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@Flamefire Flamefire commented Aug 29, 2025

(created using eb --new-pr)

When installing R-bundle-CRAN-2023.12-foss-2023a.eb the extension R.cache attempts to write to the user home (~/.cache/R folder)

This is due to rappdirs using those defaults for R_USER_DATA_DIR, R_USER_CACHE_DIR and R_USER_CONFIG_DIR env vars

Prior rappdirs versions used the XDG variables like $XDG_CACHE_HOME. Those are still used as fallbacks but setting all 6 avoids interference with user environments

I also did a small refactoring:

  • make_R_install_option had a manual str.join() implementation
  • removed some redundant checks
  • removed call to inexistent handle_installation_errors

Note that we should also remove the unused async_cmd_check, see also easybuilders/easybuild-docs#343

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Test report by @Flamefire

Overview of tested easyconfigs (in order)

  • SUCCESS SciPy-bundle-2023.07-gfbf-2023a.eb
  • SUCCESS xtensor-0.24.7-foss-2023a.eb
  • SUCCESS Perl-bundle-CPAN-5.38.0-GCCcore-13.2.0.eb
  • SUCCESS LLVM-20.1.5-GCCcore-13.3.0.eb
  • SUCCESS pyiron-0.5.1-foss-2023a.eb
  • SUCCESS MOKIT-1.2.6-gfbf-2023a.eb
  • SUCCESS XML-LibXML-2.0210-GCCcore-13.2.0.eb
  • SUCCESS R-bundle-CRAN-2023.12-foss-2023a.eb
  • SUCCESS arrow-R-14.0.1-foss-2023a-R-4.3.2.eb
  • SUCCESS R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb
  • SUCCESS Seurat-5.1.0-foss-2023a-R-4.3.2.eb

Build succeeded for 11 out of 11 (8 easyconfigs in total)
n1227 - Linux RHEL 8.9 (Ootpa), x86_64, Intel(R) Xeon(R) Platinum 8470 (sapphirerapids), Python 3.9.18
See https://gist.github.com/Flamefire/247685f27d2def48543a33b51f603a70 for a full test report.

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removed call to inexistent handle_installation_errors

@boegel See question at #2408 (comment) on what this was supposed to do

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