolveSource: {
                 dropPaths: config_1.DropPathsOption.No,

package/documentation/print-query-wiki.js

@@ -424,7 +424,7 @@ print("hello world!")
 		`;
         return `
 This query extracts all dependencies from an R script, using a combination of a ${(0, doc_query_1.linkToQueryOfName)('call-context')}
-and more advanced tracking in the [Dataflow Graph](${doc_files_1.FlowrWikiBaseRef}/Dataflow%20Graph).  
+and more advanced tracking in the [Dataflow Graph](${doc_files_1.FlowrWikiBaseRef}/Dataflow%20Graph).
 
 In other words, if you have a script simply reading: \`${exampleCode}\`, the following query returns the loaded library:
 ${await (0, doc_query_1.showQuery)(shell, exampleCode, [{
@@ -447,7 +447,7 @@ In the meantime we offer several properties to overwrite the default behavior (e
 ${await (0, doc_query_1.showQuery)(shell, longerCode, [{
                 type: 'dependencies',
                 ignoreDefaultFunctions: true,
-                libraryFunctions: [{ name: 'print', argIdx: 0, argName: 'library', resolveValue: true }],
+                libraryFunctions: [{ package: 'base', name: 'print', argIdx: 0, argName: 'library', resolveValue: true }],
                 sourceFunctions: [],
                 readFunctions: [],
                 writeFunctions: []

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@eagleoutice/flowr",
-  "version": "2.2.11",
+  "version": "2.2.12",
   "description": "Static Dataflow Analyzer and Program Slicer for the R Programming Language",
   "types": "dist/src/index.d.ts",
   "repository": {
@@ -33,6 +33,7 @@
     "wiki:search-api": "ts-node src/documentation/print-search-wiki.ts",
     "wiki:linting-and-testing": "ts-node src/documentation/print-linting-and-testing-wiki.ts",
     "wiki:interface": "ts-node src/documentation/print-interface-wiki.ts",
+    "wiki:cfg": "ts-node src/documentation/print-cfg-wiki.ts",
     "gen:readme": "ts-node src/documentation/print-readme.ts",
     "build": "tsc --project .",
     "build-dev": "npm run build && npm run build:copy-wasm",

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

@@ -109,7 +109,7 @@ function identifyLinkToLastCallRelation(from, cfg, graph, { callName, ignoreIf,
     if (ignoreIf && ignoreIf(from, graph)) {
         return found;
     }
-    (0, visitor_1.visitInReverseOrder)(cfg, from, node => {
+    (0, visitor_1.visitCfgInReverseOrder)(cfg, from, node => {
         /* we ignore the start id as it cannot be the last call */
         if (node === from) {
             return;

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

@@ -12,6 +12,11 @@ const visitor_1 = require("../../../r-bridge/lang-4.x/ast/model/processing/visit
 const assert_1 = require("../../../util/assert");
 const objects_1 = require("../../../util/objects");
 const resolve_by_name_1 = require("../../../dataflow/environments/resolve-by-name");
+const library_functions_1 = require("./function-info/library-functions");
+const source_functions_1 = require("./function-info/source-functions");
+const read_functions_1 = require("./function-info/read-functions");
+const write_functions_1 = require("./function-info/write-functions");
+const function_info_1 = require("./function-info/function-info");
 function collectNamespaceAccesses(data, libraries) {
     /* for libraries, we have to additionally track all uses of `::` and `:::`, for this we currently simply traverse all uses */
     (0, visitor_1.visitAst)(data.ast.ast, n => {
@@ -32,10 +37,10 @@ function executeDependenciesQuery(data, queries) {
     const now = Date.now();
     const [query] = queries;
     const ignoreDefault = query.ignoreDefaultFunctions ?? false;
-    const libraryFunctions = getFunctionsToCheck(query.libraryFunctions, ignoreDefault, dependencies_query_format_1.LibraryFunctions);
-    const sourceFunctions = getFunctionsToCheck(query.sourceFunctions, ignoreDefault, dependencies_query_format_1.SourceFunctions);
-    const readFunctions = getFunctionsToCheck(query.readFunctions, ignoreDefault, dependencies_query_format_1.ReadFunctions);
-    const writeFunctions = getFunctionsToCheck(query.writeFunctions, ignoreDefault, dependencies_query_format_1.WriteFunctions);
+    const libraryFunctions = getFunctionsToCheck(query.libraryFunctions, ignoreDefault, library_functions_1.LibraryFunctions);
+    const sourceFunctions = getFunctionsToCheck(query.sourceFunctions, ignoreDefault, source_functions_1.SourceFunctions);
+    const readFunctions = getFunctionsToCheck(query.readFunctions, ignoreDefault, read_functions_1.ReadFunctions);
+    const writeFunctions = getFunctionsToCheck(query.writeFunctions, ignoreDefault, write_functions_1.WriteFunctions);
     const numberOfFunctions = libraryFunctions.length + sourceFunctions.length + readFunctions.length + writeFunctions.length;
     const results = numberOfFunctions === 0 ? { kinds: {}, '.meta': { timing: 0 } } : (0, query_1.executeQueriesOfSameType)(data, ...makeCallContextQuery(libraryFunctions, 'library'), ...makeCallContextQuery(sourceFunctions, 'source'), ...makeCallContextQuery(readFunctions, 'read'), ...makeCallContextQuery(writeFunctions, 'write'));
     function getLexeme(argument, id) {
@@ -113,6 +118,9 @@ function getResults(data, results, kind, functions, makeInfo) {
         const linkedArgs = collectValuesFromLinks(args, data, linkedIds);
         const foundValues = linkedArgs ?? args;
         if (!foundValues) {
+            if (info.ignoreIf === 'arg-missing') {
+                return [];
+            }
             const record = (0, objects_1.compactRecord)(makeInfo(id, vertex, undefined, undefined, dropInfoOnLinkedIds(linkedIds)));
             return record ? [record] : [];
         }
@@ -140,7 +148,7 @@ function collectValuesFromLinks(args, data, linkedIds) {
         }
         const info = linkedId.info;
         // do not collect this one
-        if (hasAtLeastAValue && info.when !== dependencies_query_format_1.DependencyInfoLinkConstraint.Always) {
+        if (hasAtLeastAValue && info.when !== function_info_1.DependencyInfoLinkConstraint.Always) {
             continue;
         }
         // collect this one!

