Re: [R-sig-Debian] [Rd] [R] Why Rprofile.site is not built with manual installation of R devel in linux?
Thanks all for your answers.
First of all, I wrote to R-help and not R-devel, because I wanted to get help
and not discussing anything relative to R development, and also because this
issue could be due to my fault (as it was indeed), and not to the R devel
branch...
Thanks particularly to Martin, because one of his comments enlighten the issue
with my tests.
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 /etc/
Have you by chance set an R_LIBS_SITE or similar environment
variable ?
Does
env | grep '^R_'
give a hint?
Indeed, I had a ~/.Rprofile file sourcing the Rprofile.site file of Debian
stable installation, so changing its name made the issue to vanish.
Iago
De: Dirk Eddelbuettel
Enviat el: divendres, 10 de novembre de 2023 14:41
Per a: Martin Maechler
A/c: Iago Gin� V�zquez ; R-SIG-debian@r-project.org
; r-de...@r-project.org ;
Jeff Newmiller
Tema: Re: [Rd] [R] Why Rprofile.site is not built with manual installation of R
devel in linux?
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)'
bindocetc
"/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)'
bindocetc
"/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)'
bindoc
"/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 | e...@debian.org
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Re: [R-sig-Debian] [Rd] [R] Why Rprofile.site is not built with manual installation of R devel in linux?
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)'
bindocetc
"/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)'
bindocetc
"/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)'
bindoc
"/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 | e...@debian.org
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Re: [R-sig-Debian] [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 Giné Vázquez"
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 /R-devel
{which is what I do all the time; by that I can easily symlink
to more than one of different R-devel- 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 /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
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