Chapter 2 Installation Guide

2.1 Requirements

2.1.1 R environment

EZCancerTarget are collection of R scripts. Its requirement is an installed and working R environment. You can find more details on CRAN about R setup: https://cran.r-project.org/bin/windows/base/

Linux and macOS users can find download and installation instructions on these pages and can consult with their system-sepcific package management tools:

2.1.2 CLUE.IO API Key

CLUE_USER_KEY environment variable must be set on the host operating system. This key is user-specific and it can be obtained after registration on CLUE.IO (https://clue.io).

2.2 Installation Steps

Download EZCancerTarget latest ZIP bundle
Extract its content into a folder: for example C:\EzCancerTarget
Open a terminal window and enter into this directory cd C:\EzCancerTarget
Start R here by the R command
Similar output should display:


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

# Bootstrapping renv 0.15.2 --------------------------------------------------
* Downloading renv 0.15.2 ... OK
* Installing renv 0.15.2 ... Done!
* Successfully installed and loaded renv 0.15.2.
* Project '~/EZCancerTarget-main' loaded. [renv 0.15.2]
* The project library is out of sync with the lockfile.
* Use `renv::restore()` to install packages recorded in the lockfile.

Type the suggested command to install EZCancerTarget dependencies and chooes yes at prompted question . It will take a while:

> renv::restore()
The following package(s) will be updated:

# CRAN ===============================
- R6              [* -> 2.5.1]
- askpass         [* -> 1.1]
- assertthat      [* -> 0.2.1]
- bit             [* -> 4.0.4]
- bit64           [* -> 4.0.5]
- cellranger      [* -> 1.1.0]
- cli             [* -> 3.1.1]
- clipr           [* -> 0.7.1]
- cpp11           [* -> 0.4.2]
- crayon          [* -> 1.4.2]
- curl            [* -> 4.3.2]
.
.
.

Do you want to proceed? [y/N]: y

* Querying repositories for available source packages ... Done!
Retrieving 'https://cloud.r-project.org/src/contrib/R6_2.5.1.tar.gz' ...
    OK [downloaded 61.9 Kb in 0.3 secs]
Retrieving 'https://cloud.r-project.org/src/contrib/askpass_1.1.tar.gz' ...
    OK [downloaded 5.6 Kb in 0 secs]
Retrieving 'https://cloud.r-project.org/src/contrib/sys_3.4.tar.gz' ...
.
.
.


Installing whisker [0.4] ...
    OK [built from source]
Moving whisker [0.4] into the cache ...
    OK [moved to cache in 0.64 milliseconds]