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Building Git Packages for R#

R packages can come in multiple formats:

  • Source: A collection of directories and files containing source code.
  • Bundle: A specially created tar file containing bundled source code. The result of R CMD build.
  • Binary: A binary file specific to an operating system and architecture, containing compiled source code. Not an executable. The result of R CMD INSTALL.

In some configurations, RStudio Package Manager will need to run R in order to transform a package from one state to another. RStudio Package Manager uses the RStudio Job Launcher to perform this task.

Job Launcher#

The RStudio Job Launcher is a service responsible for running jobs in support of RStudio Package Manager. The Job Launcher is automatically installed when RStudio Package Manager is installed. Settings for the Job Launcher can be configured directly in the RStudio Package Manager configuration file, /etc/rstudio-pm/rstudio-pm.gcfg. See the configuration section in the appendix.

RStudio Package Manager can only use its own instance of the Job Launcher and runs all tasks locally. Other RStudio products may have separate Job Launcher instances managed independently from RStudio Package Manager. The RStudio Package Manager's Job Launcher cannot be shared by other products, nor can RStudio Package Manager use a Job Launcher instance set up for another product.

Server log messages related to this component can be shown by enabling the launcher region. More information about activating log regions is in the configuration appendix.

R Configuration#

You can optionally specify the installation of R in the RStudio Package Manager configuration file:

; /etc/rstudio-pm/rstudio-pm.gcfg
[Server]
RVersion = /opt/R/4.0.5

Replace /opt/R/4.0.5 with the path to your R installation. Use the path to the R installation directory, not the path to the binary (do not include /bin/R). While multiple versions of R may be installed on the server, only one version of R may be specified for use by RStudio Package Manager.

Note

R must be configured in order for the Job Launcher to work correctly. For more information, refer to the Job Launcher section.

If the RVersion field is included, then it must be valid, and it must only appear once in the configuration file. Check the server log after starting and stopping the RSPM process for messages relevant to the R configuration.

R Installation#

RStudio recommends that in most cases you install R from pre-compiled binaries.

To install from pre-compiled binaries, follow the instructions at Install R.

Alternatively, you can install R from source, to do this follow the instructions at Install R from source.

Git Builders#

RStudio Package Manager defines a git-builder as an entity that watches a Git endpoint, whether it be remote (e.g., git@github.com:user/example.git) or local (e.g. file:///path/to/local/git/repo), for changes and builds R package bundles.

An administrator follows these steps:

  1. Create a git source.
  2. Create a git-builder for the source, specifying whether to watch for commits to a Git branch or tags in a Git repository. The endpoint can be: HTTP, SSH (see below), or a local file path (see below). See the create git-builder command for full details, e.g., how to track a specific branch.
  3. Based on the selection specified with the create git-builder command, RStudio Package Manager clones the Git endpoint and runs an R job to transform the Git clone into a package bundle. The package bundle is made available to any repositories subscribing to the source.
  4. RStudio Package Manager polls the Git endpoint to watch for either new commits or new tags (based on the selection specified with the create git-builder command). If an update is available, RStudio Package Manager automatically pulls the new changes and launches an R job. The R job creates a package bundle from the updated Git clone and updates the package available in the git source. Previous versions are archived.
  5. Users install the package from the repository via install.packages NOT devtools.

See the Getting Started section for a specific example.

Server log messages related to this component can be shown by enabling the git region. More information about activating log regions is in the configuration appendix.

Access Restricted Git Endpoints Using Git Credentials#

If Git builders require authentication to read a repository, RStudio Package Manager can use SSH keys or HTTPS credentials to authenticate against the endpoint.

Importing an SSH key#

Begin by creating an SSH key and granting the SSH key access to the Git endpoint. Although RStudio Package Manager allows the use of SSH keys with no passphrase, it is still recommended to use a strong SSH key with a passphrase. The specific steps for granting access will depend on your Git provider.

Once you have the path to the SSH key, use the import ssh-key command to name and securely store the SSH key for later use by RStudio Package Manager. If desired, you can now remove the SSH key file from your filesystem, as it is loaded into RSPM's database as encrypted text. Multiple keys can be imported, but they must have unique names to refer to. This is the --name argument you pass to the import ssh-key command, not the filename of the key.

Because the use of a password for the key requires writing the password to a file on disk, there is some risk of leaking the password while it is on disk. To mitigate this risk, you can encrypt the password using the encrypt command prior to writing it in a file. RSPM will understand passwords in the file as either plaintext or encrypted text, and will decrypt the password as necessary to unlock your SSH key.