package/queries/catalog/dependencies-query/dependencies-query-format.d.ts

@@ -2,32 +2,8 @@ import type { BaseQueryFormat, BaseQueryResult } from '../../base-query-format';
 import type { NodeId } from '../../../r-bridge/lang-4.x/ast/model/processing/node-id';
 import Joi from 'joi';
 import { executeDependenciesQuery } from './dependencies-query-executor';
-import type { LinkTo } from '../call-context-query/call-context-query-format';
+import type { FunctionInfo } from './function-info/function-info';
 export declare const Unknown = "unknown";
-/** when to read the argument value from a linked function */
-export declare enum DependencyInfoLinkConstraint {
-    Always = "always",
-    IfUnknown = "if-unknown"
-}
-/**
- * A dependency link may have attached information. If you pass it, we try to resolve the argument value from the linked function
- * if the `when` constraint is met.
- */
-export type DependencyInfoLink = LinkTo<RegExp | string, Omit<FunctionInfo, 'name' | 'linkTo'> & {
-    when: DependencyInfoLinkConstraint;
-} | undefined>;
-export type DependencyInfoLinkAttachedInfo = DependencyInfoLink['attachLinkInfo'];
-export declare const LibraryFunctions: FunctionInfo[];
-export declare const SourceFunctions: FunctionInfo[];
-export declare const ReadFunctions: FunctionInfo[];
-export declare const WriteFunctions: FunctionInfo[];
-export interface FunctionInfo {
-    name: string;
-    argIdx?: number | 'unnamed';
-    argName?: string;
-    linkTo?: DependencyInfoLink[];
-    resolveValue?: boolean | 'library';
-}
 export interface DependenciesQuery extends BaseQueryFormat {
     readonly type: 'dependencies';
     readonly ignoreDefaultFunctions?: boolean;

