I am trying to figure out which version of R is currently being used by Rstudio. I changed the R version under: tools/global options/general/ R sessions/ R version.
But the version being used by the console seems not affected. I also tried restarting the R session under: Session/ Restart R. Running R.version in console prints the version 4.0.5 yet I have changed the version of R from global options.
here is a screenshot of what I see on Rsutio.
I have just installed some Perl modules locally in Ubuntu 18.04 LTS.
When calling them using the RStudio Server like this
system("perl -MBio::TreeIO -e 1")
I get the following error
Can't locate Bio/TreeIO.pm in #INC (you may need to install the Bio::TreeIO module) (#INC contains: /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.26.1 /usr/local/share/perl/5.26.1 /usr/lib/x86_64-linux-gnu/perl5/5.26 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.26 /usr/share/perl/5.26 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base)
When I source ~/.bashrc in the terminal everything's ok.
I tried creating a ~/.Rprofile containing:
system(". ~/.bashrc")
but no good.
According to the documentation, accessed by running help(Startup) in the R shell, you should create a file .Renviron in your home directory which will be read when starting up a new R session. For example:
.Renviron
FOOBAR=/foo/bar/foo/bar
R shell
R
R version 3.2.3 (2015-12-10) -- "Wooden Christmas-Tree"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
...
> cat(Sys.getenv("FOOBAR"), "\n")
/foo/bar/foo/bar
So just create your .Renviron file with the PERL5LIB variable set to your local perl package installation directory.
R is hanging and freezing when I try to save as, happens on scripts and graphics files. R is running:
R version 3.4.3 (2017-11-30) -- "Kite-Eating Tree"
This error message happens every time I try to save as, aswell.
objc[7900]: Class FIFinderSyncExtensionHost is implemented in both
/System/Library/PrivateFrameworks/FinderKit.framework/Versions/A/FinderKit
(0x7fffa33dfb68) and
/System/Library/PrivateFrameworks/FileProvider.framework/OverrideBundles/FinderSyncCollaborationFileProviderOverride.bundle/Contents/MacOS/FinderSyncCollaborationFileProviderOverride
(0x10993bcd8). One of the two will be used. Which one is undefined.
Have tried to use things like running R from bash like suggested in other answers to R hanging but this doesn't help.
I am attempting to compile my R package, and realized that I have multiple versions of R installed on my mac, which is giving me difficulty. When I run 'which R' from terminal, I receive this:
Home$ which R
/Users/Home/anaconda2/bin/R
Home$ R
R version 3.2.2 (2015-08-14) -- "Fire Safety"
However, when I launch RStudio from my applications folder, and type 'version' in the console, I get this:
> version
_
platform x86_64-apple-darwin13.4.0
arch x86_64
os darwin13.4.0
system x86_64, darwin13.4.0
status
major 3
minor 3.2
year 2016
month 10
day 31
svn rev 71607
language R
version.string R version 3.3.2 (2016-10-31)
nickname Sincere Pumpkin Patch
So I have 3.3.2 on RStudio (the version I want for compiling my package), and 3.2.2 from anaconda being launched in terminal when I type R in terminal.
How can I fix this? Do I have to change my path to find the correct version of R when I launch from terminal? How do I find the correct path?
Thanks!
I bet anaconda has just inserted its path at the front of your PATH variable and is overriding your newer 3.3.2 version at the terminal. If you want your 'RStudio' version to be the default version that pops up at your terminal when you type 'R', then you gotta modify your PATH. No biggie.
First, figure out which R version RStudio points to. Type the following into your RStudio console:
Sys.which("R")
I bet you'll see something like /usr/local/bin/R. So that's what you have to add to the front of your PATH (minus the '/R').
To confirm that anaconda has messed you up, open up your terminal and check out your PATH:
echo $PATH
You'll probably see /Users/YOURNAME/anaconda2/bin as the first entry in your PATH, and further down you'll see /usr/local/bin. We have to flip this order. There are a million ways to fix this. Here's the quick and dirty solution -- add the following to the bottom of your .bash_profile
export PATH="/usr/local/bin:$PATH"
And type R --version in your terminal to confirm that your default R has changed.
You might get fancy later with sed or awk if having two /usr/local/bin entries in your PATH annoys you (as it would me).
First go to the directory /Library/Frameworks/R.framework/Versions
Here you should see various versions of R that you have installed.
To change to say version 3.4 use the following sequence of commands in the Terminal:
cd /Library/Frameworks/R.framework/Versions
unlink Current
ln -s 3.4 Current
I highly recommend RSwitch. It's a tiny program that allows you to select from any installed R version, press one button, restart your R session and you'll be using the selected R version.
In order to load R with a functional rJava, I need to run R CMD javareconf first. This works if I run R from the shell, but I want to run it in ESS. How can I get ESS (that is, M-x R) to run with the effects of the javareconf?
System information:
OpenSUSE 12.2 x 64
Emacs version 24.2.1
R patched: 3.0.1 "Good Sport"