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Troubleshooting

Source: vignettes/articles/troubleshooting.qmd

Start with:

rpix::pixi_sitrep()

It checks the project’s setup, and suggests fixes for what’s wrong.

R crashes when loading a package

A crash (“segfault”, “R is aborting now”) while loading a package usually means it was built for a different R than the one loading it. Check which R you’re in, and where its packages come from:

R.home() should be inside the project’s .pixi/envs/ folder, and .libPaths() shouldn’t list any library outside it. If it does:

  • You’re in your usual R, not the environment’s. Open the project in an IDE set up with use_pixi(ide = ), or in RStudio run rpix::pixi_switch(); see Using rpix with an IDE. From a terminal, pixi run R.
  • Your personal library is listed. Keep it out of the environment; see How rpix works.
  • The project’s .Rprofile changes .libPaths(). rpix 0.3.0 and earlier added a block starting with # Pixi R library setup. use_pixi() removes it; for one in ~/.Rprofile, remove it by hand.

A package fails to load on Windows

The specified procedure could not be found, when R loads a compiled package such as dplyr, means Windows found a DLL the package needs, but an older copy, without a function it uses. Within an environment, that happens when two packages install the same file, and the older copy wins: conda-forge’s Strawberry Perl puts its own MinGW runtime (libstdc++-6.dll and others) over conda-forge’s (conda-forge/perl-feedstock#89). freetds, and so pymssql, bring perl into an environment on Windows.

pixi_sitrep() lists files that more than one package in an environment installs, and says when it’s Strawberry Perl’s runtime. To see what brings perl in:

rpix::pixi_tree("perl", invert = TRUE)

Then drop that package, or move it to an environment without R (see Several environments).

RStudio uses the wrong R

RStudio picks its R when it starts, so it has to be started from the project’s environment, as a new RStudio: set the project up with use_pixi_rstudio(), then run rpix::pixi_switch() in RStudio, which starts one (or pixi run rstudio in a terminal). See Using rpix with an IDE.

R doesn’t start in VS Code on Windows

On Windows, the environment’s R only starts when the environment is activated. Start VS Code from the project’s environment, with pixi run code .; for VSCodium, Cursor or Windsurf, pixi run codium ., pixi run cursor . or pixi run windsurf .. See Using rpix with an IDE.

A package can’t be found 

! Some packages couldn't be found.

The package may need a bioc:: or conda:: prefix, or it isn’t on conda-forge. See Finding packages.

rpix can’t find Pixi 

! Could not find Pixi.

rpix looks for Pixi on the PATH, and then where the installer puts it, ~/.pixi/bin. If you installed it somewhere else, tell rpix where:

options(rpix.pixi_path = "/path/to/pixi")

rpix can’t find the project 

! Could not find a Pixi project.

rpix looks for pixi.toml in the working directory and the folders above it. Change the working directory to your project, or set it up with use_pixi().

Still stuck?

Ask in GitHub Discussions, or open an issue.