r run task in background

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rstudio - is it possible to run a code in the background

Question regarding RStudio. Suppose I am running a code in the console:

assume that code1() prints nothing on the console, but code1() above takes an hour to complete. I want to work on something else while I wait for code1() . is it possible? Is there a function like runInBackground which I can use as follows

The alternatives are running two RStudios or writing a batch file that uses Rscript to run code1() , but I wanted to know if there is something easier that I can do without leaving the RStudio console. I tried to browse through R's help documentation but didn't come up with anything (or may be I didn't use the proper keywords).

4 Answers 4

The future package (I'm the author) provides this:

FYI, if you use

then the future expression is resolved on one of those machines. Using

will cause it to be resolved via a Slurm job scheduler queue.

This question is closely related to Run asynchronous function in R

You can always do this, which is not ideal but works for most purposes:

RStudio as of version 1.2 provides this feature. To run a script in the background select "Start Job" in the "Jobs" panel. You also have the option of copying the background job result into the working environment.

The mcparallel() function in the parallel package will do the trick, if you are on Linux, that is ...

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How to run R scripts as RStudio local background jobs

InfoWorld | May 29, 2020

See how to run lengthy R scripts as background jobs so you can continue working in your current RStudio project.

How-To's & Tips

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Running background R jobs in Shiny

How to make long running tasks persist after closing a session.

Shiny is a great tool for creating interactive dashboards and websites in R. It uses a reactive framework so that as buttons, dropdowns, and other inputs are adjusted the outputs and intermediate values are thoughtfully updated. Thanks to the reactive approach the R code in an app only needs to run when it’s relevant for the front-end. The downside of this approach is that occasionally you have activities that don’t fit into the reactive style and it’s hard to figure out how to set them up in Shiny.

One such task which has plagued me multiple times is trying to have Shiny trigger a background task. Typically this is a long-running set of code that I want to make sure both doesn’t cause the front-end to freeze while it’s running and also will continue to run after the user’s browser is closed .

This week, as part of a larger project I am working on I have found a solution that I think works really well for Shiny background tasks. It’s based on an solution I saw created by Barret Schloerke in a GitHub issue about plumber. I modified Barret’s idea slightly, but at it’s core it’s the same (and also works in Plumber too!).

The idea is to use the {callr} package, which lets you from within R start a separate R process that runs concurrently. {callr} is a really useful package when you have R tasks that you want to run without interrupting your existing R process, but it’s a bit tricky to use in Shiny since Shiny so aggressively deletes variables that aren’t reactive.

To get {callr} to run a background job with Shiny, you need to do two things:

Here is a simple example showing the background process in action. This UI contains only a button that when pressed, starts a job to save a csv file which takes ten seconds. The job will finish even if you close the browser, so long as Shiny is running.

Warning: if you use the “Run App” button in RStudio to launch the app you will have a medicore experience. In that situation closing the RStudio browser that automatically launches will cause Shiny to stop running, and thus cancel the background task. Ideally when a session ends Shiny will keep running, which is what happens in all browsers except the RStudio one. To avoid this issue, run the Shiny app with the command shiny::runApp(launch.browser = FALSE) , and then go to the URL that the message says Shiny is listening on (ex: Listening on http://127.0.0.1:3263 ).

While this is a pretty bland example, there are lots of practical applications to this, such as starting long-running data manipulations or having Shiny do HTTP calls to other services. The only thing that should interrupt the background task is the Shiny app shutting down, so take care when using services like shinyapps.io which automatically shuts down an idle server after 15 minutes.

R news and tutorials contributed by hundreds of R bloggers

Running rstudio (1.2) background jobs.

Posted on June 9, 2018 by hrbrmstr in R bloggers | 0 Comments

[social4i size="small" align="align-left"] --> [This article was first published on R – rud.is , and kindly contributed to R-bloggers ]. (You can report issue about the content on this page here ) Want to share your content on R-bloggers? click here if you have a blog, or here if you don't.

The forthcoming RStudio 1.2 release has a new “Jobs” feature for running and managing background R tasks.

I did a series of threaded screencaps on Twitter but that doesn’t do the feature justice.

So I threw together a quick ‘splainer on how to run and Python (despite RStudio not natively supporting Python) code in the background while you get other stuff done, then work with the results.

