From m@ech|er @end|ng |rom @t@t@m@th@ethz@ch  Fri Nov 10 14:19:49 2023
From: m@ech|er @end|ng |rom @t@t@m@th@ethz@ch (Martin Maechler)
Date: Fri, 10 Nov 2023 14:19:49 +0100
Subject: [Rd] 
 [R] Why Rprofile.site is not built with manual installation of
 R devel in linux?
In-Reply-To: <205A4E17-50C5-45F0-8D91-F400C1B89E6E@dcn.davis.ca.us>
References: <AM6PR02MB44230F37BC7E7A139581925F94AFA@AM6PR02MB4423.eurprd02.prod.outlook.com>
 <205A4E17-50C5-45F0-8D91-F400C1B89E6E@dcn.davis.ca.us>
Message-ID: <25934.11765.552272.1395@stat.math.ethz.ch>

>>>>> 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



[Rd] [R] Why Rprofile.site is not built with manual installation of R devel in linux?
Martin Maechler