Displaying 20 results from an estimated 8000 matches similar to: "Renviron settings for Linux Distributions: please tell me R Core's advice"
2010 Jun 03
1
How to go about getting a change in the SPEC file from which R is built on EPEL?
I asked a couple of months ago in r-sig-fedora about a difference I
noticed between Ubuntu and RedHat/Fedora. Now I think I've figured
out the cause is a little issue in packaging but I don't know how to
get it fixed.
On Ubuntu, the setup is like this. It i is controlled in a file called Renviron
R packages built/distributed in RPM are installed to /usr/lib/R/library.
R packages built
2020 Mar 19
0
R CMD check --as-cran attempts to hide R_LIBS_USER but fails
On 18 March 2020 at 19:19, Henrik Bengtsson wrote:
| AFAIU, 'R CMD check --as-cran' tries to hide any site and user package
| libraries by setting R_LIBS_SITE and R_LIBS_USER. However, contrary
What makes you think that? AFAIK --as-cran just sets a bunch of the (nearly
countless) environment variables (all described in R Inst+Admin, as I recall)
to a set of values "close to"
2020 Mar 19
2
R CMD check --as-cran attempts to hide R_LIBS_USER but fails
AFAIU, 'R CMD check --as-cran' tries to hide any site and user package
libraries by setting R_LIBS_SITE and R_LIBS_USER. However, contrary
to R_LIBS_SITE, it fails for R_LIBS_USER and the user's personal
library is still available for test scripts. Should I revise my
assumptions, or is that intentional?
The short version. Shouldn't:
$ R_LIBS_USER='' Rscript --vanilla -e
2020 Mar 19
1
R CMD check --as-cran attempts to hide R_LIBS_USER but fails
On Wed, Mar 18, 2020 at 8:04 PM Dirk Eddelbuettel <edd at debian.org> wrote:
>
>
> On 18 March 2020 at 19:19, Henrik Bengtsson wrote:
> | AFAIU, 'R CMD check --as-cran' tries to hide any site and user package
> | libraries by setting R_LIBS_SITE and R_LIBS_USER. However, contrary
>
> What makes you think that? AFAIK --as-cran just sets a bunch of the (nearly
2009 Jul 21
1
Customization options with .Renviron, R_LIBS, .Rprofile etc
Hi,
I am interested in customizing the installation of R. I have
gone through the ?R Installation and Administration? manual. But some
of the stuff is not clear to me and I would like to get clarifications
on the following points (for a Windows installation with
R_HOME=C:\\R\\R-2.9.1 ) :
1. I understand that I need to create a
file, .Renviron with the following path : R_HOME\\etc\\.Renviron where
2015 Mar 30
2
Debian Testing: ~/.Renviron seems to not being read (R_LIBS not set)
Dear Johannes, Dear Dirk,
Thanks a lot for helping. Here is the missing information.
Here is how I installed R. This is basically how Martin Maechler
showed me to install R under Ubuntu (in several versions so that they
are also recognized by ESS). My goal is to adjust this to make it work
for Debian:
1) sudo emacs /etc/apt/sources.list # then add:
deb
2017 Feb 09
0
R CMD check error
On Thu, 2017-02-09 at 09:52 -0600, Therneau, Terry M., Ph.D. wrote:
> Martin,
> ? I am aware of --vanilla; I use it myself for some testing.??In this case R_LIBS_USER was?
> set externally (part of my login) and does not involve any of the R scripts.??That means?
> it is inherited by any subprocess.??For example:
>
> tmt1495% R --vanilla --no-environ
>
> R version 3.3.1
2017 Feb 09
2
R CMD check error
Martin,
I am aware of --vanilla; I use it myself for some testing. In this case R_LIBS_USER was
set externally (part of my login) and does not involve any of the R scripts. That means
it is inherited by any subprocess. For example:
tmt1495% R --vanilla --no-environ
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
2015 Mar 30
2
Debian Testing: ~/.Renviron seems to not being read (R_LIBS not set)
Hi,
I have Debian Testing running on a Lenovo Thinkpad X1
Carbon (2015, 3rd gen.). I would like to have a package library
independent of the installed R version. Under Ubuntu, I used to
have the following line in ~/.Renviron:
R_LIBS=/usr/local/R/library:/usr/lib/R/site-library This worked
fine and /usr/local/R/library showed up in .libPaths().
However, under Debian (with the same ~/.Renviron),
2017 Feb 09
2
R CMD check error
Martyn,
No, that didn't work.
