How To Install r-cran-ape on Debian 9
Introduction
In this tutorial we learn how to install r-cran-ape on Debian 9.
What is r-cran-ape
r-cran-ape is:
This package provides functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from DNA sequences, reading and writing nucleotide sequences as well as importing from BioConductor, and several tools such as Mantel’s test, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path lengths and penalized likelihood, dating trees with non-contemporaneous sequences, translating DNA into AA sequences, and assessing sequence alignments. Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and several methods handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions call external applications (PhyML, Clustal, T-Coffee, Muscle, MAFFT) whose results are returned into R.
There are three methods to install r-cran-ape on Debian 9. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install r-cran-ape Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install r-cran-ape using apt-get by running the following command:
sudo apt-get -y install r-cran-ape
Install r-cran-ape Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install r-cran-ape using apt by running the following command:
sudo apt -y install r-cran-ape
Install r-cran-ape Using aptitude
If you want to follow this method, you might need to install aptitude first since aptitude is usually not installed by default on Debian. Update apt database with aptitude using the following command.
sudo aptitude update
After updating apt database, We can install r-cran-ape using aptitude by running the following command:
sudo aptitude -y install r-cran-ape
How To Uninstall r-cran-ape on Debian 9
To uninstall only the r-cran-ape package we can use the following command:
sudo apt-get remove r-cran-ape
Uninstall r-cran-ape And Its Dependencies
To uninstall r-cran-ape and its dependencies that are no longer needed by Debian 9, we can use the command below:
sudo apt-get -y autoremove r-cran-ape
Remove r-cran-ape Configurations and Data
To remove r-cran-ape configuration and data from Debian 9 we can use the following command:
sudo apt-get -y purge r-cran-ape
Remove r-cran-ape configuration, data, and all of its dependencies
We can use the following command to remove r-cran-ape configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge r-cran-ape
Dependencies
r-cran-ape have the following dependencies:
References
Summary
In this tutorial we learn how to install r-cran-ape package on Debian 9 using different package management tools: apt, apt-get and aptitude.