R installation and setup (Linux and Emacs)
Uninstalling R
Lets start here.
$ R
> .libPaths()
Delete these folders that you see as output,
sudo apt-get remove r-base-core
sudo apt-get remove r-base
sudo apt-get autoremove
sudo apt-get purge r-base
sudo apt-get purge r-base-dev
sudo apt-get purge r-base-core
sudo apt-get purge r-base-recommended
Just found this somewhere, not sure if this is needed. But I did it.
Installing R 3.5 for Ubuntu 16.10
sudo apt-get install r-base
This installs R version 3.2.3. But the latest version is 3.5. But it appears as of jun 10 that problematic (stack answer). Might be unstable!!! If this is the first time you are installing R then follow below.
It installs 3.2 because that’s the default in the Ubuntu 16.04 repository. If you want the most up to date version of R for Ubuntu it’s best to follow the instructions at the cran page for R on Ubuntu. - stack
Based on cran page for R on Ubuntu && Stack: add deb
https://cloud.r-project.org/bin/linux/ubuntu xenial-cran35/ to
/etc/apt/sources.list. Run the following commands:
sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys
E084DAB9
sudo apt-get update
sudo apt-get install r-base
R --version
That is it. If that didn’t go right, go to the section ‘re-installing R for Ubuntu 16.10’
Installing R-studio
Its a yak shave to install it due to the Gstreamer dependency. But thanks to the Mike Williamson and his blog and the further answer in stack, it was a very smooth install for Ubuntu 16.10 as per this stack answer.
Preparing to install R Studio
sudo apt install libjpeg62
Specifically installing for Ubuntu 16.10 (For other versions refer to the stack answer):
wget --tries=3 --timeout=120 http://ftp.ca.debian.org/debian/pool/main/g/gstreamer0.10/libgstreamer0.10-0_0.10.36-1.5_amd64.deb
wget --tries=3 --timeout=120 http://ftp.ca.debian.org/debian/pool/main/g/gst-plugins-base0.10/libgstreamer-plugins-base0.10-0_0.10.36-2_amd64.deb
sudo dpkg -i libgstreamer0.10-0_0.10.36-1.5_amd64.deb
sudo dpkg -i libgstreamer-plugins-base0.10-0_0.10.36-2_amd64.deb
sudo apt-mark hold libgstreamer-plugins-base0.10-0
sudo apt-mark hold libgstreamer0.10
Installing R Studio
wget --tries=3 --timeout=120 https://download1.rstudio.org/rstudio-xenial-1.1.383-amd64.deb
sudo dpkg -i rstudio-*-amd64.deb
rstudio
Thats it!
Note:
i386 refers to the 32-bit edition and amd64 (or x86_64) refers to the 64-bit edition for Intel and AMD processors.- stack
Re-Installing R 3.4 for Ubuntu 16.10
But the latest version is 3.5. But it appears as of jun 10 that it
could be problematic (stack answer). I didn’t have problems
until I had to install xlsx and then shit went south that all other
packages got fucked.I thought I had problems and took on a path of
multiple installing and uninstalling, when the syntax for
xmlTreeParse was wrong from my side. Without realizing this (much
later), I went for R 3.4 only!
sudo apt-get install r-base
It installs 3.2 because that’s the default in the Ubuntu 16.04 repository. If you want the most up to date version of R for Ubuntu it’s best to follow the instructions at the cran page for R on Ubuntu. - stack
Based on cran page for R on Ubuntu && Stack: add deb
https://cloud.r-project.org/bin/linux/ubuntu xenial/ to
/etc/apt/sources.list. Run the following commands:
sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys
E084DAB9
sudo apt-get update
sudo apt-get install r-base
It didn’t work for me for some reason. I got dependency error that looked something like this.
r-base : Depends: r-recommended (= 3.4.4-1xenial0) but it is not going to be installed
E: Unable to correct problems, you have held broken packages.
After hours of trying I stumbled on this stack page. This page didn’t have an answer but one of the comments took me to Unable to correct problems, you have held broken packages. From the answer here I tried (apparently aptitude will try harder to give us a solution! Amazing!):
sudo aptitude install r-base
This gave me these options
Keep the following packages at their current version:
1) r-base [Not Installed]
2) r-cran-foreign [Not Installed]
3) r-recommended [Not Installed]
Leave the following dependencies unresolved:
4) r-base-core recommends r-recommended
I didn’t know what leaving following dependencies meant so I said
n. Then I got another set of options:
The following actions will resolve these dependencies:
Install the following packages:
1) r-cran-foreign [0.8.69-1xenial0 (xenial)]
Thats it, it appears it also installed r-base-dev by
itself. Apparently according to the Cran page it is also needed
if we are going to use install-packages(), which we are.
