apt update & apt upgrade vs update.packages()

[pietro-coretto]

I followed the guidelines and set up a nice and clean install with r2u repos and bspm package.

I installed both from shell with

apt install r-cran-pkgname

and from a sudo session of R using

install.package("pkgname")

and all stuff is installed under /usr/lib/R/site-library (except bspm) as expected. This is wonderful, thanks!

My question is about updating packages. Suppose that I installed pkg_A via install.package("pkg_A") under admin privileges. When I do the next

apt update && apt dist-upgrade

do I understand correctly that pkg_A now is updated/upgraded as if it was installed under apt?

[eddelbuettel]

Yes that works that way. I have a few (long-running) machines (laptop, and ec2 instance) that operate that way. I only interface with apt and my R installation updates as well.

That is a feature and not a bug.

Of course, you can still call update.packages() as well and because it will (as needed) call install.packages() which is traced thanks to bspm it will also hit the apt code path. Still a feature.

/cc @Enchufa2

[pietro-coretto]

You saved our poor lives....
Thank you infinitely !!!

[eddelbuettel]

Thanks for the very kind words but you know what they say about open source and an itch to scratch: I had to save mine first 😆

[eddelbuettel]

See for example these two mastodon posts of mine (from a two-post thread) celebrating / illustrating this with screenshots:

• https://mastodon.social/@eddelbuettel/112464455366615093
• https://mastodon.social/@eddelbuettel/112464483600928649

[eddelbuettel]

And PS:

and from a sudo session of R using

bspm allows you enable acquiting of sudo as needed so that you can do all this from a normal user R session. See its docs, it is another option to set at startup like bspm::enable().

[pietro-coretto]

Btw, I used your setup script add_cranapt_noble.sh and It worked perfect.

Exploring the script I notice you start install r-base-core. What is it exactly? Does it contain r-base and r-base-dev in one package?

[eddelbuettel]

Do apt-cache show on the three and look carefully. r-base is the (virtual) meta package enveloping all, r-base-core is the minimal "core" package needed to run (hence a valid choice where I needed it) and -dev is the development package. We are topic drifting now so maybe open a new issue (or 'discussion' -- why are were anyway? Anyway....) to not dilute this subject's thread.