Use R files for background process

R/help/helpServer.R

@@ -0,0 +1,11 @@
+# get values from extension-set env values
+lim <- Sys.getenv("VSCR_LIM")
+
+cat(
+    lim,
+    tools::startDynamicHelp(),
+    lim,
+    sep = ""
+)
+
+while (TRUE) Sys.sleep(1)

R/rmarkdown/knit.R

@@ -0,0 +1,22 @@
+# requires rmarkdown package to run (and knitr)
+if (!requireNamespace(rmarkdown, quietly = TRUE)) {
+    stop("Knitting requires the {rmarkdown} package.")
+}
+
+# get values from extension-set env values
+
+knit_dir <- Sys.getenv("VSCR_KNIT_DIR")
+lim <- Sys.getenv("VSCR_LIM")
+knit_command <- Sys.getenv("VSCR_KNIT_COMMAND")
+
+# set the knitr chunk eval directory
+# mainly affects source calls
+knitr::opts_knit[["set"]](root.dir = knit_dir)
+
+# render and get file output location for use in extension
+cat(
+    lim,
+    eval(parse(text = knit_command)),
+    lim,
+    sep = ""
+)

R/rmarkdown/preview.R

@@ -0,0 +1,29 @@
+# requires rmarkdown package to run (and knitr)
+if (!requireNamespace(rmarkdown, quietly = TRUE)) {
+    stop("Previewing documents requires the {rmarkdown} package.")
+}
+
+# get values from extension-set env values
+
+knit_dir <- Sys.getenv("VSCR_KNIT_DIR")
+lim <- Sys.getenv("VSCR_LIM")
+file_path <- Sys.getenv("VSCR_FILE_PATH")
+output_file_loc <- Sys.getenv("VSCR_OUTPUT_FILE")
+tmp_dir <- Sys.getenv("VSCR_TMP_DIR")
+
+# set the knitr chunk eval directory
+# mainly affects source calls
+knitr::opts_knit[["set"]](root.dir = knit_dir)
+
+# render and get file output location for use in extension
+cat(
+    lim,
+    rmarkdown::render(
+        file_path,
+        output_format = rmarkdown::html_document(),
+        output_file = output_file_loc,
+        intermediates_dir = tmp_dir
+    ),
+    lim,
+    sep = ""
+)

src/helpViewer/helpProvider.ts

@@ -8,6 +8,7 @@ import * as fs from 'fs';
 import * as os from 'os';
 
 import * as rHelp from '.';
+import { extensionContext } from '../extension';
 
 export interface RHelpProviderOptions {
 	// path of the R executable
@@ -39,12 +40,14 @@ export class HelpProvider {
 		const re = new RegExp(`.*${lim}(.*)${lim}.*`, 'ms');
 
         // starts the background help server and waits forever to keep the R process running
+        const scriptPath = extensionContext.asAbsolutePath('R/help/helpServer.R');
         const cmd = (
-            `${this.rPath} --silent --slave --no-save --no-restore -e ` +
-            `"cat('${lim}', tools::startDynamicHelp(), '${lim}', sep=''); while(TRUE) Sys.sleep(1)" ` 
+            `${this.rPath} --silent --slave --no-save --no-restore -f ` +
+            `${scriptPath}`
         );
         const cpOptions = {
-            cwd: this.cwd
+            cwd: this.cwd,
+            env: { ...process.env, 'VSCR_LIM': lim }
         };
         this.cp = cp.exec(cmd, cpOptions);
 
@@ -53,7 +56,7 @@ export class HelpProvider {
         const outputPromise = new Promise<string>((resolve) => {
             this.cp.stdout?.on('data', (data) => {
                 try{
-                    // eslint-disable-next-line 
+                    // eslint-disable-next-line
                     str += data.toString();
                 } catch(e){
                     resolve('');
@@ -92,7 +95,7 @@ export class HelpProvider {
             content?: string,
             redirect?: string
         }
-    
+
         // forward request to R instance
         // below is just a complicated way of getting a http response from the help server
         let url = `http://localhost:${this.port}/${requestPath}`;
@@ -159,7 +162,7 @@ export interface AliasProviderArgs {
     cwd?: string;
 	// getAliases.R
     rScriptFile: string;
-    
+
     persistentState: Memento;
 }
 
