12 Process Management
RStudio Connect launches R to perform a variety of tasks. This includes:
- Installation of R packages
- Rendering of R Markdown documents
- Running Shiny Applications
- Running a Shiny application to customize a parameterized R Markdown document.
- Running APIs using Plumber (Beta)
The location of R defaults to whatever is in the path. Customize the
Server.RVersion setting to use a specific R installation. See Chapter ?? for details.
The RStudio Connect process runs as the
root user. It needs escalated privileges to allow binding to protected ports and to create “unshare” environments that contain the R processes.
RStudio Connect runs its R processes as an unprivileged user; both a system default and content-specific overrides are supported. See Section 12.3 for details.
The “unshare” environment created for R execution involves first establishing a number of bind mounts and then switching to the target unprivileged user. RStudio Connect uses
unshare to alter the execution context available to R processes. Within this newly established environment, a number of
mount calls are made in order to hide or isolate parts of the filesystem.
The following locations are masked during R execution:
Server.DataDirdirectory containing all variable data used by RStudio Connect.
SQLite.Dirdirectory, which can optionally be placed outside the data directory.
- Configuration directories, including
The following information is exposed during R execution:
packratdata directory (read-only except when installing packages).
Rdata directory (only when installing packages).
- The directory containing the unpackaged R code (Shiny, Plumber, and R Markdown).
- The document rendering destination directory (only for R Markdown).
- A per-process temporary directory (exposed over the original
Applications.HomeMounting is enabled, the contents of
/home are masked by an additional bind mount as follows:
- The contents of
/homeare masked by the home directory of the
- If the
RunAsdoes not have a home directory, an empty directory masks
The path to the home directory is always available through the
HOME environment variable. With
Applications.HomeMounting, the mounted path to the
HOME directory is subject to change. Avoid hard-coding paths to either
Running R applications, like Shiny apps and Plumber APIs, have write access to the directory containing the unpackaged R code. This application directory is the working directory when launching an application. Data written here will be visible to all processes associated with that application but are not visible to other R processes. Application directory data remains available until that application is next deployed to RStudio Connect. A deployment creates a new application directory containing only the deployed content.
RStudio Connect may launch multiple processes to service requests for an application. There is no coordination between these processes. Applications that write to local files could experience problems when different processes attempt to write to a single file.
For example, two different processes writing to the same file may see output incorrectly interleaved or even overwritten.
We do not recommend using the file system for data persistence.
R Markdown documents have write access to the rendering destination directory and read access to a directory containing the unpackaged R code. The source directory is the working directory when calling
rmarkdown::render. The destination directory is passed as the
output_dir while a temporary directory is passed as the
intermediates_dir. The intermediate directory is transient and not available after rendering completes. A new output directory is created whenever the document is rendered. Data created during one rendering is not visible to another.
R Markdown multi-document sites have a slightly different rendering pipeline than standalone documents. RStudio Connect uses the
rmarkdown::render_site function, which does its rendering in-place. The content from the source directory is copied into the rendering destination directory in preparation for rendering. Site rendering has write access to the destination directory. Access to the original source directory is not provided because the source content is duplicated in the destination directory
rmarkdown::render_site call usually places its output into a subdirectory (typically, ’_site’). The contents of this output subdirectory will be moved to the root of the rendering destination directory, replacing any other content. No post-rendering file movement occurs if
rmarkdown::render_site is instructed to render into the current directory instead of a subdirectory. This means that both source and output files will be available for serving.
We recommend against configuring
rmarkdown::render_siteto write its output into the current directory. Rendering the site into a subdirectory (the default) allows RStudio Connect to remove source from the output directory.
RStudio Connect serves rendered content from the document output directory. This content remains available until a subsequent rendering is successful and activated (if requested). Neither incomplete nor unsuccessful document renderings affect the availability of previously rendered content.
12.2 Shiny Applications & Plumber APIs
Note: Plumber APIs are currently in Beta.
Most of the R processes started by RStudio Connect are batch-oriented tasks. R is invoked, does a narrow set of work, and then exits. Shiny applications and Plumber APIs are different and may see an R process handle many requests for many users over their lifetimes. Both Shiny Applications and Plumber APIs are live applications that react to user requests on-demand.
RStudio Connect launches an R process tied to a live application when the first request arrives for that application. That R process will continue to service requests until it becomes idle and eventually terminated. If there is sufficient traffic against that application, RStudio Connect may launch additional processes to service those requests.
There are a number of configuration parameters which control the conditions under which processes for applications are launched and eventually reaped. The default values are appropriate for most applications but occasionally need customization in specialized environments. Section A.16 explains each of the options.
We recommend that adjustment to these runtime properties be done gradually.