To leave a comment for the author, please follow the link and comment on their blog: R – rud.is . R-bloggers.com offers daily e-mail updates about R news and tutorials about learning R and many other topics. Click here if you're looking to post or find an R/data-science job . Want to share your content on R-bloggers? click here if you have a blog, or here if you don't.

Never miss an update! Subscribe to R-bloggers to receive e-mails with the latest R posts. (You will not see this message again.)

Schedule a Background Job

Description.

Utilizes 'RStudio' job scheduler if correct environment is detected, otherwise call system command via Rscript

'RStudio' provides interfaces jobRunScript to schedule background jobs. However, this functionality only applies using 'RStudio' IDE. When launching R from other places such as terminals, the job scheduler usually result in errors. In this case, the alternative is to call system command via Rscript

The expression expr will run a clean environment. Therefore R objects created outside of the context will be inaccessible from within the child environment, and packages except for base packages will not be loaded.

There is a small difference when running within and without 'RStudio'. When running via Rscript , the environment will run under vanilla argument, which means no load, no start-up code. If you have start-up code stored at ~/.Rprofile , the start-up code will be ignored. When running within 'RStudio', the start-up code will be executed. As of rstudioapi version 0.11, there is no 'vanilla' option. This feature is subject to change in the future.

If wait=TRUE , returns evaluation results of expr , otherwise a function that can track the state of job.

taskscheduleR

Jan Wijffels

Schedule R scripts/processes with the Windows task scheduler. This allows R users working on Windows to automate R processes on specific timepoints from R itself.

Basic usage

The package allows to

Get the list of scheduled tasks

Remove a task

A task is basically a script with R code which is run through Rscript

You can schedule tasks ‘ONCE’, ‘MONTHLY’, ‘WEEKLY’, ‘DAILY’, ‘HOURLY’, ‘MINUTE’, ‘ONLOGON’, ‘ONIDLE’

The task log contains the stdout & stderr of the Rscript which was run on that timepoint. This log can be found at the same folder as the R script

Example usage:

When the task has run, you can look at the log which contains everything from stdout and stderr. The log file is located at the directory where the R script is located.

RStudio addin

If you work with RStudio as editor, you can also just use the RStudio addin. In recent versions of RStudio (0.99.893 or later), select Addins and next select ‘Schedule R scripts on Windows’. This will allow you to select a script to be scheduled at your specified timepoints. The script will be copied to the Rscript repo folder and will be launched from there each time.

Version 1.76 is now available! Read about the new features and fixes from February.

Integrate with External Tools via Tasks

Lots of tools exist to automate tasks like linting, building, packaging, testing, or deploying software systems. Examples include the TypeScript Compiler , linters like ESLint and TSLint as well as build systems like Make , Ant , Gulp , Jake , Rake , and MSBuild .

VS Code can talk to a variety of external tools

These tools are mostly run from the command line and automate jobs inside and outside the inner software development loop (edit, compile, test, and debug). Given their importance in the development life cycle, it is helpful to be able to run tools and analyze their results from within VS Code. Tasks in VS Code can be configured to run scripts and start processes so that many of these existing tools can be used from within VS Code without having to enter a command line or write new code. Workspace or folder specific tasks are configured from the tasks.json file in the .vscode folder for a workspace.

Extensions can also contribute tasks using a Task Provider , and these contributed tasks can add workspace-specific configurations defined in the tasks.json file.

Note: Task support is only available when working on a workspace folder. It is not available when editing single files.

TypeScript Hello World

Let's start with a simple "Hello World" TypeScript program that we want to compile to JavaScript.

Create an empty folder "mytask", generate a tsconfig.json file and start VS Code from that folder.

Now create a HelloWorld.ts file with the following content

Pressing ⇧⌘B (Windows, Linux Ctrl+Shift+B ) or running Run Build Task from the global Terminal menu show the following picker:

The first entry executes the TypeScript compiler and translates the TypeScript file to a JavaScript file. When the compiler has finished, there should be a HelloWorld.js file. The second entry starts the TypeScript compiler in watch mode. Every save to the HelloWorld.ts file will regenerate the HelloWorld.js file.

