R SIG Debian - Jun 2023 - why is KEYWORDS.db not in '/usr/lib/R/doc/' but in '/usr/share/R/doc/'?

Hello Johan and welcome to R-SIG-Debian!

? Tue, 6 Jun 2023 18:55:27 +0200
Johan Andresen <johan.andresen at gmail.com> ?????:
> I feel lucky to have found out that `/doc/KEYWORDS.db` is in
> `/usr/share/R/`, not in `usr/lib/R/` where rpy2 in python apparently
> looks for it when trying to search help in R from the python
> environment. it returned this error: `cannot open file
> '/usr/lib/R/doc/KEYWORDS.db': No such file or directory`.
> 
> What to do now?
> - is this a problem with rpy2 looking for `/doc/KEYWORDS.db` that
> should not be in `usr/lib/R/`? -> *edit its script to point at the
> correct path?*
It seems that R.home('doc') doesn't return the right path when
running
from under rpy2 for some reason. (With Debian packages, it should
return "/usr/share/R/doc", not "/usr/lib/R/doc".)

It's documented in ?R.home that on Unix-like OSes, the function relies
on environment variables like R_DOC_DIR being set during startup.

How does rpy2 launch R? It looks like rpy2 drives an embedded R like a
frontend. I think that at least under Unix-alikes, the required
environment variables are set by launching the frontend via `R CMD
/path/to/frontend/executable` (see WRE 8.1 [*]), except this isn't
convenient for the Python process. I guess rpy2 could obtain the
additional variables the same way it currently extracts LD_LIBRARY_PATH.
> Johan
> with his first question on a, not just thus, mail list
>	[[alternative HTML version deleted]]
One tiny detail: this mailing list (and other R project mailing lists)
removes the HTML part of the messages it processes, so it's best to
compose in plain text. But the rest of it you're doing absolutely right!

-- 
Best regards,
Ivan

[*]
https://cran.r-project.org/doc/manuals/R-exts.html#Embedding-R-under-Unix_002dalikes

Thanks, Dirk and Ivan

Now I better understand what is going on. Sweet this help is already in the
github issue.

Johan

Den tirs. 6. jun. 2023 kl. 19.25 skrev Ivan Krylov <krylov.r00t at
gmail.com>:
> Hello Johan and welcome to R-SIG-Debian!
>
> ? Tue, 6 Jun 2023 18:55:27 +0200
> Johan Andresen <johan.andresen at gmail.com> ?????:
>
> > I feel lucky to have found out that `/doc/KEYWORDS.db` is in
> > `/usr/share/R/`, not in `usr/lib/R/` where rpy2 in python apparently
> > looks for it when trying to search help in R from the python
> > environment. it returned this error: `cannot open file
> > '/usr/lib/R/doc/KEYWORDS.db': No such file or directory`.
> >
> > What to do now?
> > - is this a problem with rpy2 looking for `/doc/KEYWORDS.db` that
> > should not be in `usr/lib/R/`? -> *edit its script to point at the
> > correct path?*
>
> It seems that R.home('doc') doesn't return the right path when
running
> from under rpy2 for some reason. (With Debian packages, it should
> return "/usr/share/R/doc", not "/usr/lib/R/doc".)
>
> It's documented in ?R.home that on Unix-like OSes, the function relies
> on environment variables like R_DOC_DIR being set during startup.
>
> How does rpy2 launch R? It looks like rpy2 drives an embedded R like a
> frontend. I think that at least under Unix-alikes, the required
> environment variables are set by launching the frontend via `R CMD
> /path/to/frontend/executable` (see WRE 8.1 [*]), except this isn't
> convenient for the Python process. I guess rpy2 could obtain the
> additional variables the same way it currently extracts LD_LIBRARY_PATH.
>
> > Johan
> > with his first question on a, not just thus, mail list
>
> >       [[alternative HTML version deleted]]
>
> One tiny detail: this mailing list (and other R project mailing lists)
> removes the HTML part of the messages it processes, so it's best to
> compose in plain text. But the rest of it you're doing absolutely
right!
>
> --
> Best regards,
> Ivan
>
> [*]
>
>
https://cran.r-project.org/doc/manuals/R-exts.html#Embedding-R-under-Unix_002dalikes
>
	[[alternative HTML version deleted]]