Open Systems Pharmacology R-universe

This repository is the R-universe registry for the Open Systems Pharmacology R packages. It is not an R package itself; its only job is to hold packages.json, the list of package repositories that R-universe builds and publishes to https://open-systems-pharmacology.r-universe.dev

Why R-universe

The OSP R packages (rSharp, ospsuite, and the rest) embed pre-compiled binaries in inst/lib (the .NET assemblies and the computational core). CRAN forbids binaries in source packages, so these packages cannot be submitted to CRAN as-is. R-universe has no such restriction and no package-size limit: it builds and hosts the packages with their binary payloads intact, and it resolves the cross-package dependency chain (rSharp -> ospsuite.utils -> tlf -> ospsuite) automatically.

R-universe distributes the packages. It does not install the external .NET runtime; that remains a prerequisite on the user's machine, and on the R-universe build environment (see the caveat below).

Availability does not require passing R CMD check

A package is published and installable from this universe as soon as its source tarball builds (R CMD build succeeds). Passing R CMD check is not required. R-universe is a publishing system, not a gatekeeper: it records each platform's check result (the OK / NOTE / WARNING / ERROR badges on the dashboard) for information, but a red check does not stop the binary from being built, stored, and served.

This matters for the OSP packages because the R-universe build runners have no .NET runtime (and their Linux image ships a libxml2 whose soname differs from the one the bundled native libraries were linked against). As a result:

• The per-platform R CMD check jobs will typically show ERROR (tests, examples, and vignettes that call into .NET cannot run without the runtime). That is expected and does not block publishing.
• What must succeed is R CMD build: the package has to install and load far enough to produce a tarball. For that, its .onLoad() must not fail when the runtime is absent. rSharp and ospsuite degrade gracefully in that case (they load, record why the runtime is unavailable, and raise an actionable error only when a .NET call is actually made), so their tarballs build and they are published.

In short: build green, check red, still installable. A package only becomes unavailable if its R CMD build fails outright, or if one of its declared dependencies is not resolvable in the universe at a compatible version.

Installing from this universe

Once the universe is live, users install with plain install.packages():

install.packages(
  "ospsuite",
  repos = c(
    OSP = "https://open-systems-pharmacology.r-universe.dev",
    CRAN = "https://cloud.r-project.org"
  )
)

pak works too, once the repository is configured:

pak::repo_add(OSP = "https://open-systems-pharmacology.r-universe.dev")
pak::pak("ospsuite")

What gets built

packages.json lists the OSP R packages that publish GitHub releases. Each entry tracks the package's latest release ("branch": "*release").

Package	Source repository
rSharp	Open-Systems-Pharmacology/rSharp
ospsuite.utils	Open-Systems-Pharmacology/OSPSuite.RUtils
tlf	Open-Systems-Pharmacology/TLF-Library
ospsuite	Open-Systems-Pharmacology/OSPSuite-R
ospsuite.plots	Open-Systems-Pharmacology/OSPSuite.Plots
ospsuite.reportingengine	Open-Systems-Pharmacology/OSPSuite.ReportingEngine
ospsuite.parameteridentification	Open-Systems-Pharmacology/OSPSuite.ParameterIdentification
ospsuite.globalsensitivity	Open-Systems-Pharmacology/OSPSuite.GlobalSensitivity
ospsuite.reportingframework	Open-Systems-Pharmacology/OSPSuite.ReportingFramework

Some OSP R packages were left out for now because they do not publish GitHub releases, so they cannot be tracked with *release: ospsuite.addins, ospsuite.qualificationplaneditor, and ospsuite.VBEToolbox. Give a package a release, then add it here.

Maintaining the list

• Add a package: append an object with its package name (the Package: field from the repository's DESCRIPTION) and its url. If the package does not cut GitHub releases, drop the "branch" field so R-universe builds its default branch instead of *release. If the app is installed with "only select repositories" scope, also grant it access to the new package repository.
• Remove a package: delete its object.
• Change what is tracked: edit or remove the "branch" field on that package's entry.

Every push to this repository triggers R-universe to re-read packages.json and reconcile what it builds. packages.json is validated as strict JSON; keep it well-formed (no comments, no trailing commas).