Changing directory ownership

[snij22]

I am trying to set up a computer running Ubuntu for the first time - r2u was really helpful for rapidly getting my system up to speed. However there are a few packages (e.g. tmap) that require external packages that are not included on r2u. This makes sense, however I have installed these packages in R using install.packages() and I do not have write permissions to the /ur/R/site-lib/ folder where r2u dumped everything.

What is the recommended way to remedy the situation ?

1. Continue to maintain two separate package folders (both visible via .Libpaths()?
2. Grant write permissions to the .../site-libs/ folder so that I can add packages there?
3. Change where r2u installs packages from binaries to the personal folder?
4. Something else?

Any help/guidance you could provide is much appreciated. Thanks for building/maintaining r2u!

[eddelbuettel]

That is actually more of an 'using R on Debian / Ubuntu' question (which is the larger context of r2u. So this question is in fact decades old, and has been discussed on e.g. the (dedicated) r-sig-debian mailing list (see its archives here) and you may want to ask it there (again) for exposure to more eyes, but briefly:

• When we use apt we always are root. For r2u we have a trick via bspm so it is covered
• When we use R, we are a 'normal' user ... and by a "Policy" decision made after discussion with two R Core member well over twenty years ago (!!) we implemented the split between the three (default) directories in .libPath where i) /usr/lib/R/library is only for base R and recommended packages, and ii) /usr/lib/R/site-library is for other CRAN packages shipped as a .deb package (both inside the distro, about 1200 of them, and now r2u and lastly iii) /usr/local/lib/R/site-library is where the user installs via install.packages() (important: old focus of outside of r2u here) so there you must be member of the group owning that directory.
• You are asking a question somewhat related to that last point, and a new one. But for new one ("how/where do I install system packages") there is only one answer: as root. When you do system management on your machine you are the system administrator, and this follows standard Unix rules. So if tmap needs another lib$SOMETHING-dev library you install it as root. Standard approach, outside of r2u
• You are free to use personal folder for packages as well but be careful, R picks "first found" so both that and /usr/local/lib/R/site-library can "shadow" packages from r2u. Run e.g. bspm::shadowed_packages() to see which.

Hope this helps. And very glad ot hear r2u is helpful to you! All the preceding discussion assumes some familiarity with Linux / Ubuntu. This grows over time so just keep asking questions.

[snij22]

This is super helpful and I appreciate the quick reply. I have noticed shadowing on my system and I didn't realize bspm included methods to check and resolve this. Keep up the good work!

[eddelbuettel]

Also, with respect to tmap: What do you think is missing?

I have used it in demos (see here) as it is so widely used but it is not a package I work with daily.

[snij22]

I can't recall exactly, I think it was a leaflet dependency (maybe something Java related) that wasn't bundled in the binaries. I understand why it isn't bundled, but needed to use it. I ended up just installing is via normal install.packages() and shadowing the dependencies. I think I may have had the same issue with gt() as well.