Basilisk recently switched to a conda-less approach to setting up Python environments, see discussion in:
- https://github.com/LTLA/basilisk/pull/49, you should have been mentioned in the list of affected packages - https://github.com/LTLA/basilisk/pull/52, which provides some guidance on conda-only packages - https://github.com/LTLA/basilisk/issues/48, for an overview of the motivation - https://github.com/LTLA/basilisk/issues/20, for a typical GLIBCXX error As mentioned in #52, if your required Python dependencies are only present in conda (igblast seems to be the main culprit), you can use the repurposed basilisk.utils package to auto-provision a conda environment for you. That said: whether this conda environment can be used successfully with reticulate is another matter. It seems that, with the passage of time, the conda binaries will increasingly depend on more recent versions of system libraries. This will result in a greater rate of linker failures when attempting to use reticulate to load the associated Python packages into an R session linked against older versions of those libraries. It's probably safest to just run the conda tools via system2, like what some packages do for Python 2 environments (which aren't even supported by reticulate anymore). -A On Wed, Jun 11, 2025 at 2:48 AM Rodrigo Arcoverde Cerveira < rodrigo.arcove...@gmail.com> wrote: > Hi basilisk team, > > First, thank you for your continued work on basilisk and for the fixes and > improvements in recent versions. Also thanks to Vincent for the helpful > replies to my previous questions. > > I’ve recently run into an issue where basilisk seems to fall back to using > pip (via reticulate:::pip_install(python, packages)) instead of setting up > the environment with conda, even when all packages are available via conda. > This is happening in packages like scifer, MOFA2, and pirat, which > previously built fine. Now, builds fail with errors when trying to install > packages that are supposed to install via conda but fall on pip. > > The basilisk environment definitions still specify conda packages and > channels (bioconda, conda-forge), and nothing has changed there. Has > something changed in how basilisk sets up environments or handles fallbacks? > > Would appreciate any guidance on how to make sure conda is used as expecte > > > Best, > Rodrigo > > -- > Rodrigo Arcoverde Cerveira > PhD student in Karolinska Institutet, Sweden > Karin Loré’s research group > CMM L8:00, Visionsgatan 18 > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