12.3 User Account for R Processes
The RStudio Connect installation creates a local
rstudio-connect user account. This account runs all the R processes;
root does not invoke R. If you would like a different user to run R, customize the
Administrators can customize the
RunAs user on a content-specific level. This means that different applications and R Markdown reports can be run using different Unix accounts. This setting can be found on the Access tab when editing content settings. Publishers and Viewers are prohibited from changing the
RunAs user on a content-specific level.
If you choose to specify a custom
RunAs user for content, that user must be a member of the Unix group that is the primary group of the
rstudio-connectuser, for example, has a primary group also named
rstudio-connect. Any Unix account configured as a custom
RunAsuser for a Shiny application, Plumber API, or R Markdown report must be a member of the
Installation of R packages always happens as the
Application.RunAs user. An application or R Markdown report may override its
RunAs setting; this alters how the deployed code is executed and does not impact package installation. See Section 12.1 for more information about process sandboxing.
12.4 Current user execution
RStudio Connect can use a local Unix account associated with the currently logged-in user when executing Shiny applications or Shiny documents. This feature requires that user authentication use PAM.
See Section 10.6 for information about using PAM for user authentication.
Applications.RunAsCurrentUser property specifies that content can be configured to execute as the currently logged-in user.
[Applications] RunAsCurrentUser = true
Administrators can now customize the
RunAs settings to permit current-user execution on a content-specific level. The Access content setting tab offers the option of executing using “The Unix account of the current user”.
Content accessed anonymously will execute as the specified fallback
See Section 12.3 for more information about
Content execution settings are not altered when
RunAsCurrentUser is enabled. The
RunAsCurrentUser setting permits current-user execution but by itself does not change how R processes are launched. Each application or R Markdown report must explicitly request current-user execution.
All Unix accounts used to execute R must be members of the Unix group that is the primary group of the
Applications.RunAs user. Applications are not permitted to launch if the Unix account associated with the logged-in user does not have the proper group membership.
Applications.RunAssetting uses the
rstudio-connectuser by default. This user has a primary group also named
rstudio-connect. Any Unix account that may be used to execute applications or R Markdown reports must be a member of the
12.5 PAM sessions
Note: Please see the special instructions at the bottom of this section for running RStudio Connect on Ubuntu 14.04 (Trusty Tahr)
RStudio Connect can use PAM to establish the environment and resources available for R sessions.
See Section 10.6 for information about using PAM for user authentication.
PAM sessions are enabled with the
[PAM] UseSession = true
The default PAM service name used for PAM sessions is
su. This gives RStudio Connect the ability to launch processes as the specified user without requiring a password.
You can customize the PAM service name used for PAM sessions by customizing the
[PAM] SessionService = rstudio-connect-session
SessionService must contain the PAM directive that enables authentication with root privileges. Otherwise, basic R processes will not run, and will return error code 70.
# Allows root to su without passwords (required) auth sufficient pam_rootok.so
Ubuntu 14.04 (Trusty Tahr) uses
upstart as init by default, but also uses
systemd-logind to clean up processes from closed user sessions. There is a known issue where
PAM.UseSession causes this specific host configuration to rapidly terminate R processes, returning
error code 129.
If you enable
PAM.UseSession, you also need to edit the
upstart configuration file at
/etc/init/rstudio-connect.conf, replacing the line beginning
exec /opt/rstudio-connect/bin/connect with the following:
exec su -s /bin/sh -c 'exec "$0" "$@"' root -- /opt/rstudio-connect/bin/connect \ --config=/etc/rstudio-connect/rstudio-connect.gcfg >> /var/log/rstudio-connect.log 2>&1
This has considerable side effects because it is the equivalent of opening a
su session for root and leaving it open for the life cycle of the RStudio Connect daemon.
If this solution is unacceptable, alternative solutions may include:
- Upgrading the host to Ubuntu 16 or later
systemd-logindto be newer than v204
- Altering the init provider to use
systemd-logindon the host
12.5.1 PAM Credential Caching (Kerberos)
Note: RStudio Connect’s PAM cache is encrypted and is not stored on disk. The credentials must expire after a certain period of time.
RStudio Connect can be configured to securely cache a user’s PAM credentials when they log in to RStudio Connect. This enables RStudio Connect to let users run R processes as their current UNIX account when the PAM profile requires a user’s credentials, such as when using Kerberos.
The following config settings are required for credential caching to be enabled:
[Applications] RunAsCurrentUser = true [PAM] UseSession = true ; Enable PAM sessions ForwardPassword = true ; Forward the current user's password into the PAM session PasswordLifetime = 12h ; Cache passwords for 12 hours after login AuthenticatedSessionService = authenticated-service ; PAM service that accepts credentials
12h with the amount of time you would like credentials to be cached. Credential lifetime is counted from the moment the user logs into RStudio Connect. It is not tied to the user’s web session, except that logging in again will restart the timer for that user’s credentials.