@@ -283,7 +286,7 @@ export class AliasProvider {
         }
 
         // get from R
-        this.allPackageAliases = null; 
+        this.allPackageAliases = null;
 		const lim = '---vsc---'; // must match the lim used in R!
 		const re = new RegExp(`^.*?${lim}(.*)${lim}.*$`, 'ms');
         const tempDir = fs.mkdtempSync(path.join(os.tmpdir(), 'vscode-R-aliases-'));

src/helpViewer/index.ts

@@ -41,7 +41,7 @@ export async function initializeHelp(context: vscode.ExtensionContext, rExtensio
     const rHelpOptions: HelpOptions = {
         webviewScriptPath: context.asAbsolutePath('/html/help/script.js'),
         webviewStylePath: context.asAbsolutePath('html/help/theme.css'),
-		rScriptFile: context.asAbsolutePath('R/getAliases.R'),
+		rScriptFile: context.asAbsolutePath('R/help/getAliases.R'),
         rPath: rPath,
         cwd: cwd,
 		persistentState: persistentState

src/rTerminal.ts

@@ -98,8 +98,8 @@ export async function createRTerm(preserveshow?: boolean): Promise<boolean> {
                 shellPath: termPath,
                 shellArgs: termOpt,
             };
-            const newRprofile = extensionContext.asAbsolutePath(path.join('R', '.Rprofile'));
-            const initR = extensionContext.asAbsolutePath(path.join('R', 'init.R'));
+            const newRprofile = extensionContext.asAbsolutePath(path.join('R', 'session', '.Rprofile'));
+            const initR = extensionContext.asAbsolutePath(path.join('R', 'session','init.R'));
             if (config().get<boolean>('sessionWatcher')) {
                 termOptions.env = {
                     R_PROFILE_USER_OLD: process.env.R_PROFILE_USER,

src/rmarkdown/knit.ts

@@ -6,7 +6,7 @@ import yaml = require('js-yaml');
 
 import { RMarkdownManager, KnitWorkingDirectory, DisposableProcess } from './manager';
 import { runTextInTerm } from '../rTerminal';
-import { rmdPreviewManager } from '../extension';
+import { extensionContext, rmdPreviewManager } from '../extension';
 
 export let knitDir: KnitWorkingDirectory = util.config().get<KnitWorkingDirectory>('rmarkdown.knit.defaults.knitWorkingDirectory') ?? undefined;
 
@@ -29,18 +29,17 @@ export class RMarkdownKnitManager extends RMarkdownManager {
 	private async renderDocument(rDocumentPath: string, docPath: string, docName: string, yamlParams: IYamlFrontmatter, outputFormat?: string): Promise<DisposableProcess> {
 		const openOutfile: boolean = util.config().get<boolean>('rmarkdown.knit.openOutputFile') ?? false;
 		const knitWorkingDir = this.getKnitDir(knitDir, docPath);
-		const knitWorkingDirText = knitWorkingDir ? `'${knitWorkingDir}'` : `NULL`;
+		const knitWorkingDirText = knitWorkingDir ? `${knitWorkingDir}` : `NULL`;
 		const knitCommand = await this.getKnitCommand(yamlParams, rDocumentPath, outputFormat);
 		this.rPath = await util.getRpath();
 
 		const lim = '---vsc---';
 		const re = new RegExp(`.*${lim}(.*)${lim}.*`, 'gms');
-		const cmd =
-			`knitr::opts_knit[['set']](root.dir = ${knitWorkingDirText});` +
-			`cat('${lim}', ` +
-			`${knitCommand}, ` +
-			`'${lim}',` +
-			`sep='')`;
+		const scriptValues = {
+			'VSCR_KNIT_DIR': knitWorkingDirText,
+			'VSCR_LIM': lim,
+			'VSCR_KNIT_COMMAND': knitCommand
+		};
 
 		const callback = (dat: string) => {
 			const outputUrl = re.exec(dat)?.[0]?.replace(re, '$1');
@@ -67,7 +66,8 @@ export class RMarkdownKnitManager extends RMarkdownManager {
 			{
 				fileName: docName,
 				filePath: rDocumentPath,
-				cmd: cmd,
+				scriptArgs: scriptValues,
+				scriptPath: extensionContext.asAbsolutePath('R/rmarkdown/knit.R'),
 				rCmd: knitCommand,
 				rOutputFormat: outputFormat,
 				callback: callback

