Thanks, everyone, for responding. Here a summary of my research so
far--I do not quite understand what I am doing, but I spotted
a number of different issues, and I got the checks to work.
* I was not aware of the distinction between default and recommended
packages, and the fact that the latter is not installed by default
(although usually they are on production systems).
* in the rocker/r-devel container, R and R-devel use (partly)
overlapping lib paths: `/usr/local/lib/R/site-library` and
`/usr/lib/R/library`.
* R and R-devel have different packages installed by default, but
because both access `/usr/lib/R/library`, both seem to have access
to both default and recommended packages.
* `RD CMD check` uses a different lib path, containing
`/usr/local/lib/R/library` and a temporary folder. The latter will
contain the needed packages given they are installed in a certain
location (I still do not understand how they get there, and from
where).
* The message I got -- package _lattice_ not available -- was due to
two reasons: a) it is a recommended, not a default package; and b)
it is installed in `/usr/lib/R/library` where it is normally
accessible for both R and R-devel, and hence was not installed
again. However, from there it is not copied to the temporary folder that
R CMD check uses.
* Finally, by setting `ENV R_LIBS=/usr/local/lib/R/site-library/` in
the Dockerfile, the checks work. But I am not sure why.
It would be great to isolate R and R-devel better in the docker
image. Not sure whether it is easy to do...
Cheers,
Ott
On Tue, Aug 12, 2025 at 1:17 AM Berwin A Turlach <berwin.turl...@gmail.com>
wrote:
> On Mon, 11 Aug 2025 08:47:45 -0400
> Duncan Murdoch <murdoch.dun...@gmail.com> wrote:
>
> > Regarding Dirk's "narrower" comment: I think that is really his
> > decision about the docker container, not a property of R CMD check.
> > R CMD check needs to be able to succeed if the only packages
> > installed are the hard dependencies (Depends, Imports, plus base
> > packages), but it doesn't actually install anything. That's up to
> > you before running it.
>
> Obviously I cannot speak for Dirk and where his comment comes from :),
> but WRE has since ages the following note:
>
> Note: R CMD check and R CMD build run R processes with
> --vanilla in which none of the user’s startup files are read.
> If you need R_LIBS set (to find packages in a non-standard
> library) you can set it in the environment: also you can use
> the check and build environment files (as specified by the
> environment variables R_CHECK_ENVIRON and R_BUILD_ENVIRON; if
> unset, files55 ~/.R/check.Renviron and ~/.R/build.Renviron are
> used) to set environment variables when using these utilities.
>
> On my linux box I update and compile R patched and R devel regularly,
> and at some point I got tired of also installing a lot of packages
> (that I need for checking) each time. So I moved all of these
> additional packages to another library (where they are updated on an
> as needed basis via update.packages(ask=FALSE, CheckBuilt=TRUE)). After
> this restructure R patched and R devel could promptly not find those
> packages anymore (until I changed my scripts to create appropriate
> symbolic links, I did not want to go down the path of setting
> environment variables).
>
> Cheers,
>
> Berwin
>
>
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