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

@@ -3,156 +3,12 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.DependenciesQueryDefinition = exports.WriteFunctions = exports.ReadFunctions = exports.SourceFunctions = exports.LibraryFunctions = exports.DependencyInfoLinkConstraint = exports.Unknown = void 0;
+exports.DependenciesQueryDefinition = exports.Unknown = void 0;
 const ansi_1 = require("../../../util/ansi");
 const time_1 = require("../../../util/time");
 const joi_1 = __importDefault(require("joi"));
 const dependencies_query_executor_1 = require("./dependencies-query-executor");
 exports.Unknown = 'unknown';
-/** when to read the argument value from a linked function */
-var DependencyInfoLinkConstraint;
-(function (DependencyInfoLinkConstraint) {
-    DependencyInfoLinkConstraint["Always"] = "always";
-    DependencyInfoLinkConstraint["IfUnknown"] = "if-unknown";
-})(DependencyInfoLinkConstraint || (exports.DependencyInfoLinkConstraint = DependencyInfoLinkConstraint = {}));
-// these lists are originally based on https://github.com/duncantl/CodeDepends/blob/7fd96dfee16b252e5f642c77a7ababf48e9326f8/R/codeTypes.R
-exports.LibraryFunctions = [
-    { name: 'library', argIdx: 0, argName: 'package', resolveValue: 'library' },
-    { name: 'require', argIdx: 0, argName: 'package', resolveValue: 'library' },
-    { name: 'loadNamespace', argIdx: 0, argName: 'package', resolveValue: true },
-    { name: 'attachNamespace', argIdx: 0, argName: 'ns', resolveValue: true },
-    { name: 'attach', argIdx: 0, argName: 'what', resolveValue: true },
-    { name: 'groundhog.library', argIdx: 0, argName: 'pkg', resolveValue: true },
-    { name: 'p_load', argIdx: 'unnamed', resolveValue: 'library' }, // pacman
-    { name: 'p_load_gh', argIdx: 'unnamed', resolveValue: 'library' }, // pacman
-    { name: 'from_import', argIdx: 0, argName: 'package', resolveValue: true }, // easypackages
-    { name: 'libraries', argIdx: 'unnamed', resolveValue: true }, // easypackages
-    { name: 'shelf', argIdx: 'unnamed', resolveValue: true } // librarian
-];
-exports.SourceFunctions = [
-    { name: 'source', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'sys.source', argIdx: 0, argName: 'file', resolveValue: true }
-];
-exports.ReadFunctions = [
-    { name: 'read.table', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'read.csv', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'read.csv2', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'read.delim', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'read.dcf', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'scan', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'read.fwf', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'file', argIdx: 1, argName: 'open', resolveValue: true },
-    { name: 'url', argIdx: 1, argName: 'open', resolveValue: true },
-    { name: 'load', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'gzfile', argIdx: 1, argName: 'open', resolveValue: true },
-    { name: 'bzfile', argIdx: 1, argName: 'open', resolveValue: true },
-    { name: 'download.file', argIdx: 0, argName: 'url', resolveValue: true },
-    { name: 'pipe', argIdx: 1, argName: 'open', resolveValue: true },
-    { name: 'fifo', argIdx: 1, argName: 'open', resolveValue: true },
-    { name: 'unz', argIdx: 1, argName: 'open', resolveValue: true },
-    { name: 'matrix', argIdx: 0, argName: 'data', resolveValue: true },
-    { name: 'readRDS', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'readLines', argIdx: 0, argName: 'con', resolveValue: true },
-    { name: 'readRenviron', argIdx: 0, argName: 'path', resolveValue: true },
-    // readr
-    { name: 'read_csv', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'read_csv2', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'read_lines', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'read_delim', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'read_dsv', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'read_fwf', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'read_tsv', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'read_table', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'read_log', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'read_lines', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'read_lines_chunked', argIdx: 0, argName: 'file', resolveValue: true },
-    // xlsx
-    { name: 'read.xlsx', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'read.xlsx2', argIdx: 0, argName: 'file', resolveValue: true },
-    // data.table
-    { name: 'fread', argIdx: 0, argName: 'file', resolveValue: true },
-    // haven
-    { name: 'read_sas', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'read_sav', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'read_por', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'read_dta', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'read_xpt', argIdx: 0, argName: 'file', resolveValue: true },
-    // feather
-    { name: 'read_feather', argIdx: 0, argName: 'file', resolveValue: true },
-    // foreign