To use the newly imported SSH key with a new Git builder, specify the key name with the --credential flag in the create git-builder command.

Importing an HTTPS credential#

HTTPS credentials consist of a username and password. In applications where two-factor authentication is used, you will often need a personal access token (PAT) that serves as the password. To import an HTTPS credential, use the rspm import https-credential command.

Note that using this command requires you to input the password/PAT on the command line, which may be stored in your command history. To avoid this possible credential leak, you may first encrypt your password using the rspm encrypt command, and pass this encrypted string to the rspm import https-credential command instead.

To use the newly imported credential with a new Git builder, specify the credential name with the --credential flag in the create git-builder command.

Git Credential Security#

RStudio Package Manager encrypts and stores imported credentials in the metadata database. Any person (by default, members of the rstudio-pm unix group) with access to the admin CLI can:

  • Associate an imported credential with a Git builder using the create git-builder command
  • List the names of available Git credentials using the list git-credentials command

Users cannot access the contents of the credential, nor is the credential available for arbitrary actions. We recommend granting SSH keys and HTTPS credentials imported to RStudio Package Manager limited read-only access to only the endpoints you wish to expose as R packages.

When imported, the credentials are encrypted at rest. During Git operations which require authentication, the credentials are added to an ssh-agent or set as environment variables and thus never written to the filesystem or written to STDIN.

Changing credentials for a git-builder#

Credentials may be rotated by creating a new credential and editing an existing git-builder:

Terminal

rspm import ssh-key --name=[key name] --path=[/path/to/key]
rspm edit git-builder --name=[git-builder name] --source=[git source] --new-credential=[key name]

If you would like to change the URL type of a git builder from https to git or vice-versa, ensure that you pass a credential that matches the new URL type.

rspm edit git-builder --name=[git-builder name] --source=[git source] --new-url=git@github.com:somebody/something --new-credential=[name of ssh key]

RSPM does not change credentials aside from manually specified commands. Therefore, when changing a URL without changing the credential, RSPM will continue using any prior credential. To remove the association of the credential with the git-builder, use the edit git-builder --remove-credential command:

rspm edit git-builder --name=[git-builder name] --source=[git source] --remove-credential

Access Git Endpoints on a Local File System#

If a Git repository is available locally, it is possible to point a Git builder to watch this location and update when changes are made on a branch or tag (based on the selection specified with the create git-builder command).

To do this, the Git.AllowFileURLs configuration option must first be set to true. Once the option is set, the following command can be used to create a Git builder pointed to a local Git repository:

Terminal

rspm create git-builder --source git --url file:///path/to/local/git/repo

Commits vs Tags#

A package based on a Git endpoint can can be configured to watch one of two types of changes: "commits" or "tags". In short, "commits" watches for changes to a specified Git branch, where "tags" watches for new tags in the whole Git repository. In more detail:

  1. Commits - RStudio Package Manager will update the package any time new commits are discovered in a branch. In this mode, RStudio Package Manager automatically modifies the package's version, assigning a unique version number to each build. The version number is created based on the commit time-stamp and is designed to avoid conflicts with the version scheme used by the package author. For example, if the Description file for a package indicates a version of 1.1-3, the automatic version number would be: 1.1-3.0.0.0.1537204599. If the author updates the package with a new commit, but keeps the version in the Description file the same, the new automatic version number would reflect the new commit time-stamp, e.g. 1.1-3.0.0.0.1537218677. This process ensures that users of the package always get the correct behavior from install.packages, with newer commits being associated with a semantically higher version number.

The above version behavior for "commits" triggers may be overridden by using the Git.ForceDescriptionVersion configuration option. This will force all packages built by commits in a branch to use the exact version in the DESCRIPTION file.

  1. Tags - RStudio Package Manager will update the package any time a new Git tag is discovered. In this mode, RStudio Package Manager retains the version specified in the package's Description file. This mode is designed to work when a Git tag is used to indicate a package release. Note: The name of the tag must match the version in the Description file. For example, if your package's Description file has Version: 5.4.2 your tag must be either 5.4.2 or v5.4.2. If two tags reference the same version, preference is given to the newer tag. If a newer tag references an older version than a prior tag, the new tag is built as an archived package. If a tag is removed from a Git endpoint, any packages already built for that tag remain.

