I attempted to update R on Ubuntu by adding the line
deb http://cran.cnr.berkeley.edu/bin/linux/ubuntu/ raring/
To my sources.list file in /etc/apt
However, this is path is not found, since the code 'raring' version of Ubuntu isn't listed as an option on the R updates for ubuntu page http://cran.cnr.berkeley.edu/bin/linux/ubuntu/
(my choices being lucid, precise, quantal, etc).
Which /bin/linux/ubuntu directory could I use for this update on the 'raring' version?
Related
I am using an Rstudio Server (0.98.490) on a CentOS machine, that uses the default installation in the machine which is an older version of R. I also have a newer version of R compiled elsewhere in the system. Can I, as a non-root user, tell Rstudio to use the new installation instead of the old one when I start a session?
I'm not sure if there are any peculiarities for CentOS, but I believe you should be able to change your ~/.profile or ~/.bash_profile file to include the following line: export RSTUDIO_WHICH_R=/path/to/desired/compiled/R.
You can see which version of R RStudio is currently running by entering which R into a terminal. the export command listed above should change it to your desired build.
These links might help:
https://support.rstudio.com/hc/en-us/articles/200486138-Using-Different-Versions-of-R
Running newer version of R from terminal when older version is invoked by default
Hope this helps
The first answer was relevant RStudio, not rstudio-server as the question asks. The question is addressed in the section "RStudio Desktop and RStudio Server Open-Source".
However, adding a line like export RSTUDIO_WHICH_R=/usr/local/bin/R to my ~/.profile and ~/.bash_profile does not actually seem to affect rstudio-server for me. So I am giving up for now. The Pro version seems to have other options, as listed here.
Starting in RStudio Server 1.3 (newest version is 1.4.1106, released February 22, 2021), a user’s preferred version of R can be specified in the rstudio-prefs.json file in the global-level /etc/rstudio folder or in the user-level ~/.config/rstudio folder.
See https://blog.rstudio.com/2020/02/18/rstudio-1-3-preview-configuration/ and https://docs.rstudio.com/ide/server-pro/session-user-settings.html for user setting options in newer versions of RStudio Server.
See https://support.rstudio.com/hc/en-us/articles/200716783-RStudio-Release-History for RStudio release history and https://www.rstudio.com/products/rstudio/download-server/redhat-centos/ for Red Hat downloads of the newest version of RStudio Server.
I completely uninstalled R Framework and R Studio from my Mac.
I moved the applications to trash, and also in terminal ran the following:
sudo rm -rf /Library/Frameworks/R.framework /Applications/R.app \
/usr/bin/R /usr/bin/Rscript
I then downloaded brand new (latest versions) of R and R Studio and installed them.
When I open R Studio again after re-installing, I expect a blank, new, default environment but instead all my tabs (open R and Rmd files) are still present and open in R Studio.
How can this be??
Also, the bug I'm trying to resolve with one of my packages is still persisting
I am using RStudio 0.99.489 on a Linux machine, and for me RStudio automatically saves user settings to ~/.rstudio-desktop, for example holding:
history: ~/.rstudio-desktop/history_database
files pane settings: pcs/files-pane.pper
Since user settings were not deleted then of course the next time you re-installed RStudio, RStudio follows these histories, pane settings etc again.
To have a completely default appearance, be sure you quit RStudio first, then delete it like:
$ rm -r ~/.rstudio-desktop
Then start RStudio and it should appear with the default appearance.
I removed all environment objects, cleared the workspace, uninstalled R Framework and R Studio, and restarted my computer. This seemed to fix the issue.
I think clearing the workspace was the key after trying a re-install several times.
$ rm -r ~/.rstudio-desktop as the other answer suggests is good to try as well.
I have downloaded and installed R.
I see it here in Applications folder (I am on a Mac with Yosemite):
Fine. I can launch R.app and indeed, yes, I am running the version I want, which is 3.2.2:
So far so good. I can even open up RStudio and see that I am indeed running 3.2.2!
So after all this, I simply go to my terminal, type
r
and turns out I am running 3.1.1!
I understand the old user of my work computer probably had installed this older version.
So here's what I'm wondering:
If I just installed R.app correctly, WHY is this old version still living on my computer, and how do I get rid of it?
If this is some sort of $PATH thing, WHY doesn't the most obvious location for an app, the Applications folder, get checked for the existence of R?
Thanks.
UPDATE
Turns out the old version of R has been installed by homebrew.
Typing which r in your terminal will give you where the shell thinks R is. Then, you need only uninstall it from that location.
Since we've determined it's homebrew, all you need to do now is brew unlink r; rm -Rf /usr/local/Cellar/r/3.1.1 and you should be golden after you rehash in your shell.
It worked because you installed it using homebrew. To remove it from the system, you must first unlink it and then remove it from the system.
I am working on a remote server using RStudio. This server has no access to the Internet. I would like to install the package "stringi." I have looked at this stackoverflow article, but whenever I use the command
install.packages("stringi_0.5-5.tar.gz",
configure.vars="ICUDT_DIR=/my/directory/for/icudt.zip")
It simply tries to access the Internet, which it cannot do. Up until now I have been using Tools -> Install Packages -> Install from Packaged Archive File. However, due to this error, I can no longer use this method.
How can I install this package?