You can also define the TypeScript build or watch task as the default build task so that it is executed directly when triggering Run Build Task ( ⇧⌘B (Windows, Linux Ctrl+Shift+B ) ). To do so, select Configure Default Build Task from the global Terminal menu. This shows you a picker with the available build tasks. Select tsc: build or tsc: watch and VS Code will generate a tasks.json file. The one shown below makes the tsc: build task the default build task:

The tasks.json example above does not define a new task. It annotates the tsc: build tasks contributed by VS Code's TypeScript extension to be the default build task. You can now execute the TypeScript compiler by pressing ⇧⌘B (Windows, Linux Ctrl+Shift+B ) .

Task auto-detection

VS Code currently auto-detects tasks for the following systems: Gulp, Grunt, Jake, and npm. We are working with the corresponding extension authors to add support for Maven and the C# dotnet command as well. If you develop a JavaScript application using Node.js as the runtime, you usually have a package.json file describing your dependencies and the scripts to run. If you have cloned the eslint-starter example, then executing Run Tasks from the global menu shows the following list:

If you have not already done so, install the necessary npm modules by running npm install . Now open the server.js file and add a semicolon to the end of a statement (note the ESLint starter assumes statements without a semicolon) and execute the Run Tasks again. This time select the npm: lint task. When prompted for the problem matcher to use, select ESLint stylish

Executing the task produces one error, shown in the Problems view:

In addition, VS Code created a tasks.json file with the following content:

This instructs VS Code to scan the output of the npm lint script for problems using the ESLint stylish format.

For Gulp, Grunt, and Jake, the task auto-detection works the same. Below is an example of the tasks detected for the vscode-node-debug extension.

Tip: You can run your task through Quick Open ( ⌘P (Windows, Linux Ctrl+P ) ) by typing 'task', Space and the command name. In this case, 'task lint'.

Task auto detection can be disabled using the following settings:

Custom tasks

Not all tasks or scripts can be auto-detected in your workspace. Sometimes it is necessary to define your own custom tasks. Assume you have a script to run your tests in order to set up some environment correctly. The script is stored in a script folder inside your workspace and named test.sh for Linux and macOS and test.cmd for Windows. Run Configure Tasks from the global Terminal menu and select the Create tasks.json file from template entry. This opens the following picker:

Note: If you don't see the list of task runner templates, you may already have a tasks.json file in your folder and its contents will be open in the editor. Close the file and either delete or rename it for this example.

We are working on more auto-detection support, so this list will get smaller and smaller in the future. Since we want to write our own custom task, select Others from the list. This opens the tasks.json file with a task skeleton. Replace the contents with the following:

The task's properties have the following semantic:

You can see the full set of task properties and values with IntelliSense in your tasks.json file. Bring up suggestions with Trigger Suggest ( ⌃Space (Windows, Linux Ctrl+Space ) ) and read the descriptions on hover or with the Read More... ('i') flyout.

You can also review the tasks.json schema .

Shell commands need special treatment when it comes to commands and arguments that contain spaces or other special characters like $ . By default, the task system supports the following behavior:

Besides escaping, the following values are supported:

If the command itself contains spaces, VS Code will by default strong quote the command as well. As with arguments, the user can control the quoting of the command using the same literal style.

There are more task properties to configure your workflow. You can use IntelliSense with ⌃Space (Windows, Linux Ctrl+Space ) to get an overview of the valid properties.

In addition to the global menu bar, task commands can be accessed using the Command Palette ( ⇧⌘P (Windows, Linux Ctrl+Shift+P ) ). You can filter on 'task' and can see the various task related commands.

Compound tasks

You can also compose tasks out of simpler tasks with the dependsOn property. For example, if you have a workspace with a client and server folder and both contain a build script, you can create a task that starts both build scripts in separate terminals. If you list more than one task in the dependsOn property, they are executed in parallel by default.

The tasks.json file looks like this:

If you specify "dependsOrder": "sequence" , then your task dependencies are executed in the order they are listed in dependsOn . Any background/watch tasks used in dependsOn with "dependsOrder": "sequence" must have a problem matcher that tracks when they are "done". The following task runs task Two, task Three, and then task One.

User level tasks

You can create user level tasks that are not tied to a specific workspace or folder using the Tasks: Open User Tasks command. Only shell and process tasks can be used here since other task types require workspace information.

