Source Type Details#

The CRAN Source#

A primary use case for Package Manager is making packages in public repositories, like CRAN, available to its users. Administrators can elect to make all of CRAN available, or to make only curated subsets of CRAN available.

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

Bioconductor Sources#

Similar to CRAN, Package Manager makes packages from Bioconductor available to its users. The Bioconductor repository type includes one or more Bioconductor versions. Each of these CRAN-compatible versions is composed of component repos, including bioc, data/annotation, data/experiment, workflows, and books. There are two ways to work with Bioconductor packages:

• Using standard R commands to install packages. You'll avoid the Bioconductor repository type for this, and use the Bioconductor source instead.
• Using the BiocManager package. You'll use the Bioconductor repository type for this.

With either approach, administrators can make all of Bioconductor available, or limit Bioconductor availability to specific Bioconductor versions. Package Manager supports Bioconductor versions 3.1 (for R 3.2) and greater.

Using Bioconductor sources in CRAN-like repositories#

graph TD
    A(CRAN-like Repository) --> B(cran)
        B --> L(A3)
        B --> |Packages|M(shiny)
        B --> N(covr)
    A --> |Sources|C(bioconductor 3.13)
      C --> D(data/annotation)
      C --> |Internal sources|E(data/experiment)
        E --> F(airway)
        E --> |Packages|G(scRNAseq)
        E --> H(fission)
      C --> I(workflows)
    A --> J(git)
      J --> |Packages|O(git-built package)
    A --> K(local)
      K --> |Packages|P(uploaded package)

When you want to use install.packages in your R scripts (as opposed to something like BiocManager) and/or associate a particular Bioconductor version with another collection of R packages, such as CRAN or a local or Git package source, you'll want to use the Bioconductor source instead of a Bioconductor repository. To accomplish this, we'll first create a CRAN-like repository. This repository can only subscribe to a specific version of Bioconductor (as opposed to the Bioconductor repository). Please see the quickstart guide for a more detailed walk-through of how to create this kind of repository.

Using the Bioconductor repository with BiocManager#

graph TD
    A(Bioc Repository) --> B(bioconductor 3.17)
      A --> |Sources|C(bioconductor 3.18)
        C --> D(data/annotation)
        C --> |Internal sources|E(data/experiment)
          E --> F(airway)
          E --> |Packages|G(scRNAseq)
          E --> H(fission)
        C --> I(workflows)
      A --> J(bioconductor 3.19)

The Bioconductor repository type is composed of one or more Bioconductor versions. Unlike CRAN repositories, where you must subscribe sources, the Bioconductor repository type manages its sources itself. The sources in this repository are the Bioconductor versions that are available to BiocManager. After creating the repository and syncing it, the Bioconductor repository will be populated with all enabled Bioconductor versions:

$ rspm create repo --name bioconductor --type bioconductor
$ rspm sync --type bioconductor

There are further instructions and examples in the quickstart guide.

Advanced users wishing to limit the availability of particular Bioconductor versions should refer to the Bioconductor.EnabledVersions setting in the configuration appendix.

The PyPI Source#

Another popular use case for Package Manager is making PyPI packages in public repositories available to its users. Administrators can make all of PyPI available by following the instructions in the Python section.

Curated CRAN Sources#

Enhanced Advanced

A Curated CRAN source exposes an approved set of CRAN packages defined by a requirements.txt file. For an example, see the Serving Curated CRAN Subsets section. For more information, refer to the Curated CRAN Sources section.

CRAN Snapshot Sources#

Enhanced Advanced

CRAN Snapshot sources allow administrators to create full CRAN sources that are pinned to a specific CRAN snapshot. Administrators can periodically update the snapshot to which the source is pinned. For example:

• If your organization has previously used MRAN (Microsoft's CRAN mirror service that provides daily CRAN snapshots) snapshots, you can easily onboard to Package Manager by replicating those snapshot dates.
• If your organization has historically installed packages all at once into a system library, for instance when new R versions are provisioned, you can use a CRAN snapshot to easily achieve the same effect.
• If your organization wants to lag behind CRAN, use a CRAN Snapshot source and regularly update the source to a CRAN snapshot that trails the current CRAN release.

Curated PyPI Sources#

Enhanced Advanced

A Curated PyPI source exposes an approved set of PyPI packages defined by a requirements.txt file. For an example, refer to Serving Curated PyPI Subsets. For more information, refer to Curated PyPI Sources.

Git Sources#

Advanced

Git sources allow Package Manager to automatically expose packages tracked in Git. Git sources work with internal packages as well as external sites such as GitHub. Please see the Building Git Packages section for more information on how to use Package Manager to provide packages that are tracked in Git.

R Git sources can be supplemented with precompiled binary packages. See Adding Local and Git Binaries for more information.

Local R Sources#

Local sources allow you to expose internal R packages that are already built. For an example, refer to Distributing Local R Packages.

Local sources can be supplemented with precompiled binary packages. See Adding Local and Git Binaries for more information.

Local Python Sources#

Local Python sources allow you to expose internally-built Python packages. For an example, refer to Distributing Local Python Packages. For more information, refer to Local Python Packages.