В Tue, 21 Nov 2023 13:41:41 +0100
Ana de las Heras Molina <andel...@ucm.es> пишет:

> I am sorry for my ignorance, but what is Rgui.exe?

It's the graphical user interface that comes with R itself:
https://cran.r-project.org/bin/windows/base/README.R-4.3.2

If you haven't changed any settings while installing R, it should be
located at C:\Program Files\R\R-4.3.2\bin\x64\Rgui.exe.

You won't see the errors from
.rs.rpc.discover_package_dependencies(...), but I'm curious whether
your problems with LinDa / ANCOMBC / phyloseq can be reproduced with
plain Rgui.exe.

-- 
Best regards,
Ivan

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