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 | e...@debian.org
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