R 3.5 Is Not Available for Linux

R 3.5 is not available for linux

Do you know the reason why the latest R is not available for Linux?

Because we are volunteers.

Moreover, R 3.5 breaks the binaries of R 3.4.* and older so we have to rebuild everything first. That is work in progress (for what is mirrored at CRAN).

For Debian proper, I of course uploaded the new packages the morning of the release (as you can see in the ChangeLog) but we are now in a so-called transition where all packages need to be rebuild (which you can monitor via this tracker).

I am thinking of making interim packages available somewhere else. But I would have to find the time to build them first too.

Edit: I expanded a little in this r-sig-debian mailing list post.

Edit 2: Please see the update status described here (and same text here).

Ubuntu 18.4 install R language 3.5

Add the key before the adding the repo.

Also you need the && after every command to chain them all.
I prefer to use ; after set -uex for long chains so I can easily see which command output is coming from, particularly when it fails.

RUN set -uex; \
    apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9; \
    add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/'; \
    apt-get update; \
    apt-get install -y r-base; \
    rm -rf /var/lib/apt/lists/*

How should I deal with package 'xxx' is not available (for R version x.y.z) warning?

1. You can't spell

The first thing to test is have you spelled the name of the package correctly? Package names are case sensitive in R.

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2. You didn't look in the right repository

Next, you should check to see if the package is available. Type

setRepositories()

See also ?setRepositories.

To see which repositories R will look in for your package, and optionally select some additional ones. At the very least, you will usually want CRAN to be selected, and CRAN (extras) if you use Windows, and the Bioc* repositories if you do any biological analyses.

To permanently change this, add a line like setRepositories(ind = c(1:6, 8)) to your Rprofile.site file.

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3. The package is not in the repositories you selected

Return all the available packages using

ap <- available.packages()

See also Names of R's available packages, ?available.packages.

Since this is a large matrix, you may wish to use the data viewer to examine it. Alternatively, you can quickly check to see if the package is available by testing against the row names.

View(ap)
"foobarbaz" %in% rownames(ap)

Alternatively, the list of available packages can be seen in a browser for CRAN, CRAN (extras), Bioconductor, R-forge, RForge, and GitHub.

Another possible warnings message you may get when interacting with CRAN mirrors is:

Warning: unable to access index for repository

Which may indicate the selected CRAN repository is currently be unavailable. You can select a different mirror with chooseCRANmirror() and try the installation again.

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There are several reasons why a package may not be available.

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4. You don't want a package

Perhaps you don't really want a package. It is common to be confused about the difference between a package and a library, or a package and a dataset.

A package is a standardized collection of material extending R, e.g. providing code, data, or documentation. A library is a place (directory) where R knows to find packages it can use

To see available datasets, type

data()

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5. R or Bioconductor is out of date

It may have a dependency on a more recent version of R (or one of the packages that it imports/depends upon does). Look at

ap["foobarbaz", "Depends"]

and consider updating your R installation to the current version. On Windows, this is most easily done via the installr package.

library(installr)
updateR()

(Of course, you may need to install.packages("installr") first.)

Equivalently for Bioconductor packages, you may need to update your Bioconductor installation.

source("http://bioconductor.org/biocLite.R")
biocLite("BiocUpgrade")

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6. The package is out of date

It may have been archived (if it is no longer maintained and no longer passes R CMD check tests).

In this case, you can load an old version of the package using install_version()

library(remotes)
install_version("foobarbaz", "0.1.2")

An alternative is to install from the GitHub CRAN mirror.

library(remotes)
install_github("cran/foobarbaz")

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7. There is no Windows/OS X/Linux binary

It may not have a Windows binary due to requiring additional software that CRAN does not have. Additionally, some packages are available only via the sources for some or all platforms. In this case, there may be a version in the CRAN (extras) repository (see setRepositories above).

If the package requires compiling code (e.g. C, C++, FORTRAN) then on Windows install Rtools or on OS X install the developer tools accompanying XCode, and install the source version of the package via:

install.packages("foobarbaz", type = "source")

# Or equivalently, for Bioconductor packages:
source("http://bioconductor.org/biocLite.R")
biocLite("foobarbaz", type = "source")

On CRAN, you can tell if you'll need special tools to build the package from source by looking at the NeedsCompilation flag in the description.

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8. The package is on GitHub/Bitbucket/Gitorious

It may have a repository on GitHub/Bitbucket/Gitorious. These packages require the remotes package to install.

library(remotes)
install_github("packageauthor/foobarbaz")
install_bitbucket("packageauthor/foobarbaz")
install_gitorious("packageauthor/foobarbaz")

(As with installr, you may need to install.packages("remotes") first.)

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9. There is no source version of the package

Although the binary version of your package is available, the source version is not. You can turn off this check by setting

options(install.packages.check.source = "no")

as described in this SO answer by imanuelc and the Details section of ?install.packages.

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10. The package is in a non-standard repository

Your package is in a non-standard repository (e.g. Rbbg). Assuming that it is reasonably compliant with CRAN standards, you can still download it using install.packages; you just have to specify the repository URL.

install.packages("Rbbg", repos = "http://r.findata.org")

RHIPE on the other hand isn't in a CRAN-like repository and has its own installation instructions.

Install latest version of R with all the packages on Ubuntu 16.04

You have to install the newest version of R from a different PPA:

1. Add the PPA:

Currently, there are two different ones. For R 3.5 and above:

sudo add-apt-repository "deb [arch=amd64,i386] https://cran.rstudio.com/bin/linux/ubuntu $(lsb_release -cs)-cran35/"

And one for R 3.4 (obviously the newer version is recommended):

sudo add-apt-repository "deb [arch=amd64,i386] https://cran.rstudio.com/bin/linux/ubuntu $(lsb_release -cs)/"

2. Next, you need to add R to your keyring.

sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9

3. Update apt and install R (or r-base-dev if you wish to compile packages from source):

sudo apt-get update && sudo apt-get install r-base

4. (optional) install RStudio via gdebi:

sudo apt-get install gdebi-core
wget https://download1.rstudio.org/desktop/xenial/amd64/rstudio-1.2.5019-amd64.deb
sudo gdebi -n rstudio-1.2.5019-amd64.deb
rm rstudio-1.2.5019-amd64.deb

Steps are from this PDF.

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