One other thing in the mix (which I don't think is the issue) is that I call one of the
C-entry points of expm. So the DESCRIPTION file imports expm, the NAMESPACE file imports
expm, and the init.c file is
#include "R.h"
#include "R_ext/Rdynload.h"
/* Interface to expm package. */
typedef enum {Ward_2, Ward_1, Ward_buggy_octave}
2014 Apr 25
0
Preventing $R_HOME/site-library/ via R_LIBS_SITE=":" (no other way?)
(As a non-root/non-admin), I've just tried to figure out how to
prevent a default $R_HOME/site-library/ to be added to the library
path. The solution I found was to environment variable R_LIBS_SITE to
":" (preferably in ~/.Renviron). Note that setting R_LIBS_SITE to en
empty string will cause it to fall back to using
$R_HOME/site-library/. This "hack" is based on the
2010 Jan 30
2
Can I install debs over packages installed via R?
[ Kevin sent this to me but agreed that it's better to have this discussed here. ]
On 30 January 2010 at 12:18, Kevin Donnelly wrote:
| Hi
|
| I'm beginning to learn R,a nd I've just discovered cran2deb - what a terrific
| resource! Thanks for making it.
|
| I was wondering what happens if I want to use cran2deb versions instead of the
| versions installed via R itself. I'm
2015 Mar 10
1
R_HOME default setting
Dear All,
I would like to reset default R_HOME PATH for R.3.1.3.
I installed R-devel in /usr/local/R-devel but I can't install many packages
as tcltk.
I uninstalled R-devel and I would reuse R.3.1.3 but the PATH is remaining
to /usr/local/R-devel.
I touch ~.Renviron file with
R_HOME=/usr/lib/R/bin/
RSTUDIO_R_HOME=/usr/lib/R/bin/
R_LIBS=~/R/x86_64-pc-linux-gnu-library/3.1
2008 May 07
0
how to define .Renviron to work with different R-versions
Hi,
I have a simple R script for printing arguments
cat > printargs.R << EOF
args = commandArgs()
print(args)
q()
EOF
To run this script, first I set PATH to ~/src/R-2.6.2 and execute >
R --no-save < printargs.R
I want to run this script with different R versions by defining an
.Renviron file in the same directory as printargs.R
cat >
2010 May 09
2
running a locally built R-devel with libraries from Debian installation
Hi,
What is the best way to tell a locally-built R-devel (somewhere in the
user home directory) to use the libraries from the Debian installation
(i.e. /usr/local/lib/R/site-library and /usr/lib/R/site-library). I
suppose this would take setting one or all of R_LIBS, R_LIBS_SITE,
R_LIBS_USER in ~/.Renviron, but that would also affect the Debian R in
the system so is not an option. How do R
2011 Nov 21
1
Setting hostname in the .Renvironment
This is a follow-up to a question I asked a few years back. We have a pair
of computers that share a common home directory (and therefor a common
.Renviron) with identical hardware, but very different sets of libraries
such that using a "shared" R_LIBS between two computers does not work.
They both use this as the default library for user installations:
2010 Feb 04
1
Improving RPM packaging for R; ideas gathered from the Debian folks
Hi, everybody.
I've got some Centos Linux systems and some Ubuntu Linux systems. R's
basically the same in either place, but the packaging of R for Debian
systems seems better to me than it is on Fedora/Redhat/Centos.
I joined R-sig-debian and we talk about package management issues
there sometimes. One of the really handy R packaging ideas they have
is to customize R environment so
2019 Jan 06
2
change default path for installing r-cran packages by sudo apt r-cran...?
dear dirk,
i am following up on our thread on r-help-mailinglist. you advised me to
bring it over here.
when installing packages from within R, they usually go to a directory
defined in R_LIBS_USER, which i have it set in .Renviron.
when installing packages via sudo apt install r-cran-.., they go to
/usr/lib/R/site-library.
is there a possibility to have packages installed to the R_LIBS-USER
2010 Jul 01
1
How best to set library search path so user libraries come first
I want my local libraries to have priority over the system installed
ones, which, as far as I can make out from help(".libPaths"), means they
have to come first in that list (it doesn't actually_say_ so, but that
seems to be the idea).
We have R_LIBS_USER which looks made for specifying where I keep my own
libraries. Unfortunately it comes last in .libPaths() [which appears to
2013 Nov 21
1
R CMD check (v-3.0.2) not loading $R_CHECK_ENVIRON
Hi all,
I'm trying to check a package using R CMD check --as-cran <package>. When
I do so, the check fails upon not finding the dependencies which I have
installed in a non-standard location. Per the manual, I created
~/.R/check.Renviron :
$ cat ~/.R/check.Renviron
R_LIBS=/usr/lib64/R/library:/usr/lib64/R/var
R_LIBS_SITE=/usr/lib64/R/library:/usr/lib64/R/var
No luck. I tried