-    { name: 'read.arff', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'read.dbf', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'read.dta', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'read.epiinfo', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'read.mtp', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'read.octave', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'read.spss', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'read.ssd', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'read.systat', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'read.xport', argIdx: 0, argName: 'file', resolveValue: true },
-    // car
-    { name: 'Import', argIdx: 0, argName: 'file', resolveValue: true },
-];
-const OutputRedirects = [
-    { type: 'link-to-last-call', callName: 'sink', attachLinkInfo: { argIdx: 0, argName: 'file', when: DependencyInfoLinkConstraint.IfUnknown, resolveValue: true } }
-];
-exports.WriteFunctions = [
-    { name: 'save', argName: 'file', resolveValue: true },
-    { name: 'save.image', argIdx: 1, argName: 'file', resolveValue: true },
-    { name: 'write', argIdx: 1, argName: 'file', resolveValue: true },
-    { name: 'dput', argIdx: 1, argName: 'file', resolveValue: true },
-    { name: 'dump', argIdx: 1, argName: 'file', resolveValue: true },
-    { name: 'write.table', argIdx: 1, argName: 'file', resolveValue: true },
-    { name: 'write.csv', argIdx: 1, argName: 'file', resolveValue: true },
-    { name: 'saveRDS', argIdx: 1, argName: 'file', resolveValue: true },
-    // write functions that don't have argIndex are assumed to write to stdout
-    { name: 'print', linkTo: OutputRedirects, resolveValue: true },
-    { name: 'cat', linkTo: OutputRedirects, argName: 'file', resolveValue: true },
-    { name: 'message', linkTo: OutputRedirects, resolveValue: true },
-    { name: 'warning', linkTo: OutputRedirects, resolveValue: true },
-    // readr
-    { name: 'write_csv', argIdx: 1, argName: 'file', resolveValue: true },
-    { name: 'write_csv2', argIdx: 1, argName: 'file', resolveValue: true },
-    { name: 'write_delim', argIdx: 1, argName: 'file', resolveValue: true },
-    { name: 'write_dsv', argIdx: 1, argName: 'file', resolveValue: true },
-    { name: 'write_fwf', argIdx: 1, argName: 'file', resolveValue: true },
-    { name: 'write_tsv', argIdx: 1, argName: 'file', resolveValue: true },
-    { name: 'write_table', argIdx: 1, argName: 'file', resolveValue: true },
-    { name: 'write_log', argIdx: 1, argName: 'file', resolveValue: true },
-    // heaven
-    { name: 'write_sas', argIdx: 1, argName: 'file', resolveValue: true },
-    { name: 'write_sav', argIdx: 1, argName: 'file', resolveValue: true },
-    { name: 'write_por', argIdx: 1, argName: 'file', resolveValue: true },
-    { name: 'write_dta', argIdx: 1, argName: 'file', resolveValue: true },
-    { name: 'write_xpt', argIdx: 1, argName: 'file', resolveValue: true },
-    // feather
-    { name: 'write_feather', argIdx: 1, argName: 'file', resolveValue: true },
-    // foreign
-    { name: 'write.arff', argIdx: 1, argName: 'file', resolveValue: true },
-    { name: 'write.dbf', argIdx: 1, argName: 'file', resolveValue: true },
-    { name: 'write.dta', argIdx: 1, argName: 'file', resolveValue: true },
-    { name: 'write.foreign', argIdx: 1, argName: 'file', resolveValue: true },
-    // xlsx
-    { name: 'write.xlsx', argIdx: 1, argName: 'file', resolveValue: true },
-    { name: 'write.xlsx2', argIdx: 1, argName: 'file', resolveValue: true },
-    // graphics
-    { name: 'pdf', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'jpeg', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'png', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'windows', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'postscript', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'xfix', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'bitmap', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'pictex', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'cairo_pdf', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'svg', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'bmp', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'tiff', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'X11', argIdx: 0, argName: 'file', resolveValue: true },
-    { name: 'quartz', argIdx: 0, argName: 'file', resolveValue: true },
-    // car
-    { name: 'Export', argIdx: 0, argName: 'file', resolveValue: true },
-];
 function printResultSection(title, infos, result, sectionSpecifics) {
     if (infos.length <= 0) {
         return;
@@ -175,6 +31,7 @@ function printResultSection(title, infos, result, sectionSpecifics) {
 }
 const functionInfoSchema = joi_1.default.array().items(joi_1.default.object({
     name: joi_1.default.string().required().description('The name of the library function.'),
+    package: joi_1.default.string().optional().description('The package name of the library function'),
     argIdx: joi_1.default.number().optional().description('The index of the argument that contains the library name.'),
     argName: joi_1.default.string().optional().description('The name of the argument that contains the library name.'),
 })).optional();

