Language Extensions: Packages, Modules, et al.

Last Update: 2025-09-29

Vanilla R or plain Python would be pretty hard to use, yes? (And rather boring!) The Red Team is working to provide on-demand capabilities for researchers to download various language extentions from authoritative, external sources while simultaneously meeting security and compliance obligations.

Packages & Modules via Posit Package Manager

"Posit Package Manager (PPM) provides a secure, reliable, and scalable way to distribute and manage R and Python packages across an organization. Built-in vulnerability reporting and management bolsters your security and compliance efforts. Posit Package Manager can even provide an air-gapped source of CRAN, PyPI, and other packages for high-security environments."

PPM is available for both the RES and PC/OOD compute environments; and is configured for CRAN, PyPI, and BioConductor. PPM works by having an on-demand conduit to the external, authoritative public repositories, and responds to your request for a download. Like virus scanners on current desktops and laptops, PPM scans the download for malicious code, malware, and known vulnerabilities (as documented in the CVE (Common Vulnerabilities and Exposures) catalog); and will release the files to you only if cleen.

The following sections include notable and configuration information for your particular environments, IDEs, etc.

Python

This capability is available in both PC/OOD and RES. Configure pip, the Python installer, to contact our internal mirror to download Python modules and related files:

$ pip config set global.index-url https://mirrors.sanitization.red.rc.harvard.edu/pypi/latest/simple
$ pip config set global.trusted-host mirrors.sanitization.red.rc.harvard.edu

Continue as usual with subsequent pip install ... commands.

Note that, as a global setting, this will persist across sessions as this is stored in your home directory.

R

This capability is available in both PC/OOD and RES. Configure your R/RStudio environment to contact our internal mirror to download R packages and related files:

# For Linux sessions (RES or PC/OOD)
options(repos=c(CRAN="https://mirrors.sanitization.red.rc.harvard.edu/cran/__linux__/rhel9/latest", 
                  pRSPM="https://mirrors.sanitization.red.rc.harvard.edu/bioconductor-3.21/__linux__/rhel9/latest"
                 )
         )

# For WindowsOS sessions (esp. in RES)
Sys.setenv(R_LIBCURL_SSL_REVOKE_BEST_EFFORT=TRUE)
options(repos = c(CRAN = "https://mirrors.sanitization.red.rc.harvard.edu/cran/latest",
                  pRSPM="https://mirrors.sanitization.red.rc.harvard.edu/bioconductor-3.21/latest"
                 )
         )

Continue as usual with subsequent install.packages() commands.

Note that this command is ephemeral and works only for this session. If you wish this to persist across working sessions, create an ".Rprofile" file with this options command, and store it in the top level of your home directory.

BioConductor

BioConductor (BioC) is special as compared to R and CRAN, in that BioConductor releases are tied to particular versions of R, and installs are traditionally handled through the BiocManager::install() command. With BioConductor and PPM in ReD, we have chosen initially to funnel all BioC install requests through install.packages() , with later plans to deploy a BioConductor-style mirror. Given that we provide multiple versions of R, we will be mirroring mutliple BioC versions as well. From BioC's website on release versions, the compatiblity maps as:

To install BioConductor packages, issue the options command listed above as for using R, substituting in the appropriate BioC version in the pRSPM mirror URL. Then continue as usual with BioC installs by using the install.packages() command. We strongly recommend that you do not use the BiocManager::install() function.

Visual Studio Code Extensions

VSCode extensions are available for both RES and PC/OOD for Python and Jupypter. To install: 1. Run VSCode.

1. Select the Extensions icon in the left navigation pane, usually the bottom icon that looks like a stack of squares.
2. At the top of the column that lists installed and recommended extensions, select the Options pop-up elipsis (three horizontal dots, "...").
3. From the pop-up menu, select "Install from VSIX..."
4. In the path navigator, enter :
5. For LinuxOS, use the path /shared/software/central-installation/code_extensions/
6. For WinOS, use the path Net use P: \\10.7.34.49\res-urc-software-pgks\vscode_extensions. ('pgks' and not 'pkgs'. Sorry!)

1. Select each VSIX file for installation or (if possible) all the files at once. Some extensions may take up to 30 seconds to fully install and load.

Stata Plugins

Update 4/8/25: This is still under consideration. Please contact the ReD Team if your requirements include particular Stata plugins.