Fix VM setup issues: WebGestaltR/cargo, ggridges - #38
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Adds ggridges to the CRAN package list in the setup page (required by enrichplot::ridgeplot(), was missing and had to be added manually on the workshop VMs). Also adds a note explaining that WebGestaltR compiles Rust source during installation and needs a working cargo toolchain, pointing at rustup as the fix when an older distro-packaged cargo fails. Also clarifies in the STRINGdb chapter that an empty data frame from get_interactions(crabp2, sema3a) is expected, not a bug: STRING has no direct interaction annotated between these two genes.
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Summary
Addresses three issues found while colleagues set up workshop VMs:
01-02-setup.Rmd; required byenrichplot::ridgeplot(), wasn't listed and had to be added manually on the VMs.01-02-setup.Rmdexplaining it compiles Rust source during install and needs a workingcargotoolchain, pointing at rustup as the fix.08-2-stringdb.Rmdexplaining that an empty data frame fromget_interactions(crabp2, sema3a)is expected, since STRING has no direct interaction annotated between these two genes.Test plan
bookdown::render_book()completes cleanly.bookdown-renderjob to be confirmed green before merge.