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build: make pixi run setup work on a cluster node - #45
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pak compiled R packages from source and failed on missing tools and libraries: fs needs cmake, rsvg needs librsvg and glib's headers (found through PKG_CONFIG_PATH), and igraph links libxml2 and lzma. pak also upgraded packages the conda environment already provides, so setup now passes upgrade = FALSE and the compile-heavy packages come from conda-forge as binaries. Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
devtools::load_all() needs it to register the package's cpp11 code. Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
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pixi run setupfails on a cluster node:pakcompiles R packages from source and the environment lacks what they need.fsbuilds its bundled libuv with cmake, which was not installed (cmake: command not found,Makevars:44: libuv Error 127). Addedcmake.rsvgneeds librsvg's headers and glib'sglibconfig.h. Addedpkg-config,librsvgandglib, and setPKG_CONFIG_PATHto the environment'slib/pkgconfigandshare/pkgconfig.local_install_dev_deps()upgrades packages by default, so it replaced working conda builds (rlang,xml2,withr, ...) with CRAN source builds that failed:rlangfailed its load check becausecliwas not installed yet, andxml2linked against the host's/usr/include/libxml2. It now runs withupgrade = FALSE.igraphlinks libxml2 and lzma, which are not in the environment.igraph,V8,systemfonts,vroom,isoband,stringi,sassandRcppArmadillonow come from conda-forge as binaries.devtools::load_all()needsdecorto register the cpp11 code; added to thepaklist (there is no conda package).Checked on an Alpine compute node:
pixi run setupcompletes, thenpixi run testgivesFAIL 0 | WARN 0 | SKIP 0 | PASS 536. That run used the files from #44 (the Sprinzl fix and its new regression test), so those pass too.The lock file is regenerated; pixi also upgraded it from format v6 to v7.