I want to be able to install the latest stable R release for Ubuntu 18.04, I had the ubuntu version installed and so I removed it and then followed several guides like in this link.
No matter what I do I get the following output when I issue a sudo apt-get install r-base:
sudo apt install r-base
Reading package lists... Done
Building dependency tree
Reading state information... Done
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:
The following packages have unmet dependencies:
r-base : Depends: r-base-core (>= 3.6.1-3disco) but it is not going to be installed
Depends: r-recommended (= 3.6.1-3disco) 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.
What's wrong?
Related
I was having trouble with R packages so I decided to uninstall to do fresh install. Now I cannot even re-install R. I am using Linux Mint. what I did is:
Removed all directories found with .libPaths()
And in the terminal:
sudo apt-get remove r-base-core
sudo apt-get remove r-base
sudo apt-get autoremove
Now when I try to install R following https://cran.r-project.org/ tutorial, I get many errors:
sudo apt update -qq
E: The repository 'https://cloud.r-project.org/bin/linux/ubuntu una-cran40/ Release' does not have a Release file.
apt install --no-install-recommends r-base
Reading package lists... Done
Building dependency tree
Reading state information... Done
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:
The following packages have unmet dependencies:
r-base : Depends: r-recommended (= 3.6.3-2) but it is not going to be installed
E: Unable to correct problems, you have held broken packages.
apt install r-recommended
Reading package lists... Done
Building dependency tree
Reading state information... Done
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:
The following packages have unmet dependencies:
r-recommended : Depends: r-cran-foreign (>= 0.7-2) but it is not going to be installed
E: Unable to correct problems, you have held broken packages.
apt install r-cran-foreign
Reading package lists... Done
Building dependency tree
Reading state information... Done
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:
The following packages have unmet dependencies:
r-cran-foreign : Depends: r-base-core (>= 4.0.0-1.2004.0) but 3.6.3-2 is to be installed
Depends: r-api-4.0 but it is not installable
E: Unable to correct problems, you have held broken packages.
Does anyone have a good approach to installing R on Ubuntu 20.04? I can't seem to find a solution for this specific to 20.04 focal through apt.
No LSB modules are available.
Distributor ID: Ubuntu
Description: Ubuntu 20.04 LTS
Release: 20.04
Codename: focal
Edit: after going through the link here and adding the entry to sources.list, I ran into issues with dependencies:
Reading package lists... Done
Building dependency tree
Reading state information... Done
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:
The following packages have unmet dependencies:
r-base : Depends: r-base-core (>= 4.0.2-1.2004.0) but it is not going to be installed
Depends: r-recommended (= 4.0.2-1.2004.0) 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.
Per #DirkEddelbuettel's comment, I ran sudo apt install r-base-core r-recommended r-base-html to see next level dependencies:
Reading package lists... Done
Building dependency tree
Reading state information... Done
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:
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
Depends: liblapack3 but it is not installable or
liblapack.so.3 but it is not installable
Depends: libtcl8.6 (>= 8.6.0) but it is not installable
Depends: libtk8.6 (>= 8.6.0) but it is not installable
Recommends: r-base-dev but it is not going to be installed
Recommends: r-doc-html but it is not going to be installed
r-recommended : Depends: r-cran-kernsmooth (>= 2.2.14) but it is not going to be installed
Depends: r-cran-mgcv (>= 1.1.5) but it is not going to be installed
Depends: r-cran-rpart (>= 3.1.20) but it is not going to be installed
Depends: r-cran-survival (>= 2.13.2-1) but it is not going to be installed
Depends: r-cran-matrix but it is not going to be installed
E: Unable to correct problems, you have held broken packages.
There was a more underlying issue when I worked on trying to install r-base. I ended up finding out that I had problems with unmet dependencies after adding a PPA. I used this link here to fix the underlying problem of unmet dependencies, which in turn allowed me to apt install and not have any issues installing.
Here is what I do in the Rocker container r-ubuntu for the 20.04 image:
Install software-properties-common to be able to say add-apt-repository
Add the rrutter4.0 PPA for R itself (same as CRAN)
add-apt-repository --enable-source --yes "ppa:marutter/rrutter4.0"
Add the c4d4u.teams repo for over 4k CRAN packages:
add-apt-repository --enable-source --yes "ppa:c2d4u.team/c2d4u4.0+"
Run apt install r-base (and a few more).
In a narrow sense you only need 2 (as you likely do not 1 on a full Ubuntu system) and 4 but you may as well do 3.
