Archive

Posts Tagged ‘install’

apt-get: install software/packages in specific version

February 5, 2018 Leave a comment

Sometimes there is a need to install a specific version of software for it to be compatible to other software, already have certain bug fixed, or because we need specific features. And sometimes there are multiple versions of the software available in the repos of your Linux machine, which allows for selecting the version that you want to have instead of just installing the default version. With apt this is possible – however, be careful to not install incompatible versions of software that causes conflicts with other things on your machine.

We are now going to demonstrate installing a specific version of fish, the user friendly interactive shell. At the time of writing there is only version 2.2.0.3 available in the Ubuntu 16.04.3 repositories, but we need at least version 2.3.x, as this is where fish became compatible to fzf, the fuzzy command-line finder (which is a very helpful tool btw). At the time of writing the latest version of fish in the Ubuntu PPA of fish 2.x is 2.7.x. We therefore at first need to add its PPA to make the version we need available to apt:

sudo apt-add-repository ppa:fish-shell/release-2
sudo apt-get update
sudo apt-get install fish

Now, to see all versions of the desired package available for installation on your machine with apt execute:

apt-cache madison fish

In our example we see:

fish | 2.7.0-1~xenial | http://ppa.launchpad.net/fish-shell/release-2/ubuntu xenial/main amd64 Packages
fish |    2.2.0-3 | http://fi.archive.ubuntu.com/ubuntu xenial/universe amd64 Packages

We can also look at some more details with:

apt-cache policy fish

In our example we see:

fish:
  Installed: (none)
  Candidate: 2.7.0-1~xenial
  Version table:
     2.7.0-1~xenial 500
        500 http://ppa.launchpad.net/fish-shell/release-2/ubuntu xenial/main amd64 Packages
     2.2.0-3 500
        500 http://fi.archive.ubuntu.com/ubuntu xenial/universe amd64 Packages
        100 /var/lib/dpkg/status

where 2.7.0-1~xenial is the exact identifier of the version we want to install for our scenario. We can now install this version using apt by setting the additional SW parameter:

sudo apt-get install SW=version

which in case of our example is:

sudo apt-get install fish=2.7.0-1~xenial

Done!

Install R from source: a simple way to compile R from source and use it in RStudio or on servers without X

Sometimes we need to use special versions of R (e.g. the latest version of R is not available in the repositories of the machine we need to use). This post describes a simple way of compiling R from sources and using it in RStudio or on servers without X.

Get latest R source

Get the source of your desired R version from https://www.r-project.org/. You want to obtain a file named R.x.y.z.tar from there and untar it using tar -xf R-x.y.z.tar.gz. Change into the untar-ed folder then.

More details on this are available at https://cran.r-project.org/doc/manuals/r-release/R-admin.html#Getting-and-unpacking-the-sources

Build R from source for RStudio

Built R using the following commands. Be aware that there are a number of prerequisites to this compilation, like having gcc and g++ installed.

./configure --enable-R-shlib
make
make check
make check-all

 

Passing the checks creates the R and Rscript frontends in ./bin/ — those are what you most likely need. You can call these directly, link to them, or use them in RStudio (see below). If you forgot to add the –enable-R-shlib parameter to configure you need to delete and re-extract the tar before redoing the process — otherwise make will fail.

More details on this are available at https://cran.r-project.org/doc/manuals/r-release/R-admin.html#Simple-compilation

Define the R to use with RStudio

RStudio uses the R defined by which R. Hence we can add the following to the ~/.profile file to define which R is used by RStudio:

# export RSTUDIO_WHICH_R=/path/to/your/R # this is what RStudio usually uses
export RSTUDIO_WHICH_R=/usr/local/bin/R  # this is what we use
. ~/.profile # reloads the profile without requiring us to logout+login again

More details on this are available at https://support.rstudio.com/hc/en-us/articles/200486138-Using-Different-Versions-of-R

Build R for environments without X/without Java

Do the same steps as above, but use this configure instead:

./configure --with-x=no --disable-java

More details on this are available at https://cran.r-project.org/doc/manuals/r-release/R-admin.html#Essential-programs-and-libraries

Hint for “package not available for R version x.z.y…” errors

If package installations fail because your repositories don’t contain the required SW, try the Berkeley mirror: from our experience, they host lots of packages in many versions. For example:

install.packages("ggplot2", repos="http://cran.cnr.berkeley.edu")

Alternatively, the URL to the source archive can be specified directly:

packageurl <- "http://cran.r-project.org/src/contrib/Archive/XXXX/XXXX_A.B.C.tar.gz"
install.packages(packageurl, contriburl=NULL, type="source")

More details on this are available at http://stackoverflow.com/questions/17998543/what-to-do-when-a-package-is-not-available-for-our-r-version

Yet another option is to use devtools to fetch code e.g. directly from GitHub:

devtools::install_github("hadley/lineprof")

More details on this example can be found at http://adv-r.had.co.nz/Profiling.html

 

Categories: Data Analysis Tags: , , , , , , ,