package/queries/catalog/dependencies-query/function-info/function-info.d.ts

@@ -0,0 +1,24 @@
+import type { LinkTo } from '../../call-context-query/call-context-query-format';
+/** when to read the argument value from a linked function */
+export declare enum DependencyInfoLinkConstraint {
+    Always = "always",
+    IfUnknown = "if-unknown"
+}
+/**
+ * A dependency link may have attached information. If you pass it, we try to resolve the argument value from the linked function
+ * if the `when` constraint is met.
+ */
+export type DependencyInfoLink = LinkTo<RegExp | string, Omit<FunctionInfo, 'name' | 'linkTo' | 'package'> & {
+    when: DependencyInfoLinkConstraint;
+} | undefined>;
+export type DependencyInfoLinkAttachedInfo = DependencyInfoLink['attachLinkInfo'];
+export interface FunctionInfo {
+    package?: string;
+    name: string;
+    /** the index if the argument can be positional, unnamed in case of something like `...`, if the argument must be given with the name, please leave undefined */
+    argIdx?: number | 'unnamed';
+    argName?: string;
+    linkTo?: DependencyInfoLink[];
+    resolveValue?: boolean | 'library';
+    ignoreIf?: 'arg-missing';
+}

package/queries/catalog/dependencies-query/function-info/function-info.js

@@ -0,0 +1,10 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.DependencyInfoLinkConstraint = void 0;
+/** when to read the argument value from a linked function */
+var DependencyInfoLinkConstraint;
+(function (DependencyInfoLinkConstraint) {
+    DependencyInfoLinkConstraint["Always"] = "always";
+    DependencyInfoLinkConstraint["IfUnknown"] = "if-unknown";
+})(DependencyInfoLinkConstraint || (exports.DependencyInfoLinkConstraint = DependencyInfoLinkConstraint = {}));
+//# sourceMappingURL=function-info.js.map

package/queries/catalog/dependencies-query/function-info/library-functions.d.ts

@@ -0,0 +1,2 @@
+import type { FunctionInfo } from './function-info';
+export declare const LibraryFunctions: FunctionInfo[];

package/queries/catalog/dependencies-query/function-info/library-functions.js

@@ -0,0 +1,18 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.LibraryFunctions = void 0;
+exports.LibraryFunctions = [
+    { package: 'base', name: 'library', argIdx: 0, argName: 'package', resolveValue: 'library' },
+    { package: 'base', name: 'require', argIdx: 0, argName: 'package', resolveValue: 'library' },
+    { package: 'base', name: 'loadNamespace', argIdx: 0, argName: 'package', resolveValue: true },
+    { package: 'base', name: 'attachNamespace', argIdx: 0, argName: 'ns', resolveValue: true },
+    { package: 'base', name: 'attach', argIdx: 0, argName: 'what', resolveValue: true },
+    { package: 'groundhog', name: 'groundhog.library', argIdx: 0, argName: 'pkg', resolveValue: true },
+    { package: 'pacman', name: 'p_load', argIdx: 'unnamed', resolveValue: 'library' },
+    { package: 'pacman', name: 'p_load_gh', argIdx: 'unnamed', resolveValue: 'library' },
+    { package: 'easypackages', name: 'from_import', argIdx: 0, argName: 'package', resolveValue: true },
+    { package: 'easypackages', name: 'libraries', argIdx: 'unnamed', resolveValue: true },
+    { package: 'librarian', name: 'shelf', argIdx: 'unnamed', resolveValue: true },
+    { package: 'devtools', name: 'load_all', argIdx: 0, argName: 'path', resolveValue: true }
+];
+//# sourceMappingURL=library-functions.js.map

package/queries/catalog/dependencies-query/function-info/read-functions.d.ts

@@ -0,0 +1,2 @@
+import type { FunctionInfo } from './function-info';
+export declare const ReadFunctions: FunctionInfo[];

