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

Hi r-sig-debian,

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?*
- or is it a problem with R for debian bullseye putting  `/doc/KEYWORDS.db`
in '/usr/share/R/doc/' where it should not be? -> why does it do
that?
Should it be this way? Can I change it?

To be sure, searching help in RStudio and `help('help`) in R from the
terminal both worked. I installed both the way you suggest on lib.stat.cmu/R
/CRAN/bin/linux/debian/.

See also https://github.com/rpy2/rpy2/issues/1033

Johan
with his first question on a, not just thus, mail list

	[[alternative HTML version deleted]]

Hi Johan,

On 6 June 2023 at 18:55, Johan Andresen wrote:
| Hi r-sig-debian,
| 
| 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?*

Yes, in essence.  The longer story is that for (many, MANY) years we followed
_Debian_ Policy where architecture-dependent files are in /usr/lib and
architecture-indepdendent files are in /usr/share.  As such we (ie Debian)
differ from a "plain vanilla from source" installation.  But then all
(or
most) other distros do too.  It is the right (and/or was when multi-arch ie
32 and 64 bit was more common).

Even R itself recently patched another accessor because the right way to do
this is to expand the R.home() function rather than to append to the
environment variable R_HOME (or RHOME).

To show, on my system:

   > file.path( R.home("doc"), "KEYWORDS.db" )
   [1] "/usr/share/R/doc/KEYWORDS.db"
   > 

So ideally rpy2 to should try to figure out where doc/ is for R and then
append KEYWORDS.db. I am CCing Laurent now.

| - or is it a problem with R for debian bullseye putting  `/doc/KEYWORDS.db`
| in '/usr/share/R/doc/' where it should not be? -> why does it do
that?
| Should it be this way? Can I change it?

It was change brought to me (as Debian maintainer) by other Debian developers
/ Debian Policy.  As such it is pretty irreversible.

But "R known" and access via e.g. R.home() is the right way. Also not
that
/etc/R/Makeconf has, inter alia

   '--datadir=/usr/share/R/share'

and

   include $(R_SHARE_DIR)/make/vars.mk
   MKINSTALLDIRS = "$(R_HOME)/bin/mkinstalldirs"
   R_XTRA_CPPFLAGS =  -I"$(R_INCLUDE_DIR)" -DNDEB

so R does have the notion of different directories just fine. Also:

   > envs <- Sys.getenv()
   > envs[grepl("^R_", names(envs))]
   R_ARCH                                                      
   R_BROWSER                                                   xdg-open
   R_BZIPCMD                                                   /bin/bzip2
   R_DOC_DIR                                                   /usr/share/R/doc
   R_GZIPCMD                                                   /bin/gzip -n
   R_HOME                                                      /usr/lib/R
   R_INCLUDE_DIR                                              
/usr/share/R/include
   R_LIBS_SITE                                                
/usr/local/lib/R/site-library:/usr/lib/R/site-library
   R_LIBS_USER                                                 
   R_MAX_NUM_DLLS                                              500
   R_PAPERSIZE                                                 letter
   R_PAPERSIZE_USER                                            letter
   R_PDFVIEWER                                                 /usr/bin/xdg-open
   R_PLATFORM                                                 
x86_64-pc-linux-gnu
   R_PRINTCMD                                                  /usr/bin/lpr
   R_RD4PDF                                                   
times,inconsolata,hyper
   R_SESSION_TMPDIR                                            /tmp/RtmpoU2ifO
   R_SHARE_DIR                                                
/usr/share/R/share
   R_STRIP_SHARED_LIB                                          strip
--strip-unneeded
   R_STRIP_STATIC_LIB                                          strip
--strip-debug
   R_SYSTEM_ABI                                               
linux,gcc,gxx,gfortran,gfortran
   R_TEXI2DVICMD                                               /usr/bin/texi2dvi
   R_UNZIPCMD                                                  /usr/bin/unzip
   R_ZIPCMD                                                    /usr/bin/zip
   >
   
| To be sure, searching help in RStudio and `help('help`) in R from the
| terminal both worked. I installed both the way you suggest on lib.stat.cmu/R
| /CRAN/bin/linux/debian/.
| 
| See also https://github.com/rpy2/rpy2/issues/1033

Oh, nice, I should link back to this reply once it hits the mailing list
archive.

| Johan
| with his first question on a, not just thus, mail list

Thanks for the detailed and high-quality post. Keep'em coming!

Dirk

-- 
dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org

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