I tried to install R 4.1 on a newly set-up Ubuntu 20.04. After some struggle with the repositories and keys, I chose to install from source.
Visited https://www.r-project.org/ to download latest version of R. Ran ./configure multiple times to note the requirement of various libraries which you may note as follows. I am hoping this will save significant amount of time for anyone intending to build from source. Suggestions welcome for speeding up the process or better solution. However my intention is to share entire set of libraries that I had to install on a naked installation of 20.04 on which the very first package I tried to install was R 4.1 (from source).
Directory where you downloaded the tar.gz (e.g. R-4.1.2.tar.gz in my case)
cd Downloads
Untar
tar -xvzf R-4.1.2.tar.gz
Enter directory
cd R-4.1.2
As root
sudo su
Try validating configuration (encountered many errors throughout and following libraries were installed)
./configure
Installed various libraries:
apt-get install build-essential
apt-get install gfortran
apt-get install fort77
apt-get install libreadline-dev
apt-get install xorg-dev
apt-get install liblzma-dev libblas-dev
apt-get install gcc-multilib
apt-get install libbz2-dev
apt-get install libpcre2-dev
apt-get install libcurl4-openssl-dev
apt install default-jdk
make
make install
The above set worked for me and I am hopeful it may be of help.
Related
The problem:
I'm trying to install the devtools package for R. I'm using Ubuntu 18.04 LTS on WSL, the Windows Subsystem for Linux.
I'm able to install some packages just fine with a simple call to install.packages() from within R on WSL. However, other packages seem to give me trouble.
None of the following methods I've tried seem to work:
* I've tried installing the package with install.packages().
* I've tried installing from source into /usr/local/lib/R/site-library.
* I've tried installing from source into a personal library.
Error message:
I was recieving an error message like that discussed here, but I was unable to fix the problem by editing unpackPkgZip because it didn't exist.
The Question:
How can I install devtools on WSL?
Solution:
I was able to fix the problem by starting over. I uninstalled Ubuntu and then reinstalled it. With a fresh install of Ubuntu 18.04 I followed these instructions. There are other online tutorials which probably work just fine, but I followed this one. You can ignore the bit about installing an rstudio server and the fsl package if you wish.
# Install R on WSL
sudo apt-get update -qq -y
sudo apt-get install -y wget git
OS_DISTRIBUTION=$(lsb_release -cs)
wget -O- http://neuro.debian.net/lists/${OS_DISTRIBUTION}.us-nh.full | sudo tee /etc/apt/sources.list.d/neurodebian.sources.list
sudo apt-key adv --recv-keys --keyserver hkp://pool.sks-keyservers.net:80 0xA5D32F012649A5A9
sudo apt-get update
sudo apt-get install libopenblas-base r-base
sudo apt-get update -qq -y
sudo apt-get install -y libgit2-dev
sudo apt-get install -y libcurl4-openssl-dev libssl-dev
sudo apt-get install -y zlib1g-dev libssh2-1-dev libpq-dev libxml2-dev
#sudo apt-get install -y libhdf5 # This didn't work.
Now try installing devtools in R.
# Install devtools
install.packages("devtools", repos = "https://cran.rstudio.com/")
Permission error:
If you encounter a permission error like the following...
Warning in install.packages("edgeR") :'lib = "/usr/local/lib/R/site-library"' is not writable Would you like to use a personal library instead? (y/n)
...you need to provide the user with write access to the directory where R packages are installed (see here). Try changing the group ownership of this directory:
# Who has ownership of /usr/local/lib/R/site-library/?
ls -l /usr/local/lib/R/
# drwxrwsr-x 1 root staff 512 Jul 18 21:38 site-library
# Change ownership.
sudo chgrp twesleyb /usr/local/lib/R/site-library/
ls -l /usr/local/lib/R/
#drwxrwxr-x 1 root twesleyb 512 Jul 18 21:38 site-library
# In this case I have write access, but in case you need to add it, try:
# $ sudo chmod g+w /usr/local/lib/R/site-library
You should now be able to install.packages("package").
I'm a linux novice, but I think this is an okay thing to do.
Update:
You can also try following duckmayr's instructions.
I am getting this error and i have tried every other solution related to this given on stackoverflow but still not able to install the package.Please suggest a solution.And how can i install any R package using source on linux?
You can try the following:
In shell:
sudo yum install -y epel-release
sudo yum install glibc-common
sudo yum install -y rpm-build make wget tar libxml2-devel
In R:
install.packages('xml2')
Instructions are adapted from https://github.com/opencpu/opencpu-server/tree/master/rpm#readme
Please let me know if it works.
Is there any way to have apt install a package from a specific launchpad repository?
I would like to set up a little test server and install all of the 1000+ r-cran-* packages from the cran2deb4ubuntu launchpad repository. As of last month, all packages in this repository are build for R 3.0.1. So I install a copy of R 3.0.1 and then do:
sudo add-apt-repository marutter/c2d4u
sudo apt-get update
sudo apt-get install r-cran-*
However, this will also install all of the r-cran-* packages form universe which are build for R 2.15, and hence will fail to load. Is there an easy way to install the packages only from c2d4u? Or alternatively, is there a way to blacklist the r-cran- packages in universe from apt?