Output behavior

Sometimes you want to control how the Integrated Terminal panel behaves when running tasks. For instance, you may want to maximize editor space and only look at task output if you think there is a problem. The behavior of the terminal can be controlled using the presentation property of a task. It offers the following properties:

You can modify the terminal panel behavior for auto-detected tasks as well. For example, if you want to change the output behavior for the npm: run lint from the ESLint example from above, add the presentation property to it:

You can also mix custom tasks with configurations for detected tasks. A tasks.json that configures the npm: run lint task and adds a custom Run Test tasks looks like this:

Run behavior

You can specify a task's run behaviors using the runOptions property:

Customizing auto-detected tasks

As mentioned above, you can customize auto-detected tasks in the tasks.json file. You usually do so to modify presentation properties or to attach a problem matcher to scan the task's output for errors and warnings. You can customize a task directly from the Run Task list by pressing the gear icon to the right to insert the corresponding task reference into the tasks.json file. Assume you have the following Gulp file to lint JavaScript files using ESLint (the file is taken from https://github.com/adametry/gulp-eslint ):

Executing Run Task from the global Terminal menu will show the following picker:

Press the gear icon. This will create the following tasks.json file:

Usually you would now add a problem matcher (in this case $eslint-stylish ) or modify the presentation settings.

Processing task output with problem matchers

VS Code can process the output from a task with a problem matcher. Problem matchers scan the task output text for known warning or error strings, and report these inline in the editor and in the Problems panel. VS Code ships with several problem matchers 'in-the-box':

You can also create your own problem matcher, which we'll discuss in a later section .

Binding keyboard shortcuts to tasks

If you need to run a task frequently, you can define a keyboard shortcut for the task.

For example, to bind Ctrl+H to the Run tests task from above, add the following to your keybindings.json file:

Variable substitution

When authoring tasks configurations, it is useful to have a set of predefined common variables such as the active file ( ${file} ) or workspace root folder ( ${workspaceFolder} ). VS Code supports variable substitution inside strings in the tasks.json file and you can see a full list of predefined variables in the Variables Reference .

Note: Not all properties will accept variable substitution. Specifically, only command , args , and options support variable substitution.

Below is an example of a custom task configuration that passes the current opened file to the TypeScript compiler.

Below is an example of a custom task configuration, which executes autopep8 on the current file using the autopep8 executable defined by the python.formatting.autopep8Path setting:

If you want to specify the selected Python interpreter used by the Python extension for tasks.json or launch.json , you can use the ${command:python.interpreterPath} command.

If simple variable substitution isn't enough, you can also get input from the user of your task by adding an inputs section to your tasks.json file.

For more information about inputs , see the Variables Reference .

Operating system specific properties

The task system supports defining values (for example, the command to be executed) specific to an operating system. To do so, put an operating system specific literal into the tasks.json file and specify the corresponding properties inside that literal.

Below is an example that uses the Node.js executable as a command and is treated differently on Windows and Linux:

Valid operating properties are windows for Windows, linux for Linux, and osx for macOS. Properties defined in an operating system specific scope override properties defined in the task or global scope.

Global tasks

Task properties can also be defined in the global scope. If present, they will be used for specific tasks unless they define the same property with a different value. In the example below, there is a global presentation property, which defines that all tasks should be executed in a new panel:

Tip: To get access to the global scope tasks.json file, open the Command Palette ( ⇧⌘P (Windows, Linux Ctrl+Shift+P ) ) and run the Tasks: Open User Tasks command.

Character escaping in PowerShell

When the default shell is PowerShell, or when a task is configured to use PowerShell, you might see unexpected space and quote escaping. The unexpected escaping only occurs with cmdlets because VS Code doesn't know if your command contains cmdlets. Example 1 below shows a case where you'll get escaping that doesn't work with PowerShell. Example 2 shows the best, cross-platform, way to get good escaping. In some cases, you might not be able to follow example 2 and you'll need to do the manual escaping shown in example 3.

Changing the encoding for a task output

Tasks frequently act with files on disk. If these files are stored on disk with an encoding different than the system encoding, you need to let the command executed as a task know which encoding to use. Since this depends on the operating system and the shell used, there is no general solution to control this. Below are advice and examples on how to make it work.