package/queries/catalog/dependencies-query/function-info/read-functions.js

@@ -0,0 +1,101 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.ReadFunctions = void 0;
+exports.ReadFunctions = [
+    { package: 'base', name: 'parse', argName: 'file', resolveValue: true, ignoreIf: 'arg-missing' },
+    { package: 'base', name: 'read.table', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'utils', name: 'read.csv', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'utils', name: 'read.csv2', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'utils', name: 'read.delim', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'base', name: 'read.dcf', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'base', name: 'scan', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'utils', name: 'read.fwf', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'base', name: 'file', argIdx: 1, argName: 'open', resolveValue: true },
+    { package: 'base', name: 'url', argIdx: 1, argName: 'open', resolveValue: true },
+    { package: 'base', name: 'load', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'base', name: 'gzfile', argIdx: 1, argName: 'open', resolveValue: true },
+    { package: 'base', name: 'bzfile', argIdx: 1, argName: 'open', resolveValue: true },
+    { package: 'utils', name: 'download.file', argIdx: 0, argName: 'url', resolveValue: true },
+    { package: 'base', name: 'pipe', argIdx: 1, argName: 'open', resolveValue: true },
+    { package: 'base', name: 'fifo', argIdx: 1, argName: 'open', resolveValue: true },
+    { package: 'base', name: 'unz', argIdx: 1, argName: 'open', resolveValue: true },
+    { package: 'base', name: 'matrix', argIdx: 0, argName: 'data', resolveValue: true },
+    { package: 'base', name: 'readRDS', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'base', name: 'readLines', argIdx: 0, argName: 'con', resolveValue: true },
+    { package: 'base', name: 'readRenviron', argIdx: 0, argName: 'path', resolveValue: true },
+    { package: 'readr', name: 'read_csv', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'readr', name: 'read_csv2', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'readr', name: 'read_lines', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'readr', name: 'read_delim', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'readr', name: 'read_dsv', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'readr', name: 'read_fwf', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'readr', name: 'read_tsv', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'readr', name: 'read_table', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'readr', name: 'read_log', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'readr', name: 'read_lines_raw', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'readr', name: 'read_lines_chunked', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'readr', name: 'read_rds', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'readr', name: 'clipboard' },
+    { package: 'xlsx', name: 'read.xlsx', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'xlsx', name: 'read.xlsx2', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'data.table', name: 'fread', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'haven', name: 'read_sas', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'haven', name: 'read_sav', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'haven', name: 'read_por', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'haven', name: 'read_dta', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'haven', name: 'read_xpt', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'feather', name: 'read_feather', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'foreign', name: 'read.arff', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'foreign', name: 'read.dbf', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'foreign', name: 'read.dta', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'foreign', name: 'read.epiinfo', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'foreign', name: 'read.mtp', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'foreign', name: 'read.octave', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'foreign', name: 'read.spss', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'foreign', name: 'read.ssd', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'foreign', name: 'read.systat', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'foreign', name: 'read.xport', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'car', name: 'Import', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'magick', name: 'image_read', argIdx: 0, argName: 'path', resolveValue: true },
+    { package: 'magick', name: 'image_read_svg', argIdx: 0, argName: 'path', resolveValue: true },
+    { package: 'magick', name: 'image_read_pdf', argIdx: 0, argName: 'path', resolveValue: true },
+    { package: 'magick', name: 'image_read_video', argIdx: 0, argName: 'path', resolveValue: true },
+    { package: 'LIM', name: 'Read', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'sourcetools', name: 'read', argIdx: 0, argName: 'path', resolveValue: true },
+    { package: 'sourcetools', name: 'read_lines', argIdx: 0, argName: 'path', resolveValue: true },
+    { package: 'sourcetools', name: 'read_bytes', argIdx: 0, argName: 'path', resolveValue: true },
+    { package: 'sourcetools', name: 'read_lines_bytes', argIdx: 0, argName: 'path', resolveValue: true },
+    { package: 'sourcetools', name: 'tokenize', argName: 'file', resolveValue: true, ignoreIf: 'arg-missing' },
+    { package: 'sourcetools', name: 'tokenize_file', argIdx: 0, argName: 'path', resolveValue: true },
+    { package: 'expss', name: 'read_spss', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'expss', name: 'read_spss_to_list', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'SimPhe', name: 'read.geno', argIdx: 0, argName: 'fname', resolveValue: true },
+    { package: 'ape', name: 'read.tree', argName: 'file', resolveValue: true, ignoreIf: 'arg-missing' },
+    { package: 'geomorph', name: 'readland.tps', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'readxl', name: 'read_excel', argIdx: 0, argName: 'path', resolveValue: true },
+    { package: 'readxl', name: 'read_xls', argIdx: 0, argName: 'path', resolveValue: true },
+    { package: 'readxl', name: 'read_xlsx', argIdx: 0, argName: 'path', resolveValue: true },
+    { package: 'sf', name: 'read.sf', argIdx: 0, argName: 'dsn', resolveValue: true },
+    { package: 'sf', name: 'st_read', argIdx: 0, argName: 'dsn', resolveValue: true },
+    { package: 'rgdal', name: 'readOGR', argIdx: 0, argName: 'dsn', resolveValue: true },
+    { package: 'rgdal', name: 'ogrInfo', argIdx: 0, argName: 'dsn', resolveValue: true },
+    { package: 'rgdal', name: 'ogrFIDs', argIdx: 0, argName: 'dsn', resolveValue: true },
+    { package: 'rgdal', name: 'OGRSpatialRef', argIdx: 0, argName: 'dsn', resolveValue: true },
+    { package: 'rgdal', name: 'ogrListLayers', argIdx: 0, argName: 'dsn', resolveValue: true },
+    { package: 'rgdal', name: 'readGDAL', argIdx: 0, argName: 'fname', resolveValue: true },
+    { package: 'readstata13', name: 'read.dta13', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'arrow', name: 'read_parquet', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'maptools', name: 'readShapePoly', argIdx: 0, argName: 'fn', resolveValue: true },
+    { package: 'XLConnect', name: 'readWorksheetFromFile', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'XLConnect', name: 'readNamedRegionFromFile', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'XLConnect', name: 'loadWorkbook', argIdx: 0, argName: 'filename', resolveValue: true },
+    { package: 'DiagrammeR', name: 'import_graph', argIdx: 0, argName: 'graph_file', resolveValue: true },
+    { package: 'DiagrammeR', name: 'open_graph', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'highcharter', name: 'download_map_data', argIdx: 0, argName: 'url', resolveValue: true },
+    { package: 'rvest', name: 'read_html', argIdx: 0, argName: 'x', resolveValue: true },
+    { package: 'rvest', name: 'read_html_live', argIdx: 0, argName: 'url', resolveValue: true },
+    { package: 'stats', name: 'read.ftable', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'DBI', name: 'dbReadTable', argIdx: 1, argName: 'name', resolveValue: true },
+    { package: 'DBI', name: 'dbReadTableArrow', argIdx: 1, argName: 'name', resolveValue: true },
+];
+//# sourceMappingURL=read-functions.js.map

