Hello,
I have upgraded to R 4.2.0 on Ubuntu Ubuntu 20.04.4 LTS.
Something changed since now when invoking R as "R --vanilla" does not pick
up "/usr/local/lib/R/site-library" library anymore.
I tried to look at "6.2 Managing libraries" in
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html and
set R_LIBS_SITE in Renviron.site but with no success.
What am I missing? Thanks.
If I run R as "R --vanilla" this is what I get:
$ R --vanilla
R version 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
If I run R as "R" correct libraries are picked up:
$ R
R version 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
| I have upgraded to R 4.2.0 on Ubuntu Ubuntu 20.04.4 LTS.
|
| Something changed since now when invoking R as "R --vanilla" does not pick
| up "/usr/local/lib/R/site-library" library anymore.
I noticed that too when beta testing the earlier builds. It has to do with us
(previously) setting value to unset variables ... which are now set.
For the Debian package I managed the change by moving the setting to
Renviron.site:
## edd Apr 2003 Allow local install in /usr/local, also add a directory for
## Debian packaged CRAN packages, and finally the default dir
## edd Jul 2007 Now use R_LIBS_SITE, not R_LIBS
## edd Mar 2022 Now in Renviron.site reflecting R_LIBS_SITE
R_LIBS_SITE="/usr/local/lib/R/site-library/:${R_LIBS_SITE}:/usr/lib/R/library'"
If you have those three lines you should be fine. I am (also on Uubuntu 20.04
which a binary from my PPA):
# lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description: Ubuntu 20.04.4 LTS
Release: 20.04
Codename: focal
# Rscript --version
Rscript (R) version 4.2.0 (2022-04-22)
# Rscript -e '.libPaths()'
[1] "/usr/local/lib/R/site-library" "/usr/lib/R/site-library"
[3] "/usr/lib/R/library"
#
Dirk
dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
Dirk, thank you.
I do have the following lines in /usr/lib/R/etc/Renviron.site (see below):
## edd Apr 2003 Allow local install in /usr/local, also add a directory
for
## Debian packaged CRAN packages, and finally the default
dir
## edd Jul 2007 Now use R_LIBS_SITE, not R_LIBS
## edd Mar 2022 Now in Renviron.site reflecting R_LIBS_SITE
R_LIBS_SITE="/usr/local/lib/R/site-library/:${R_LIBS_SITE}:/usr/lib/R/library'"
Unfortunately, somehow it doesn't work for me and I don't have a clue why:
username at usernameVB:~$ lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description: Ubuntu 20.04.4 LTS
Release: 20.04
Codename: focal
username at usernameVB:~$ Rscript --version
Rscript (R) version 4.2.0 (2022-04-22)
username at usernameVB:~$ Rscript -e '.libPaths()'
[1] "/usr/local/lib/R/site-library" "/usr/lib/R/site-library"
[3] "/usr/lib/R/library"
username at usernameVB:~$ Rscript --vanilla -e '.libPaths()'
[1] "/usr/lib/R/site-library" "/usr/lib/R/library"
username at usernameVB:~$ cat /usr/lib/R/etc/Renviron.site
## Emacs please make this -*- R -*-
## empty Renviron.site for R on Debian
##
## Copyright (C) 2008 - 2022 Dirk Eddelbuettel and GPL'ed
##
## see help(Startup) for documentation on ~/.Renviron and Renviron.site
# ## Example ~/.Renviron on Unix
# R_LIBS=~/R/library
# PAGER=/usr/local/bin/less
# ## Example .Renviron on Windows
# R_LIBS=C:/R/library
# MY_TCLTK="c:/Program Files/Tcl/bin"
# ## Example of setting R_DEFAULT_PACKAGES (from R CMD check)
# R_DEFAULT_PACKAGES='utils,grDevices,graphics,stats'
# # this loads the packages in the order given, so they appear on
# # the search path in reverse order.
## # We comment out this line in the default Renviron, you can re-enable it
here
## # @R_PLATFORM@ can be eg x86_64-pc-linux-gnu, see /etc/R/Renviron for
R_PLATFORM
## # @MAJ_MIN_VERSION@ is likely something like '3.4', see /etc/R/Renviron
too
## #
## # Also note that you set this per-user via '%p' and '%v' for platform
and version
#R_LIBS_USER=${R_LIBS_USER-'~/R/@R_PLATFORM at -library/@MAJ_MIN_VERSION@'}
## edd May 2019
##
## Debian (and its derivatives) impose a set of compiler flags to prevent
some known
## security issues with compiled code. These flags then become defaults
for R as well
## (see eg /etc/R/Makeconf) but nevertheless confuse R as warnings get
triggers. Users,
## on the other hand, are often stumped about these. So with this variable
we declare
## these options as known for the local checks on the machine this file is
on.
##
## See Section 8 of the R Internals manual for many more options to
customize tests.
_R_CHECK_COMPILATION_FLAGS_KNOWN_='-Wformat -Werror=format-security
-Wdate-time'
## edd Apr 2003 Allow local install in /usr/local, also add a directory for
## Debian packaged CRAN packages, and finally the default dir
## edd Jul 2007 Now use R_LIBS_SITE, not R_LIBS
## edd Mar 2022 Now in Renviron.site reflecting R_LIBS_SITE
R_LIBS_SITE="/usr/local/lib/R/site-library/:${R_LIBS_SITE}:/usr/lib/R/library"
username at usernameVB:~$
Best,
Sam
On Mon, Apr 25, 2022 at 9:44 PM Dirk Eddelbuettel <edd at debian.org> wrote:
On 25 April 2022 at 21:12, Sam H wrote:
| I have upgraded to R 4.2.0 on Ubuntu Ubuntu 20.04.4 LTS.
|
| Something changed since now when invoking R as "R --vanilla" does not
pick
| up "/usr/local/lib/R/site-library" library anymore.