What I ended up doing is simply install all packages and then remove the ones with an old build. I.e.
sudo add-apt-repository ppa:marutter/c2d4u -y
sudo add-apt-repository ppa:marutter/rrutter -y
sudo apt-get update
sudo apt-get install r-bioc-*
sudo apt-get install r-cran-
And then in R:
which(installed.packages()[,"Built"] < 3.0)
I am newbie to both Ubuntu and R.
I am trying to install R 2.15.2 on ubuntu. Since the latest version of R is 3.0.X, I specified the version in /etc/apt/sources.list
deb http://cran.ma.imperial.ac.uk/bin/linux/ubuntu precise 2.15.2
Then I ran sudo apt-get install r-base.
It installs, but when I check version, it is 2.14.1, not 2.15.2
I tried to specify version in command line, such as:
sudo apt-get install r-base_2.15.2_1precision1
Always seeing:
E: Unable to locate package r-base_2.15.2_1precision1.
E: Couldn't find any package by regex 'r-base_2.15.2_1precision1'
Any suggestion? Thanks.
If I run command:
sudo apt-get install r-base=2.15.2-1precise0
See the following message:
The following packages have unmet dependencies:
r-base : Depends: r-recommended (= 2.15.2-1precise0) but 3.0.1-1precise0precise2 is to be installed
Recommends: r-base-html but it is not going to be installed
Find the solution.
I need to install like:
sudo apt-get install r-base-core=2.15.3-1precise0precise1
sudo apt-get install r-recommended=2.15.3-1precise0precise1
sudo apt-get install r-doc-html=2.15.3-1precise0precise1
sudo apt-get install r-base=2.15.3-1precise0precise1
Okay so the URL for where the packages are found has changed :^) on the cran.ma site:
Change the debian url to:
deb http://cran.ma.imperial.ac.uk/bin/linux/ubuntu precise/
do an apt-get update and try reinstalling
The complete instructions are on:
http://cran.ma.imperial.ac.uk/bin/linux/ubuntu/
I used aptitude install to install a package, Ubuntu 11.10 oneiric, that apparently I couldn't install because of dependencies. I removed a couple of more libraries while doing it. I uninstalled Rstudio but still can't install R on my machine. I'm on ubuntu and this is what I get while running
sudo apt-get install r-base
The following packages have unmet dependencies:
r-base : Depends: r-base-core (>= 2.15.3-1quantal0) but it is not going to be installed
Depends: r-recommended (= 2.15.3-1quantal0) but it is not going to be installed
Recommends: r-base-html but it is not going to be installed
E: Unable to correct problems, you have held broken packages.
any ideas how to start from scratch and get R running again?
More of the Error log:
The following packages have unmet dependencies r-base-core : Depends: libblas3 but it is not installable or libblas.so.3 but it is not installable or libatlas3-base but it is not installable Depends: libc6 (>= 2.15) but 2.13-20ubuntu5.3 is to be installed Depends: liblapack3 but it is not installable or liblapack.so.3 but it is not installable or libatlas3-base but it is not installable Depends: liblzma5 (>= 5.1.1alpha+20120614) but it is not installable –
Try this
If you have added a line from new ubuntu repository to /etc/apt/sources.list, erase the line.
Then, run the commands
sudo add-apt-repository ppa:marutter/rrutter
sudo apt-get update
sudo apt-get upgrade
It worked for me, the answer comes from here
http://r.789695.n4.nabble.com/Upgrading-on-Ubuntu-from-2-11-1-to-2-15-1-td4636965.html
Uninstall previous R installation:
sudo R --no-save
pkgList <- installed.packages(priority='NA')
remove.packages(pkgList)
q()
sudo apt-get remove --purge r-cran* r-base*
Follow instructions (for R part) from:
How to install R, JGR and Deducer in Ubuntu
To list what you installed with aptitude type the following
xyz#sxyzcom~$ sudo apt-get remove
This should list what remains of your R install and possibly anything else missing dependencies Then you can run
xyz#sxyzcom~$ sudo apt-get autoremove
and that should get you back to square one.
If you are facing problems regarding Broken packages then first of all remove that package by first checking dependencies and then forcefully remove that package, and don't ever forget to reboot when you do make enormous changes in your system. To remove that package use these shell commands
$ sudo su
Then Enter your password
# apt-cache rdepends package-name
# apt-get --purge remove --force package-name
Use these shell commands
# apt-get clean
# apt-get autoclean
# apt-get update
# apt-get upgrade
# apt-get dist-upgrade
# reboot
This worked for me, Try this, I believe this will fix all your problems, Good luck.
If you want to remove the package forcefully,you can do
sudo dpkg --remove --force-remove-reinstreq package_name
and then
sudo apt-get update