If you need to tweak the encoding, you should check whether it makes sense to change the default encoding used by your operating system or at least change it for the shell you use by tweaking the shell's profile file.

If you only need to tweak it for a specific task, then add the OS-specific command necessary to change the encoding to the tasks command line. The following example is for Windows using code page of 437 as its default. The task shows the output of a file containing Cyrillic characters and therefore needs code page 866. The task to list the file looks like this assuming that the default shell is set to cmd.exe :

If the task is executed in PowerShell , the command needs to read like this chcp 866; more russian.txt . On Linux and macOS, the locale command can be used to inspect the locale and tweak the necessary environment variables.

Examples of tasks in action

To highlight the power of tasks, here are a few examples of how VS Code can use tasks to integrate external tools like linters and compilers.

Transpiling TypeScript to JavaScript

The TypeScript topic includes an example that creates a task to transpile TypeScript to JavaScript and observe any related errors from within VS Code.

Transpiling Less and SCSS into CSS

The CSS topic provides examples of how to use Tasks to generate CSS files.

Defining a problem matcher

VS Code ships some of the most common problem matchers 'in-the-box'. However, there are lots of compilers and linting tools out there, all of which produce their own style of errors and warnings so you may want to create your own problem matcher.

We have a helloWorld.c program in which the developer mistyped printf as prinft . Compiling it with gcc will produce the following warning:

We want to produce a problem matcher that can capture the message in the output and show a corresponding problem in VS Code. Problem matchers heavily rely on regular expressions . The section below assumes you are familiar with regular expressions.

Tip: We have found the RegEx101 playground , which has an ECMAScript (JavaScript) flavor, to be a great way to develop and test regular expressions.

A matcher that captures the above warning (and errors) looks like this:

Note that the file, line, and message properties are mandatory. The fileLocation specifies whether the file paths that are produced by the task output and matched in the problem are absolute or relative . If the task produces both absolute and relative paths, you can use the autoDetect file location. With autoDetect , paths are first tested as absolute paths, and if the file doesn't exist then the path is assumed to be relative.

Here is a finished tasks.json file with the code above (comments removed) wrapped with the actual task details:

Running it inside VS Code and pressing ⇧⌘M (Windows, Linux Ctrl+Shift+M ) to get the list of problems gives you the following output:

Note: The C/C++ extension includes problem matchers for GCC so there is no need to define our own.

There are a couple more properties that can be used inside a pattern. These are:

You can also define a problem matcher that captures only a file. To do so, define a pattern with the optional kind attribute set to file . In this case, there is no need to provide a line or location property.

Note: A functional pattern must at least provide a match group for file and message if the kind property is set to file . If no kind property is provided or the kind property is set to location , a function pattern must provide a line or location property as well.

Note: The problem matcher only parses output from the given command. If you want to parse output written to separate file (e.g. a log file), make the command that you run print out lines from the separate file before it finishes executing.

Defining a multiline problem matcher

Some tools spread problems found in a source file over several lines, especially if stylish reporters are used. An example is ESLint ; in stylish mode it produces output like this:

Our problem matcher is line-based so we need to capture the file name (test.js) with a different regular expression than the actual problem location and message (1:0 error Missing "use strict" statement).

To do this, use an array of problem patterns for the pattern property. This way you define a pattern per each line you want to match.

The following problem pattern matches the output from ESLint in stylish mode - but still has one small issue that we need to resolve next. The code below has a first regular expression to capture the file name and the second to capture the line, column, severity, message, and error code:

However, this pattern will not work if there is more than one problem on a resource. For instance, imagine the following output from ESLint:

The pattern's first regular expression will match "test.js", the second "1:0 error ...". The next line "1:9 error ..." is processed but not matched by the first regular expression and so no problem is captured.

To make this work, the last regular expression of a multiline pattern can specify the loop property. If set to true, it instructs the task system to apply the last pattern of a multiline matcher to the lines in the output as long as the regular expression matches.

The information captured by the first pattern, which in this case matches test.js , will be combined with each of the subsequent lines that match the loop pattern to create multiple problems. In this example, six problems would be created.