package/queries/catalog/dependencies-query/function-info/source-functions.d.ts

@@ -0,0 +1,2 @@
+import type { FunctionInfo } from './function-info';
+export declare const SourceFunctions: FunctionInfo[];

package/queries/catalog/dependencies-query/function-info/source-functions.js

@@ -0,0 +1,11 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.SourceFunctions = void 0;
+// these lists are originally based on https://github.com/duncantl/CodeDepends/blob/7fd96dfee16b252e5f642c77a7ababf48e9326f8/R/codeTypes.R
+exports.SourceFunctions = [
+    { package: 'base', name: 'source', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'base', name: 'sys.source', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'devtools', name: 'source_url', argIdx: 0, argName: 'url', resolveValue: true },
+    { package: 'devtools', name: 'source_gist', argIdx: 0, argName: 'id', resolveValue: true }
+];
+//# sourceMappingURL=source-functions.js.map

package/queries/catalog/dependencies-query/function-info/write-functions.d.ts

@@ -0,0 +1,2 @@
+import { type FunctionInfo } from './function-info';
+export declare const WriteFunctions: FunctionInfo[];

package/queries/catalog/dependencies-query/function-info/write-functions.js

@@ -0,0 +1,87 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.WriteFunctions = void 0;
+const function_info_1 = require("./function-info");
+const OutputRedirects = [
+    { type: 'link-to-last-call', callName: 'sink', attachLinkInfo: { argIdx: 0, argName: 'file', when: function_info_1.DependencyInfoLinkConstraint.IfUnknown, resolveValue: true } }
+];
+exports.WriteFunctions = [
+    { package: 'base', name: 'save', argName: 'file', resolveValue: true },
+    { package: 'base', name: 'save.image', argIdx: 1, argName: 'file', resolveValue: true },
+    { package: 'base', name: 'write', argIdx: 1, argName: 'file', resolveValue: true },
+    { package: 'base', name: 'dput', argIdx: 1, argName: 'file', resolveValue: true },
+    { package: 'base', name: 'dump', argIdx: 1, argName: 'file', resolveValue: true },
+    { package: 'utils', name: 'write.table', argIdx: 1, argName: 'file', resolveValue: true },
+    { package: 'utils', name: 'write.csv', argIdx: 1, argName: 'file', resolveValue: true },
+    { package: 'base', name: 'saveRDS', argIdx: 1, argName: 'file', resolveValue: true },
+    // write functions that don't have argIndex are assumed to write to stdout
+    { package: 'base', name: 'print', linkTo: OutputRedirects, resolveValue: true },
+    { package: 'base', name: 'cat', linkTo: OutputRedirects, argName: 'file', resolveValue: true },
+    { package: 'base', name: 'message', linkTo: OutputRedirects, resolveValue: true },
+    { package: 'base', name: 'warning', linkTo: OutputRedirects, resolveValue: true },
+    { package: 'readr', name: 'write_csv', argIdx: 1, argName: 'file', resolveValue: true },
+    { package: 'readr', name: 'write_csv2', argIdx: 1, argName: 'file', resolveValue: true },
+    { package: 'readr', name: 'write_delim', argIdx: 1, argName: 'file', resolveValue: true },
+    { package: 'readr', name: 'write_dsv', argIdx: 1, argName: 'file', resolveValue: true },
+    { package: 'readr', name: 'write_fwf', argIdx: 1, argName: 'file', resolveValue: true },
+    { package: 'readr', name: 'write_tsv', argIdx: 1, argName: 'file', resolveValue: true },
+    { package: 'readr', name: 'write_table', argIdx: 1, argName: 'file', resolveValue: true },
+    { package: 'readr', name: 'write_log', argIdx: 1, argName: 'file', resolveValue: true },
+    { package: 'readr', name: 'write_lines', argIdx: 1, argName: 'file', resolveValue: true },
+    { package: 'readr', name: 'write_rds', argIdx: 1, argName: 'file', resolveValue: true },
+    { package: 'heaven', name: 'write_sas', argIdx: 1, argName: 'file', resolveValue: true },
+    { package: 'heaven', name: 'write_sav', argIdx: 1, argName: 'file', resolveValue: true },
+    { package: 'heaven', name: 'write_por', argIdx: 1, argName: 'file', resolveValue: true },
+    { package: 'heaven', name: 'write_dta', argIdx: 1, argName: 'file', resolveValue: true },
+    { package: 'heaven', name: 'write_xpt', argIdx: 1, argName: 'file', resolveValue: true },
+    { package: 'feather', name: 'write_feather', argIdx: 1, argName: 'file', resolveValue: true },
+    { package: 'foreign', name: 'write.arff', argIdx: 1, argName: 'file', resolveValue: true },
