R devel - Nov 2023 - [R] Why Rprofile.site is not built with manual installation of R devel in linux?

>>>>> Jeff Newmiller via R-help 
>>>>>     on Thu, 09 Nov 2023 12:08:07 -0800 writes:
    > No clue. Tip: R-devel is the mailing list for anything
    > related to development versions of R. Off-topic here.

Yes.  Alternatively, as he uses Debian, there's the
R-SIG-Debian  mailing list, too.

--> I'm CC'ing  both R-devel and R-SIG-Debian instead of R-help.

    > On November 9, 2023 2:59:44 AM PST, "Iago Gin? V?zquez"
<iago.gine at sjd.es> wrote:
    >> Hi all,
    >> 
    >> I downloaded R-devel as explicited in
https://developer.r-project.org/SVNtips.html
    >> Then, I tried to install it through instructions in
https://cran.r-project.org/doc/manuals/r-devel/R-admin.html#Installation
    >> (taking into account also
https://stat.ethz.ch/pipermail/r-devel/2016-May/072777.html)
    >> So:
    >> export REPOS=https://svn.r-project.org/R
    >> export RTOP=~ #adjust as necessary
    >> cd $RTOP
    >> svn co $REPOS/trunk r-devel/R
    >> cd r-devel/R
    >> tools/rsync-recommended
    >> mkdir ../build-R
    >> cd ../build-R
    >> ../R/configure --prefix=/where/you/want/R/to/go
    >> make
    >> make check

all fine till here.

I never do the following two (they are not necessary, if you
keep your  .../r-devel/build-R/  directory and  symlink the
.../r-devel/build-R/bin/R  to some  <in_our_PATH>/R-devel
{which is what I do all the time; by that I can easily symlink
to more than one of different R-devel-<foo> versions etc}

Still I cannot believe that these are the problem.

    >> make install
    >> make install-tests

    >> cd tests
    >> ## followed by one of
    >> ../bin/R CMD make check
    >> ../bin/R CMD make check-devel

I've never used    ../bin/R CMD make check
instead of simply  make check
(which you already did earlier),
and ditto replacing 'check' with 'check-devel'.

But even if I do that now, I don't get your error,
*and*  I have not made use of an  Rprofile.site  for a very long time
(and do *not* have any inside (my variant of your) build-R/


    >> And here I get the following error
    >> checking package 'base'
    >> Error in file(filename, "r", encoding = encoding) :
    >> cannot open the connection
    >> Calls: source -> file
    >> In addition: Warning message:
    >> In file(filename, "r", encoding = encoding) :
    >> cannot open file '.../etc/Rprofile.site': No such file or
directory
    >> Execution halted

You must have forgotten to tell us a bit more about your setup.
I never get the above error,
and I do *not* have an  Rprofile.site  either in my  <build-R>/etc/

Have you by chance set an R_LIBS_SITE or similar environment
variable ?
Does
	env | grep '^R_'

give a hint?

    >> where the dots ... specify the path to the build-R folder where
R-devel was built. And I check the etc folder and indeed there is no the
Rprofile.site
    >> -rw-r--r-- 1 iago iago  209 Nov  9 08:27 javaconf
    >> -rw-r--r-- 1 iago iago  770 Nov  9 08:35 ldpaths
    >> -rw-r--r-- 1 iago iago 6672 Nov  9 08:35 Makeconf
    >> -rw-r--r-- 1 iago iago 3336 Nov  9 08:27 Makefile
    >> -rw-r--r-- 1 iago iago 1853 Nov  9 08:27 Renviron
    >> -rw-r--r-- 1 iago iago 1173 Nov  9 08:32 repositories


    >> I note that make install installed R in the path I specified in 
../R/configure --prefix=/where/you/want/R/to/go
    >> however
    >> 1. make install-tests installed the tests folder in build-R .

Are your sure?  I don't see how it would do this when I do

    make -n install-tests

(the `-n` "simulates" the make and tells you what make *would* do if
you left away the `-n`)
Rather it would (try to) install to the same place that

    make -n install

would do , namely the  $PREFIX/tests/  directory.
Maybe you are just confused, because indeed, your
.../build-R/tests/  directory also contains many of the files
needed for the tests {but not e.g. the crucial *.R  ones !}.


    >> 2.  In the installed R in /where/you/want/R/to/go, there is no even
etc folder, there are only the folders bin, lib and share.

    >> Am I  skipping some step? I am on Debain 12.
Deb*ia*n  {Debora(h) + Ian }

Could it be that the Debian/Ubuntu default (for *their* build of
/usr/bin/R ) where they indeed use an  Rprofile.site and hence
that Debian-specific setup is hurting you here  in some way?

I'm close to sure that Debian users may be able to help you one
step further.

Martin

    >> Thank you!
    >> Iago

On 10 November 2023 at 14:19, Martin Maechler wrote:
|     >> 2.  In the installed R in /where/you/want/R/to/go, there is no
even etc folder, there are only the folders bin, lib and share.

That would appear to be an error in the locally installed R.

What the package does has been discussed before. Per the Linux Filesystem
Standard (or Filesystem Hierarchy or whatever it is called), Linux distro
such as Debian and Ubuntu use _both_ /usr/lib _and_ /usr/share so the
directories are split. Use the `R.home()` function to find them:

    $ Rscript -e 'sapply(c("bin", "doc",
"etc"), R.home)'
                   bin                doc                etc 
      "/usr/lib/R/bin" "/usr/share/R/doc"  
"/usr/lib/R/etc"
    $ 

That is from the packaged R via r-base-core.

The behaviour can easily be validated by invoking, say, a Docker container
based on these same (Debian) packages. One of the containers I look after in
the Rocker Project has also been aliased to just 'r-base' for years by
Docker
itself so just prefix the above by 'docker run --rm -ti r-base' to run
in a
clean container:

    $ docker run --rm -ti r-base Rscript -e 'sapply(c("bin",
"doc", "etc"), R.home)'
                   bin                doc                etc 
      "/usr/lib/R/bin" "/usr/share/R/doc"  
"/usr/lib/R/etc"
    $ 

Being able to run Docker for such tests is a good superpower and on most
systems these days only one package installation away.

For a locally built one (my r-devel build here) it works the same but points
of course to a different directory:

    $ RDscript -e 'sapply(c("bin", "doc",
"etc"), R.home)'
                                   bin                                doc
    "/usr/local/lib/R-devel/lib/R/bin"
"/usr/local/lib/R-devel/lib/R/doc"
                                   etc 
    "/usr/local/lib/R-devel/lib/R/etc"
    $ 

As suggested, question for 'R on Debian, Ubuntu, ...' should probably go
to
r-sig-debian which is now CCed.  As usual, you must be subscribed to post or
else you will get mistaken for a spammer and ignored.

Dirk

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