If you have no internet access on local machines, you can build a distributable source package that includes all the required
ICU data files (for off-line use) by omitting some relevant lines in
the .Rbuildignore file. The following command sequence should do the trick:
wget https://github.com/gagolews/stringi/archive/master.zip -O stringi.zip
unzip stringi.zip
sed -i '/\/icu..\/data/d' stringi-master/.Rbuildignore
R CMD build stringi-master
Assuming the most recent development version is 1.3.1,
a file named stringi_1.3.1.tar.gz is created in the current working directory.
The package can now be installed (the source bundle may be propagated via
scp etc.) by executing:
R CMD INSTALL stringi_1.3.1.tar.gz
or by calling install.packages("stringi_1.3.1.tar.gz", repos=NULL),
from within an R session.
For a Linux machine the easiest way is from my point of view:
Download the release you need from Rexamine in tar.gz format to your local pc. In opposition to the version on CRAN it already contains the icu55\data\ folder.
Move the archive to your target linux machine without internet access
run R CMD INSTALL stringi-1.0-1.tar.gz (in case of release 1.0-1)
You provided the wrong value of configure.vars.
It indicates that you have to give the directory's name, not a final file name.
Correct your code to the following:
install.packages("stringi_0.5-5.tar.gz",
configure.vars="ICUDT_DIR=/my/directory/for/")
Regards,
Sean
Follow the steps below
Download icudt55l.zip seperately from server where you have internet access with
wget http://www.mini.pw.edu.pl/~gagolews/stringi/icudt55l.zip
Copy the downloaded packages to the server where you want to install stringi
Execute the following command
R CMD INSTALL --configure-vars='ICUDT_DIR=/tmp/ALL' stringi_1.1.6.tar.gz
icudt55l.zip is copied to /tmp/ALL
The suggestion from #gagolews almost worked for me. Here's what actually did the trick with RStudio.
Download the master.zip file that will save as stringi-master.zip.
Unzip the file onto your desktop. The unzipped folder should be stringi-master.
Edit the .Rbuildignore file by removing ^src/icu55/data and ^src/icu61/data or similar lines.
Move the folder from your desktop to the home directory of your server.
Create a New Project in RStudio with ~/stringi-master as the Existing Directory
From RStudio's menu, select Build and Build Source Package. (You may need to first select Configure Build Tools. For Project build tools choose Package then select OK.)
It should create a tar.gz file, in the following format: stringi_x.x.(x+1).tar.gz. For example, if the current version of stringi is 1.5.3, it will create version 1.5.4. (I received a few warnings that didn't seem to affect the outcome.)
Move the newly created package to your local repository. Update the repository index. And install the package.
I'm trying to get R to recognize that I have installed Rtools.exe. I've tried installing it in several different locations. However, whenever I restart R and load devtools I get the same error:
> library(devtools)
WARNING: Rtools is required to build R packages, but is not currently installed.
Please download and install Rtools 3.0 from http://cran.r-project.org/bin/windows
/Rtools/ and then run find_rtools().
Naturally, whenever I try the function find_rtools() I get the same error message. I'm done trying to figure this out with help files, as the devtools help doesn't offer much. I've tried installing in several of the locations returned by get_path() but the problem persists.
FYI, currently my R is installed at D:/R.
Has anyone else had this problem, and more importantly, can anyone help me?
I'm sorry if this is a duplicate, and I've tried to include as many relevant details as possible so if you need any clarification please let me know.
Thanks,
Nick
Grab the batch file Rpathset.bat from batchfiles, edit the SET statements in it appropriately and then run R like this from the Windows console:
Rpathset
Rgui
I ran into this issue running a Windows 7 machine without admin rights. I leveraged G. Grothendieck's response, with a few additional steps.
Get Rpathset.bat from https://code.google.com/p/batchfiles/
Edit the Set statements in Rpathset.bat to your paths
Run CMD and change directories to where Rpathset.bat is stored
In the command prompt, run rpathset.bat > mypath.txt
Open mypath.txt with a text editor
Click Windows Start and search for environment
Click Edit environment variables for your account
Click path and then edit
Copy and paste the entire path from mypath.txt into the Windows path (everything after the path statement)
Restart RStudio and check that devtools::find_rtools() is TRUE
This file rtools.r contains the code for find_rtools(). It looks like it is trying to find ls and gcc in your system path (and then does some more checks based on the version) and if that fails it tries to look up SOFTWARE\R-core\Rtools in the the Windows registry.
As Thomas mentioned here, "Rtools is not a package." This is what I did to install Rtools. My RStudio is running R version 3.1.3. So I downloaded Rtools31.exe from https://cran.r-project.org/bin/windows/Rtools/. I executed the exe file, selected all the default options in the Setup Wizard and installed. (I had admin privilege on the computer I was using but I am not sure if that makes any difference.) To check that it was properly installed, you can enter find_rtools() in the R prompt which should return TRUE if Rtools installed properly.
For R 3.0, you probably just need to download Rtools30.exe and follow the same steps above.
I ran into this problem trying to install Rtools33 to use Hadley Wickham's lineprof package. I got that error multiple times. I'm running Windows 7 on a laptop.
I was able to fix the problem by running the Rtools installation file as the windows Admin (i.e. right-click the Rtools33.exe and choose "Run as administrator")
I also made sure to point the path to the R source directory, which I kept in C:\Rtools\ (which contains C:\Rtools\bin\ and C:\Rtools\gcc-4.6.3\).
This solved the problem for me and I am now able to install lineprof from GitHub and make use of it.