I noticed that too when beta testing the earlier builds. It has to do with
us
(previously) setting value to unset variables ... which are now set.
For the Debian package I managed the change by moving the setting to
Renviron.site:
## edd Apr 2003 Allow local install in /usr/local, also add a directory
for
## Debian packaged CRAN packages, and finally the default
dir
## edd Jul 2007 Now use R_LIBS_SITE, not R_LIBS
## edd Mar 2022 Now in Renviron.site reflecting R_LIBS_SITE
R_LIBS_SITE="/usr/local/lib/R/site-library/:${R_LIBS_SITE}:/usr/lib/R/library'"
If you have those three lines you should be fine. I am (also on Uubuntu
20.04
which a binary from my PPA):
# lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description: Ubuntu 20.04.4 LTS
Release: 20.04
Codename: focal
# Rscript --version
Rscript (R) version 4.2.0 (2022-04-22)
# Rscript -e '.libPaths()'
[1] "/usr/local/lib/R/site-library" "/usr/lib/R/site-library"
[3] "/usr/lib/R/library"
#
Dirk
--
dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
Best regards,
Sam
[[alternative HTML version deleted]]
Sam,
Please try to debug locally. There are command-line switches to R that allow
you to turn sourcing of initializations files off, you can also try to see if
it is different for 'root' as opposed to you account.
When I chase something like that his I typically
a) add lines like message("running from file foo") in Rprofile,
Rprofile.site, ~/.Rprofile etc
b) set env vars in each Renviron / Renviron.site / ~/.Renviron file to see
which are being hit.
Something somewhere turns some values off for you. I can't tell from here
what caused it.
Dirk
dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
Dirk, thanks.
I will try to debug locally. Thanks for the instructions.
Just to make sure it is only me: when you run the following commands ($
Rscript -e '.libPaths()') without and with --vanilla on your system you get
the same output (as you see below I don't):
username at usernameVB:~$ Rscript -e '.libPaths()'
[1] "/usr/local/lib/R/site-library" "/usr/lib/R/site-library"
[3] "/usr/lib/R/library"
username at usernameVB:~$ Rscript --vanilla -e '.libPaths()'
[1] "/usr/lib/R/site-library" "/usr/lib/R/library"
Thanks.
Best regards,
Sam
On Mon, Apr 25, 2022 at 10:21 PM Dirk Eddelbuettel <edd at debian.org> wrote:
Sam,
Please try to debug locally. There are command-line switches to R that
allow
you to turn sourcing of initializations files off, you can also try to see
if
it is different for 'root' as opposed to you account.
When I chase something like that his I typically
a) add lines like message("running from file foo") in Rprofile,
Rprofile.site, ~/.Rprofile etc
b) set env vars in each Renviron / Renviron.site / ~/.Renviron file to
see
which are being hit.
Something somewhere turns some values off for you. I can't tell from here
what caused it.
Dirk
--
dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
Best regards,
Sam
[[alternative HTML version deleted]]
| Just to make sure it is only me: when you run the following commands ($
| Rscript -e '.libPaths()') without and with --vanilla on your system you get
| the same output (as you see below I don't):
| username at usernameVB:~$ Rscript -e '.libPaths()'
| [1] "/usr/local/lib/R/site-library" "/usr/lib/R/site-library"
| [3] "/usr/lib/R/library"
| username at usernameVB:~$ Rscript --vanilla -e '.libPaths()'
| [1] "/usr/lib/R/site-library" "/usr/lib/R/library"
I see the same on Ubuntu with R 4.2.0.
This is likely due to me having to move the setting for
/usr/local/lib/R/site-library
from R's own Renviron to Renviron.site and --vanilla skip reading that.
Dirk
dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
So in short: If you want to run R with --vanilla you have to change the
local set up file. Because R now ships with this
R_LIBS_USER=${R_LIBS_USER:-'%U'}
R_LIBS_SITE=${R_LIBS_SITE:-'%S'}
you could set R_LIBS_USER and/or R_LIBS_SITE in a file read by the OS before
R starts -- a short text snippet in /etc/profile.d/ may work -- to ensure
R_LIBS_USER and R_LIBS_SITE are set to your liking.
Sorry for missing the hint about --vanilla from your first email.
Dirk
dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
Dirk, thanks.
Changing /etc/R/Renviron by adding
*R_LIBS_SITE="/usr/local/lib/R/site-library/:${R_LIBS_SITE}:/usr/lib/R/library"*
after *R_LIBS_SITE=${R_LIBS_SITE:-'%S'}* seems to solve my problem. So my
/etc/R/Renviron in specified place now looks like this
R_LIBS_USER=${R_LIBS_USER:-'%U'}
R_LIBS_SITE=${R_LIBS_SITE:-'%S'}
R_LIBS_SITE="/usr/local/lib/R/site-library/:${R_LIBS_SITE}:/usr/lib/R/library"
On Mon, Apr 25, 2022 at 11:00 PM Dirk Eddelbuettel <edd at debian.org> wrote:
So in short: If you want to run R with --vanilla you have to change the
local set up file. Because R now ships with this
R_LIBS_USER=${R_LIBS_USER:-'%U'}
R_LIBS_SITE=${R_LIBS_SITE:-'%S'}
you could set R_LIBS_USER and/or R_LIBS_SITE in a file read by the OS
before
R starts -- a short text snippet in /etc/profile.d/ may work -- to ensure
R_LIBS_USER and R_LIBS_SITE are set to your liking.
Sorry for missing the hint about --vanilla from your first email.
Dirk
--
dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
Best regards,
Sam
[[alternative HTML version deleted]]