Here is a problem matcher to fully capture ESLint stylish problems:

Note : If you have multiple problems that occur on the same resource with the exact same line and column, then only one problem will be shown. This applies to all problem matchers, not just multiline problem matchers.

Modifying an existing problem matcher

If an existing problem matcher is close to what you need, you can modify it in your tasks.json task. For example, the $tsc-watch problem matcher only applies to closed documents. If you want to have it apply to all documents you can modify it:

Other modifiable problem matcher properties include background , fileLocation , owner , pattern , severity , and source .

Background / watching tasks

Some tools support running in the background while watching the file system for changes and then triggering an action when a file changes on disk. With Gulp such functionality is provided through the npm module gulp-watch . The TypeScript compiler tsc has built in support for this via the --watch command line option.

To provide feedback that a background task is active in VS Code and producing problem results, a problem matcher has to use additional information to detect these state changes in the output. Let's take the tsc compiler as an example. When the compiler is started in watch mode, it prints the following additional information to the console:

When a file changes on disk that contains a problem, the following output appears:

Looking at the output shows the following pattern:

To capture this information, a problem matcher can provide a background property.

For the tsc compiler, an appropriate background property looks like this:

In addition to the background property on the problem matcher, the task itself has to be marked as isBackground so that the task keeps running in the background.

A full handcrafted tasks.json for a tsc task running in watch mode looks like this:

That was tasks - let's keep going...

Common questions

Can a task use a different shell than the one specified for the integrated terminal.

Yes. You can use the "terminal.integrated.automationProfile.*" setting to set the shell that will be used for all automation in VS Code, which includes Tasks.

Alternatively, you can override a task's shell with the options.shell property. You can set this per task, globally, or per platform. For example, to use cmd.exe on Windows, your tasks.json would include:

Can a background task be used as a prelaunchTask in launch.json?

Yes. Since a background task will run until killed, a background task on its own has no signal that it has "completed". To use a background task as a prelaunchTask , you must add an appropriate background problemMatcher to the background task so that there is a way for the task system and debug system to know that the task "finished".

Your task could be:

Note: The $tsc-watch is a background problem matcher, as is required for a background task.

You can then use the task as a prelaunchTask in your launch.json file:

For more on background tasks, go to Background / watching tasks .

Why do I get "command not found" when running a task?

The message "command not found" happens when the task command you're trying to run is not recognized by your terminal as something runnable. Most often, this occurs because the command is configured as part of your shell's startup scripts. Tasks are run as non-login and non-interactive, which means that the startup scripts for your shell won't be run. nvm in particular is known to use startup scripts as part of its configuration.

There are several ways to resolve this issue:

The above npm task will run bash with a command ( -c ), just like the tasks system does by default. However, this task also runs bash as a login shell ( -l ).

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COMMENTS

rstudio
RStudio as of version 1.2 provides this feature. To run a script in the background select "Start Job
RStudio User Guide
A “background job” is an R script that runs in a separate, dedicated R session. Any R script can be run in a separate session by: from the Background Job tab in
How to run R scripts as RStudio local background jobs
If you don't want to use the RStudio dialog box to source a script as a local job, you can use the rstudioapi package and its jobRunScript()
Running background R jobs in Shiny
How to make long running tasks persist after closing a session · Use the function callr::r_bg() which will start the new R process in the
Run Scripts in the Background Using RStudio
Brief video showing how to run #Rscripts in the background using #RStudio . You can run the script in the background which will allow you to
How to run R scripts as RStudio local background jobs
See how to run lengthy R scripts as background jobs so you can continue working in your current RStudio project.Follow Sharon on Twitter:
Running RStudio (1.2) Background Jobs
The forthcoming RStudio 1.2 release has a new “Jobs” feature for running and managing background R tasks. I did a series of threaded
Schedule a Background Job
When running via Rscript , the environment will run under vanilla argument, which means no load, no start-up code. If you have start-up code stored at ~/.
taskscheduleR
Basic usage · A task is basically a script with R code which is run through Rscript · You can schedule tasks 'ONCE', 'MONTHLY', 'WEEKLY', 'DAILY'
Tasks in Visual Studio Code
Tasks in VS Code can be configured to run scripts and start processes so that many of ... Any background/watch tasks used in dependsOn with "dependsOrder":