Skip to contents

FAQ and troubleshooting

Source: vignettes/faq.Rmd
faq.Rmd

This vignette collects answers to common questions that come up when using sysreqr or, more generally, when installing R packages from source on GNU/Linux.

My install failed but sysreqr reports nothing missing

Not every install failure is caused by a missing system library. Other causes:

  • R version too old. Some CRAN packages require recent R. Run R.version.string.
  • Package source too old. A pinned older package version may need a library you no longer have at that version. Try a newer package version.
  • Disk full or read-only library path. Check with df -h and .libPaths().
  • Network failure mid-download. Re-run.
  • Locked package. A 00LOCK-<name> directory in your library path from a previous failed install. Remove it.

When in doubt, run setup_advice() to confirm the broader checklist, then ask for help with the specific log.

I’m on a server without sudo. What now?

Use admin_request() to draft a message you can send to your administrator:

plan <- check_packages(c("xml2", "curl"), platform = "ubuntu-22.04")
cat(admin_request(plan))

The message lists the missing system packages, which R packages need them, and the exact install command. Many administrators appreciate having all of that in one place.

How does sysreqr differ from pak, remotes, and renv?

Tool Strengths Limitations
pak::pkg_sysreqs() Authoritative live resolver Requires pak; no log diagnosis
remotes::system_requirements() Light; widely available No log diagnosis, no project scanner
renv::sysreqs() Project-oriented; integrates with renv workflow Requires renv
sysreqr Zero runtime deps; log diagnosis; beginner UX Bundled DB is small; biased to apt

sysreqr can use pak as one of its backends (backend = "pak") when it is installed. The two tools are complementary, not competitors.

I’m in Docker and platform detection seems wrong

When you run detect_platform() outside a container, R sees the host operating system. When you run it inside a container, R sees the container operating system. If you are generating a Dockerfile from your laptop for a different base image, always specify the platform argument explicitly:

dockerfile(check_packages("xml2", platform = "ubuntu-22.04"))

See the Docker vignette for more detail.

How do I keep the bundled database current?

The bundled database is refreshed with each package release. There is no runtime “update” function, because CRAN policy forbids packages from writing to their installed location.

If you need newer data than the latest release, use backend = "ppm" for live Posit Package Manager data, or backend = "pak" for live pak resolution.

Why is sysreqr suggesting r-base-dev?

r-base-dev is the Debian/Ubuntu package that contains the development headers and Makefile fragments needed to compile R packages from source. You only need it if you build R packages from source (which is the default on Linux). setup_advice() includes it in the build-tools step.

On Fedora/RHEL, the equivalent comes with the R package itself. On openSUSE, the equivalent is R-base.

I’m on Alpine. What’s supported?

Alpine uses apk and is detected as alpine. Install commands use apk add --no-cache. The bundled fallback database currently uses Debian/Ubuntu names, so prefer the ppm or pak backend on Alpine. Many common system libraries on Alpine are in the community repository.

I’m behind a corporate proxy. PPM queries fail

Posit Package Manager queries use utils::download.file(). Set the standard http_proxy and https_proxy environment variables before starting R, or configure them in your .Renviron.

If outbound HTTP is blocked entirely, use backend = "bundled" or backend = "pak" (pak has its own download tooling and may already be configured for your network).

What do the confidence levels mean?

  • high: direct evidence: a missing-header or linker error pattern was matched in the log, or live upstream metadata reported the requirement.
  • medium: indirect evidence: a tool failure (such as pkg-config not found) or a failed-package lookup against the bundled fallback database.
  • low: reserved for future, broader heuristics.

A medium-confidence result is still useful, but it is not proof. R version mismatches, locked libraries, and permission problems can all cause failed installs unrelated to system requirements.

sysreqr says the platform is unsupported but I want to try anyway

Use the platform argument with an explicit platform string. If you supply backend = "ppm", the package will ask Posit Package Manager which is authoritative.

If you are experimenting with an unknown platform, please open an issue at https://github.com/choxos/sysreqR/issues with the contents of /etc/os-release so support can be added properly.

Why does this package use a custom JSON parser?

A small custom parser keeps the package free of runtime dependencies, in line with its design goal. jsonlite would also work, but it would add a dependency that the rest of the package does not need. The parser is exercised by the test suite and handles unicode escapes, nested arrays, and the JSON dialect used by Posit Package Manager and renv.lock.

See also