Commit mode is recommended for bleeding edge repositories, whereas tag mode is suitable for exposing stable releases of packages.

A git source can support different packages with different modes. However, a given package can only have one mode in a source. If you would like to surface the same package in both commit and tag mode, you must create two git sources.

Git Directories#

By default, packages will be built from the git root directory. If the R package exists in a different location, it can be specified using the --sub-dir flag when adding a git package.

Managing Packages from Git#

The git-builder (described above) watches the Git endpoint for changes, automatically handling package updates and archives. There might be cases where you wish to remove packages, or to stop package building altogether.

Packages can be removed at any time using the remove command.

To stop automatic package building, but keep the existing packages, use the delete git-builder command. To resume package building, simply create a new git-builder with the same metadata.

Terminal

# To remove previously-built packages from git:
rspm remove --source=[name of source] --name=[name of package and scope]
# To stop automatic package building, but keep the packages:
rspm delete git-builder --name=[name of package] --source=[name of source]

To view information about the current Git endpoints that are being tracked, use:

Terminal

rspm list git-builders

Editing git-builders#

Git builders have a few fields which may be edited: credentials, URLs, sub directories, and branches (for "commits" triggers). The git-builders cannot be changed from SSH to HTTP URLs or vice versa.

Terminal

rspm edit git-builder --name=[git-builder name] --source=[git source name] --new-url=[HTTP/SSH URL]
rspm edit git-builder --name=[git-builder name] --source=[git source name] --new-credential=[credential name]
rspm edit git-builder --name=[git-builder name] --source=[git source name] --new-branch=[branch name]
rspm edit git-builder --name=[git-builder name] --source=[git source name] --new-sub-dir=[sub directory path]
rspm edit git-builder --name=[git-builder name] --source=[git source name] --remove-credential
rspm edit git-builder --name=[git-builder name] --source=[git source name] --remove-sub-dir

Combining Packages from Git with Other Package Sources#

Local packages cannot be added manually to a git source, but a repository can surface packages from a git source alongside local packages and CRAN packages by subscribing to multiple sources. Take care when managing a repository's subscriptions as order is important, see the Multiple Sources section.

Polling Frequency#

You can control how frequently RStudio Package Manager checks for updates using the Git.PollInterval configuration field. If multiple commits occur between checks, RStudio Package Manager will create a single version representing all of the changes. If multiple tags are created or removed between checks, RStudio Package Manager will build each tag individually, automatically archiving tags representing older versions of the package.

Repository Versioning is identical in all source types, including git sources.

Tracking Changes and Errors#

If a repository subscribes to a git source, you can view the git source's history in the Activity Log. The Activity Log will identify each change to a package including the new version, and a message will indicate the associated Git tag or commit as appropriate. If an error is encountered attempting to clone, poll, or bundle a package, the Activity Log will record the attempt and include a message with the CLI command to be run to view a full error log.

You can also use the following RSPM CLI commands to quickly check your active Git builders and view the logs:

Terminal

$ rspm list git-builders
<< Git Builders:
<< - [git package name]
<<     Source: [source name]
<<     URL: [source url]
<<     Trigger: [git package trigger]
<<     Key: none

Terminal

$ rspm list git-builds --source=[source name] --name=[git package name]
<< Git Builds:
<< - [git package name]
<<     Transaction ID: [transaction ID]
<<     SHA: [SHA]
<<     Tag: [tag]
<<     Status: [job status]
<<     Time: [time of run]
<< Only showing latest build, for more builds use the --count and --page flags
<< For more information run: rspm logs --transaction-id=[transaction ID]

Terminal

$ rspm logs --transaction-id=[transaction ID]
<< ...
<< [git package run logs]
<< ...

RStudio Package Manager automatically tries to build updates from a Git source three times. If the build fails more than three times, the update causing the failure is ignored. New updates are still discovered and built.

To retry a failed update, or to force a Git builder to rebuild the latest package version, use the rerun command:

Terminal

rspm rerun git-builder   \
  --name=[package name]  \
  --source=[source name] \
  --tag=[tag to rebuild, only required if the build trigger is tags]

To aid in debugging, it can help to view output from the git commands that are run as well as output from the SSH connection when applicable. To enable debugging, refer to the Debug.Log configuration property in the configuration appendix. To enable the debug log temporarily without restarting the server use the rspm config command:

Terminal

rspm config debug logger activate git

Process Management#

See Process Management for information on how RStudio Package Manager securely runs R processes when building R packages for git sources.