R --version
All Good!
Now let’s see how the packages installation will go.
Setting up R with Emacs
R-bloggers, suggests to install package ESS and
ESS-smart-underscore and some other org and org-ref type of
packages. The org stuff seem to be unnecessary for me, so I skip them
for now. Further more r-bloggers link to their github repository
and the minimum-working-init-file for our reference.
The init-file linked above shows that we need to add require
ess-site. I don’t understand what it is and why we need it. I stick
to installing the required packages ESS and
ESS-smart-underscore. This can be manually installed with M-x
package-list-packages RET or you can add it to the init file. In my
case I add the packages to my package-init.el file which will
automatically install it. Furthermore the following is added to the
init.el based on r-bloggers-init-file:
;; Line numbers
(add-hook 'ess-mode-hook 'linum-mode)
This allows for line numbers during the usage of ESS.
Testing if the above works
Yes it works.
To get a console simply do:
M-x R
The setup we now want to have is R editor on the left and R console on
the right. Create testing.R file. Run C-x 3 to split the
window. Go to the other window (C-x 0). Open the console using M-x
R. The following command will run the file in the console:
C-c C-l
Toodles! Some more helpful configuration things are given in here. This shall be taken into account later if needed.
Writing R code
_ key is bound to <- by default in the ESS
mode. ESS-smart-underscore tries to overcome this issue (I have not
yet tested how).
Time taken to understand and install and procrastinate
1hr 35 mins.
Upgrading R 3.4.4 to next version for MASS library
From this stack answer made on may 18,
sudo nano /etc/apt/sources.list
deb https://cloud.r-project.org/bin/linux/ubuntu/ version/
gpg --keyserver keyserver.ubuntu.com --recv-key E084DAB9
gpg -a --export E084DAB9 | sudo apt-key add -
sudo apt-get update && sudo apt-get upgrade
It appears that R has already upgraded!
sudo apt-get install r-base-dev
Reading package lists... Done
Building dependency tree
Reading state information... Done
r-base-dev is already the newest version (3.6.0-1xenial).
r-base-dev set to manually installed.
The following packages were automatically installed and are no longer required:
cdbs libaio1 libevent-core-2.0-5 snapd-login-service
Use 'sudo apt autoremove' to remove them.
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Seemless integration into ESS emacs
But packages are missin!
But all packages are missin! BUT!!!!!
library(ggplot2)
NOT FOUND!
For this we follow the same guy on this answer!
Recover your old packages following the solution that best suits to you (see this). For instance, to recover all the packages (not only those from CRAN) the idea is:
– copy the packages from R-oldversion/library to R-newversion/library, (do not overwrite a package if it already exists in the new version!).
– Run the R command update.packages(checkBuilt=TRUE, ask=FALSE).
So we first look at .libPaths() in R to see where 3.6 packages are!
and we get
[2] "/usr/local/lib/R/site-library"
[3] "/usr/lib/R/site-library"
[4] "/usr/lib/R/library"
And found that /usr/lib/R/library has the packages of the current
folders of packages. I test many of them using library(MASS) for
example! It works!
When you ask to update packages (also install packages I think), it
puts in a different folder which is writable. I found 3.4 packages in
/home/eghx/R/x86_64-pc-linux-gnu-library/3.4 and 3.6 packages go
into /home/eghx/R/x86_64-pc-linux-gnu-library/3.6 when you
update.packages(checkBuilt=TRUE, ask=FALSE)
Conclusion
In conclusion, what needs to be done is,
sudo cp -rn R/x86_64-pc-linux-gnu-library/3.4/ggplot2 /usr/lib/R/library/ggplot2
for all folders
or
just copy paste from R/x86_64-pc-linux-gnu-library/3.4 to
R/x86_64-pc-linux-gnu-library/3.6. Do not replace any folders in 3.6
and then type in R
update.packages(checkBuilt=TRUE, ask=FALSE)
You will have a lot of warnings, maybe errors even. But thats how it’s going to be! But I guess it’s ok!