src/rmarkdown/manager.ts

@@ -20,7 +20,8 @@ const rMarkdownOutput: vscode.OutputChannel = vscode.window.createOutputChannel(
 interface IKnitArgs {
 	filePath: string;
 	fileName: string;
-	cmd: string;
+	scriptArgs: Record<string, string>;
+	scriptPath: string;
 	rCmd?: string;
 	rOutputFormat?: string;
 	callback: (...args: unknown[]) => boolean;
@@ -61,18 +62,23 @@ export abstract class RMarkdownManager {
 
 		return await new Promise<DisposableProcess>(
 			(resolve, reject) => {
-				const cmd = args.cmd;
+				const scriptArgs = args.scriptArgs;
+				const scriptPath = args.scriptPath;
 				const fileName = args.fileName;
+
 				const processArgs = [
 					`--silent`,
 					`--slave`,
 					`--no-save`,
 					`--no-restore`,
-					`-e`,
-					cmd
+					`-f`,
+					`${scriptPath}`
 				];
 				const processOptions = {
-					env: process.env
+					env: {
+						...process.env,
+						...scriptArgs
+					}
 				};
 
 				let childProcess: DisposableProcess;

src/rmarkdown/preview.ts

@@ -283,21 +283,20 @@ export class RMarkdownPreviewManager extends RMarkdownManager {
 
     private async previewDocument(filePath: string, fileName?: string, viewer?: vscode.ViewColumn, currentViewColumn?: vscode.ViewColumn): Promise<DisposableProcess> {
         const knitWorkingDir = this.getKnitDir(knitDir, filePath);
-        const knitWorkingDirText = knitWorkingDir ? `'${knitWorkingDir}'` : `NULL`;
+        const knitWorkingDirText = knitWorkingDir ? `${knitWorkingDir}` : `NULL`;
         this.rPath = await getRpath();
 
         const lim = '---vsc---';
         const re = new RegExp(`.*${lim}(.*)${lim}.*`, 'ms');
         const outputFile = path.join(tmpDir(), crypto.createHash('sha256').update(filePath).digest('hex') + '.html');
-        const cmd = (
-            `knitr::opts_knit[['set']](root.dir = ${knitWorkingDirText});` +
-            `cat('${lim}', rmarkdown::render(` +
-            `'${filePath.replace(/\\/g, '/')}',` +
-            `output_format = rmarkdown::html_document(),` +
-            `output_file = '${outputFile.replace(/\\/g, '/')}',` +
-            `intermediates_dir = '${tmpDir().replace(/\\/g, '/')}'), '${lim}',` +
-            `sep='')`
-        );
+        const scriptValues = {
+            'VSCR_KNIT_DIR' : knitWorkingDirText,
+            'VSCR_LIM': lim,
+            'VSCR_FILE_PATH': filePath.replace(/\\/g, '/'),
+            'VSCR_OUTPUT_FILE': outputFile.replace(/\\/g, '/'),
+            'VSCR_TMP_DIR': tmpDir().replace(/\\/g, '/')
+        };
+
 
         const callback = (dat: string, childProcess: DisposableProcess) => {
             const outputUrl = re.exec(dat)?.[0]?.replace(re, '$1');
@@ -329,7 +328,8 @@ export class RMarkdownPreviewManager extends RMarkdownManager {
             {
                 fileName: fileName,
                 filePath: filePath,
-                cmd: cmd,
+                scriptPath: extensionContext.asAbsolutePath('R/rmarkdown/preview.R'),
+                scriptArgs: scriptValues,
                 rOutputFormat: 'html preview',
                 callback: callback,
                 onRejection: onRejected

src/session.ts

@@ -43,7 +43,7 @@ export function deploySessionWatcher(extensionPath: string): void {
     console.info(`[deploySessionWatcher] extensionPath: ${extensionPath}`);
     resDir = path.join(extensionPath, 'dist', 'resources');
 
-    const initPath = path.join(extensionPath, 'R', 'init.R');
+    const initPath = path.join(extensionPath, 'R', 'session', 'init.R');
     const linkPath = path.join(homeExtDir(), 'init.R');
     fs.writeFileSync(linkPath, `local(source("${initPath.replace(/\\/g, '\\\\')}", chdir = TRUE, local = TRUE))\n`);