AuthenticatedSessionService setting is similar to
SessionService, except that it should accept user credentials and validate them. For example, a PAM service that uses the host’s Kerberos configuration to expose functionality could be:
auth required pam_krb5.so account [default=bad success=ok user_unknown=ignore] pam_krb5.so password sufficient pam_krb5.so use_authtok session requisite pam_krb5.so
12.6 Path Rewriting
The sandboxing used by RStudio Connect involves bind mounts which map physical locations on disk onto different directory structures at runtime. Paths used by your R code use these sandboxed locations. If you need to find the physical file on disk, you will need to undo the path transformation.
This section gives some examples of path rewriting and offer some ways of finding the file you need.
Let’s start with an
app.R file that describes a Shiny application. This file will be in the
apps/XX/YY/ directory underneath the
Server.DataDir location. The
YY path components correspond to the application ID and bundle (or deployment) ID for this version of your application. This directory is available at runtime as
The directory structure of
/opt/rstudio-connect/mnt/ is just a number of empty directories. The “unshare” environment created during sandboxing allows RStudio Connect to associate different application directories with these mount directories.
Here are some common path transformations that may be helpful. All of the physical paths are beneath the
Server.DataDir hierarchy that defaults to
/var/lib/rstudio-connect. All of the sandbox paths are beneath the mount directory
/opt/rstudio-connect/mnt/. This location is not customizable.
|Physical path||Sandbox path|
Here are some actual path transformations using the default
# A source Shiny application /var/lib/rstudio-connect/apps/4/7/app.R => /opt/rstudio-connect/mnt/app/app.R # A source Plumber API /var/lib/rstudio-connect/apps/38/10/plumber.R => /opt/rstudio-connect/mnt/app/plumber.R # A source R Markdown document /var/lib/rstudio-connect/apps/8/12/index.Rmd => /opt/rstudio-connect/mnt/app/index.Rmd # An HTML document rendered from that R Markdown document /var/lib/rstudio-connect/reports/8.2/index.html => /opt/rstudio-connect/mnt/report/index.html # A staticly deployed document /var/lib/rstudio-connect/apps/17/21/index.html => /opt/rstudio-connect/mnt/app/index.html # The Shiny package inside the packrat cache /var/lib/rstudio-connect/packrat/3.2.5/v2/library/shiny/ 28d6903a44dc53bd4823fa43ccdc08e5/shiny => /opt/rstudio-connect/mnt/packrat/3.2.5/v2/library/shiny/ 28d6903a44dc53bd4823fa43ccdc08e5/shiny
12.7 Program Supervisors
You may need to modify the environment or resources available to R processes prior to R being launched. This can be accomplished using a program supervisor using the
Applications.Supervisor configuration setting.
The supervisor command is provided the full R command-line, which MUST be invoked by the supervisor. The process exit code from R MUST be returned as the exit code of the supervisor. The file descriptors for standard input, output, and error MUST NOT be intercepted by the supervisor.
A supervisor is executed as the appropriate
RunAs user. Package installation always uses the
Applications.RunAs user. Other R processes will use the content-specific
RunAs account, falling back to
Applications.RunAs if no override was configured. See Section 12.3 for details.
Supervisors run within the sandbox established for any R process. See Section 12.1 for more information about process sandboxes.
RStudio Connect configures the
RSTUDIO_PANDOC environment variables for launched R processes. RStudio Connect also manages package installation and references. Avoid altering any of this behavior in program supervisors.
12.7.1 Example Supervisors
Here is a configuration that uses the
nice command to lower the priority of all R processes. See http://linux.die.net/man/1/nice for details about
nice. Because process supervisors are run as a
RunAs user and not as
root or another super-user, you may not be permitted to assign a negative (higher priority) privilege.
[Applications] Supervisor = nice -n 2
Here is a configuration that uses a custom script to prepare a custom execution environment before finally running R.
[Applications] Supervisor = /some/script/that/prepares/an/environment.sh
Here is an example supervisor that echos its arguments, sets an environment variable, then invokes whatever arguments have been passed.
#!/bin/bash echo arguments: "$@" echo export COMPANY_DATA_HOME="/data/resides/here" exec "$@"
Your organization may use shell initialization scripts to establish a particular environment. This environment might not be completely compatible with how RStudio Connect attempts to launch R.
We recommend building supervisor scripts gradually and carefully. Changes to the environment can alter how your content executes or even prevent R from running correctly.
12.8 Using the
config package makes it easy to manage environment specific configuration values in R code. For example, you might want to use one value for a variable locally, and another value when deployed on RStudio Connect. The package vignette contains more information.
The desired configuration is identified to the
config package by the
R_CONFIG_ACTIVE environment variable. By default, R processes launched by RStudio Connect set
rsconnect. The value can be changed by modifying the
Applications.RConfigActive configuration setting. Note that the value of
R_CONFIG_ACTIVE is not available during package installation.