You can of course also just to docker pull rocker/r-ubuntu:20.04 and get that container pre-made, but I use both: a container for tests, and these settings on my 20.04 machine(s).
Prerequisites
You will need an Ubuntu 20.04 with:
at least 1GB of RAM
a root user / non-root user with sudo privileges
Installing R
Because R is a fast-moving project, the latest stable version isn’t always available from Ubuntu’s repositories, so we’ll start by adding the external repository maintained by CRAN.
Note: CRAN maintains the repositories within their network, but not all external repositories are reliable. Be sure to install only from trusted sources.
Let’s first add the relevant GPG key.
sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
Note that if you’re not using 20.04, you can find the relevant repository from the R Project Ubuntu list, named for each release. Ubuntu 20.04 is referred to as Focal Fossa, and the most recent version of R is 4.0.0, hence the naming convention of the repository below — focal-cran40.
sudo add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/'
Now, we’ll need to run update after this in order to include package manifests from the new repository.
sudo apt update
At this point, we’re ready to install R with the following command.
sudo apt install r-base
If prompted to confirm installation, press y to continue.
Finally get into R shell-
sudo -i R
This confirms that we’ve successfully installed R and entered its interactive shell.
Recently I had to update R from 3.4.4 to 3.5 for installing bioconductor packages. For doing that I followed the steps on this link.
But now I have the problem that r studio do not work for the problem:
R shared library (/usr/local/lib/R/lib/libR.so) not found. If this is
a custom build of R, was it built with the --enable-R-shlib option?
For that reason I tried to reinstall R 3.4.4 with the command:
sudo apt-get install r-base
But it returns me this error:
Reading package lists... Done
Building dependency tree
Reading state information... Done
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:
The following packages have unmet dependencies:
r-base : Depends: r-recommended (= 3.5.1-2xenial) but it is not
going to be installed
E: Unable to correct problems, you have held broken packages.
Does anyone know how to remove completely R (3.5) and installing again the 3.4 version?
Thank you all.
Edit: R works on command line with the 3.5 version and I cannot install other packages like:
$ sudo apt-get install libgdal-dev
Reading package lists... Done
Building dependency tree
Reading state information... Done
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:
The following packages have unmet dependencies:
libgdal-dev : Depends: libarmadillo-dev but it is not going to be installed
Depends: libdap-dev but it is not going to be installed
Depends: libgeotiff-dev but it is not going to be installed
Depends: libgif-dev but it is not going to be installed
Depends: libhdf4-alt-dev but it is not going to be installed
Depends: libhdf5-dev but it is not going to be installed
Depends: libjpeg-dev
Depends: libmysqlclient-dev but it is not going to be installed
Depends: libnetcdf-dev but it is not going to be installed
Depends: libpoppler-private-dev but it is not going to be installed
Depends: libpq-dev but it is not going to be installed
Depends: libtiff-dev
Depends: libxml2-dev but it is not going to be installed
E: Unable to correct problems, you have held broken packages.
I'm trying to install R from the terminal following this site:
https://www.r-bloggers.com/how-to-install-r-on-linux-ubuntu-16-04-xenial-xerus/
When I execute sudo apt-get install r-base, I get the following error:
Reading package lists... Done
Building dependency tree
Reading state information... Done
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:
The following packages have unmet dependencies:
r-base : Depends: r-base-core (>= 3.3.2-1xenial0) but it is not going to be installed
Depends: r-recommended (= 3.3.2-1xenial0) 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.
Add the two others to the command, and see the errors it generates, ie do
sudo apt-get install r-base r-base-core r-recommended
You likely you have something installed which conflicts. Many (and I mean thousands) of us run these packages just fine.
You can also consider the r-sig-debian mailing list.
I keep getting this error when trying to install R
sudo apt-get install r-base
Reading package lists... Done
Building dependency tree
Reading state information... Done
Some packages could not be installed. This may mean that you have
requested an impossible situation or if you are using the unstable
distribution that some required packages have not yet been created
or been moved out of Incoming.
The following information may help to resolve the situation:
The following packages have unmet dependencies:
r-base : Depends: r-base-core (>= 3.2.0-3trusty) but it is not going to be installed
Depends: r-recommended (= 3.2.0-3trusty) 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 one knows how to solve this?
Try installing all at once
sudo apt-get install r-base r-base-core r-recommended r-base-html
but from your description is not clear how you manage to get into this situation in the first place. This should not happen under normal use.