pak clobbers system source installs about pak

[gaborcsardi]

pak only detects proper system packages, that were installed with the system package manager. If you install packages other ways, e.g. the traditional ./configure; make install way, those are not detected. This is usually not a big problem, even if pak installs extra packages, because the manually installed packages go into /usr/local/, which takes priority over system packages in /usr.

Nevertheless, you can opt out from system dependency installation by setting the PKG_SYSREQS=false env var or the pkg.sysreqs=FALSE option: https://pak.r-lib.org/reference/pak-config.html#pak-configuration

[mdsumner]

ok thanks!

it still installs though it looks promisingly like it's not going to do that, I'll keep exploring since this is not a very familar area for me - I guess the installs are bundled with everything somehow on the setup I'm using.

options(pkg.sysreqs=FALSE)
> pak::pak("terra")
v Loading metadata database ... done

> Will update 1 package.
> Will download 1 package with unknown size.
+ terra 1.7-69 > 1.7-65 [dl] + x libgdal-dev, x gdal-bin, v libgeos-dev, v libproj-dev, v libsqlite3-dev
x Missing 2 system packages. You'll probably need to install them manually:
+ gdal-bin     - terra
+ libgdal-dev  - terra
? Do you want to continue (Y/n) Y
i Getting 1 pkg with unknown size
v Got terra 1.7-65 (x86_64-pc-linux-gnu-ubuntu-22.04) (4.21 MB)
v Downloaded 1 package (4.21 MB) in 3.4s
v Installed terra 1.7-65  (1s)
v 1 pkg + 1 dep: kept 1, upd 1, dld 1 (4.21 MB) [18.2s]
> terra::gdal()
[1] "3.4.1"

(would be 3.8.2 with rocker as above)

EDIT:
ok, i'm sorry - it's right on the rocker example, my bad. I'm doing something wrong in my docker setup elsewhere. Please ignore