+    { package: 'foreign', name: 'write.dbf', argIdx: 1, argName: 'file', resolveValue: true },
+    { package: 'foreign', name: 'write.dta', argIdx: 1, argName: 'file', resolveValue: true },
+    { package: 'foreign', name: 'write.foreign', argIdx: 1, argName: 'file', resolveValue: true },
+    { package: 'xlsx', name: 'write.xlsx', argIdx: 1, argName: 'file', resolveValue: true },
+    { package: 'xlsx', name: 'write.xlsx2', argIdx: 1, argName: 'file', resolveValue: true },
+    { package: 'graphics', name: 'pdf', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'graphics', name: 'jpeg', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'graphics', name: 'png', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'graphics', name: 'windows', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'graphics', name: 'postscript', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'graphics', name: 'xfix', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'graphics', name: 'bitmap', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'graphics', name: 'pictex', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'graphics', name: 'cairo_pdf', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'graphics', name: 'svg', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'graphics', name: 'bmp', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'graphics', name: 'tiff', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'graphics', name: 'X11', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'graphics', name: 'quartz', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'car', name: 'Export', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'LIM', name: 'PrintMat', linkTo: OutputRedirects, resolveValue: true },
+    { package: 'sjmisc', name: 'write_spss', argIdx: 1, argName: 'path', resolveValue: true },
+    { package: 'sjmisc', name: 'write_stata', argIdx: 1, argName: 'path', resolveValue: true },
+    { package: 'sjmisc', name: 'write_sas', argIdx: 1, argName: 'path', resolveValue: true },
+    { package: 'ape', name: 'write.tree', argIdx: 1, argName: 'file', resolveValue: true },
+    { package: 'ape', name: 'write.nexus', argIdx: 1, argName: 'file', resolveValue: true },
+    { package: 'ape', name: 'write.phyloXML', argIdx: 1, argName: 'file', resolveValue: true },
+    { package: 'Claddis', name: 'write_nexus_matrix', argIdx: 1, argName: 'file_name', resolveValue: true },
+    { package: 'Claddis', name: 'write_tnt_matrix', argIdx: 1, argName: 'file_name', resolveValue: true },
+    { package: 'rgdal', name: 'writeOGR', argIdx: 1, argName: 'dsn', resolveValue: true },
+    { package: 'rgdal', name: 'writeGDAL', argIdx: 1, argName: 'fname', resolveValue: true },
+    { package: 'arrow', name: 'write_parquet', argIdx: 1, argName: 'sink', resolveValue: true },
+    { package: 'sf', name: 'st_write', argIdx: 1, argName: 'dsn', resolveValue: true },
+    { package: 'sf', name: 'write_sf', argIdx: 1, argName: 'dsn', resolveValue: true, ignoreIf: 'arg-missing' },
+    { package: 'maptools', name: 'writePolyShape', argIdx: 1, argName: 'fn', resolveValue: true },
+    { package: 'XLConnect', name: 'writeNamedRegionToFile', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'XLConnect', name: 'writeWorksheetToFile', argIdx: 0, argName: 'file', resolveValue: true },
+    { package: 'visNetwork', name: 'visSave', argIdx: 1, argName: 'file', resolveValue: true },
+    { package: 'DiagrammeR', name: 'save_graph', argIdx: 1, argName: 'file', resolveValue: true },
+    { package: 'DiagrammeR', name: 'export_graph', argName: 'file_name', resolveValue: true },
+    { package: 'ggplot', name: 'ggsave', argIdx: 0, argName: 'filename', resolveValue: true },
+    { package: 'cowplot', name: 'ggsave2', argIdx: 0, argName: 'filename', resolveValue: true },
+    { package: 'tinyplot', name: 'tinyplot', argName: 'file', resolveValue: true, ignoreIf: 'arg-missing' },
+    { package: 'tinyplot', name: 'plt', argName: 'file', resolveValue: true, ignoreIf: 'arg-missing' },
+    { package: 'rasterpdf', name: 'raster_pdf', argIdx: 0, argName: 'filename', resolveValue: true },
+    { package: 'rasterpdf', name: 'agg_pdf', argIdx: 0, argName: 'filename', resolveValue: true },
+    { package: 'highcharter', name: 'hc_exporting', argName: 'filename', resolveValue: true },
+];
+//# sourceMappingURL=write-functions.js.map