On 6 June 2023 at 22:29, Johan Andresen wrote:
| Thanks, Dirk and Ivan
|
| Now I better understand what is going on. Sweet this help is already in the
| github issue.
It's an issue somewhere between Laurent (for rpy2) and me (for the R package
and his rpy2 on Debian) and we should be able to sort it out. Maybe easiest
at the GH issue, I am sure I will hear from Laurent about it too. (CCing
Laurent again: not sure if you were CCed on Ivan's message quoted below:
looks like rpy2 comes up with the wrong value on Debian.)
Best, Dirk
| Johan
|
| Den tirs. 6. jun. 2023 kl. 19.25 skrev Ivan Krylov <krylov.r...@gmail.com>:
|
| > Hello Johan and welcome to R-SIG-Debian!
| >
| > В Tue, 6 Jun 2023 18:55:27 +0200
| > Johan Andresen <johan.andre...@gmail.com> пишет:
| >
| > > 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]]
|
| _______________________________________________
| R-SIG-Debian mailing list
| R-SIG-Debian@r-project.org
| https://stat.ethz.ch/mailman/listinfo/r-sig-debian
--
dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
_______________________________________________
R-SIG-Debian mailing list
R-SIG-Debian@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-debian
