Instruction are provided separately for each OS:

- Install on Linux systems
- Install on Windows
- Install on MacOS

Alternatively, sen 2 r can be used in a Docker container.

## On Linux systems

### Installing dependencies

Before installing sen 2 r, it is recommended to check R (v. 3.4.4 or higher) and the following libraries to be present:

- GDAL, PROJ and GEOS (required by rgdal and rgeos);
- jq (required by jqr);
- protobuf (required by protolite);
- V8 (required by geojsonio);
- openssl (required by openssl);
- cairo (required by gdtools);
- libcurl (required by curl);
- NetCDF (required by ncdf4);
- libxml2 (required by XML).

Other binaries are required (or suggested), since they are used in runtime by the package:

- GDAL (with support for JP2OpenJPEG format): this is a mandatory dependency, needed for all the processing operations and to retrieve metadata from SAFE products;
- Sen2Cor is used to perform atmospheric correction of Sentinel-2 Level-1C products: it is required by the package, unless you choose not to correct products locally (using only Level-1C – TOA products or downloading directly Level-2A products).
- aria2 is an alternative downloader which can be used to faster the download of SAFE archives; it can be optionally installed and used.

To install both package dependencies and runtime binaries (excepting sen2cor, which is installed by sen 2 r):

- On Ubuntu:

      sudo apt-get install -y r-base gdal-bin python-gdal aria2 libpython-dev libudunits2-dev libgdal-dev libjq-dev libprotobuf-dev protobuf-compiler libv8-dev libssl-dev libcairo2-dev

  On Ubuntu 16.04 LTS Xenial and 14.04 LTS Trusty, the repositories ubuntugis and opencpu must be added before installing the packages:

      sudo add-apt-repository -y ppa:opencpu/jq
      sudo add-apt-repository -y ppa:ubuntugis/ubuntugis-unstable
      sudo apt-get update -q

  Installation was tested over Ubuntu 18.04 LTS Bionic; newer versions should work, like Ubuntu 16.04 LTS Xenial and 14.04 LTS Trusty should also do. Other releases (Ubuntu non-LTS < 18.04; Ubuntu LTS ≤ 12.04) are not supported.

- On Debian:

      sudo apt-get install -y r-base gdal-bin python-gdal aria2 libpython-dev libudunits2-dev libgdal-dev libjq-dev libprotobuf-dev protobuf-compiler libnode-dev libssl-dev libcairo2-dev proj-epsg

  Installation was tested over Debian 9 Stretch; older releases are not supported.

- On Fedora:

      sudo yum install R gdal gdal-python aria2 python-devels gdal-devel proj-devel geos-devel udunits2-devel jq-devel protobuf-devel v8-devel openssl-devel cairo-devel libcurl-devel netcdf-devel libxml2-devel

  Installation was tested over Fedora 29.

- On ArchLinux:

      sudo pacman -S --noconfirm r base-devel gcc-fortran python-gdal wget aria2 jq protobuf git
      cd /tmp; git clone https://aur.archlinux.org/gyp-git.git
      cd gyp-git; makepkg -si --noconfirm
      cd /tmp; git clone https://aur.archlinux.org/v8-3.14.git
      cd v8-3.14; makepkg -si --noconfirm
      cd /tmp; git clone https://aur.archlinux.org/udunits.git
      cd udunits; makepkg -si --noconfirm

  Installation was tested on date 2018-11-21.

### Installing sen 2 r

Before proceeding, it is suggested to update the existing R packages:

    update.packages(ask = FALSE)

Doing that, the following warning could appear:

    Warning in install.packages(update[instlib == l, "Package"], l, contriburl = contriburl,  :
      'lib = "/usr/lib/R/library"' is not writable
    Would you like to use a personal library instead?  (y/n)

If so, press `y` and continue. Moreover, if no personal libraries already exist, it is asked to create a new one: ask `y` and continue.

After that, the package can be installed from CRAN:

    install.packages("sen2r")

Alternatively, the development version can be installed from GitHub with the R package remotes. To do it:

1. install the package remotes, if missing:

       install.packages("remotes")

2. load it and install sen 2 r:

       library(remotes)
       install_github("ranghetti/sen2r")

This will install the R package along with its package dependencies, containing all the functions necessary to preprocess data.

Finally, Sen2Cor can be installed from R:

    library(sen2r)
    install_sen2cor()

## On Windows

### Installing sen 2 r

R must be installed before proceeding.

In the case it was already installed, it is suggested to update the existing R packages:

    update.packages(ask = FALSE)

sen 2 r can be installed from CRAN:

    install.packages("sen2r")

Alternatively, the development version can be installed from GitHub with the R package remotes. To do it:

1. install the package remotes, if missing:

       install.packages("remotes")

2. load it and install sen 2 r:

       library(remotes)
       install_github("ranghetti/sen2r")

This will install the R package along with its package dependencies, containing all the functions necessary to preprocess data.

### Installing runtime dependencies

To run the functions correctly, some external dependences are required:

- GDAL (with support for JP2OpenJPEG format): this is a mandatory dependency, needed for all the processing operations and to retrieve metadata from SAFE products. To avoid incompatibilities, starting from sen 2 r v. 1.1.0 it is strictly mandatory to use a GDAL installation provided with the OSGeo4W installer: if this requirement is not satisfied, it is possible to install GDAL with OSGeo4W directly from R (see below);
- Sen2Cor is used to perform atmospheric correction of Sentinel-2 Level-1C products: it is required by the package, unless you choose not to correct products locally (using only Level-1C – TOA products or downloading directly Level-2A products).
- aria2 is an alternative downloader which can be used to faster the download of SAFE archives; it can be optionally installed and used.

These dependences can be graphically checked launching the function

    library(sen2r)
    check_sen2r_deps()

This function opens a GUI which help to check that they are satisfied; if some of them are missing, the GUI allows to install them directly.

Alternatively, they can be installed individually from the command line with the three following functions (see their respective references for further details):

    check_gdal()
    install_sen2cor()
    install_aria2()

## On MacOS

### Installing GDAL

In order to avoid incompatibilities with GDAL, starting from sen 2 r v. 1.1.0 it is strictly mandatory to use a GDAL installation provided with the OSGeo Homebrew repository. To do it:

1. if Homebrew is missing on your system, install it opening a terminal and typing:

       /usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

   (see the Homebrew webpage for details);

2. install GDAL by typing:

       brew tap osgeo/osgeo4mac
       brew install osgeo-gdal-python

   (see the OSGeo Homebrew webpage for details). At this step, an error could be returned in case another GDAL installation was already present; in this case, follow the instruction returned in the terminal to solve it (probably some packages must be unlinked with the instructions `brew unlink <package>`).

### Installing sen 2 r

R must be installed before proceeding.

In the case it was already installed, it is suggested to update the existing R packages:

    update.packages(ask = FALSE)

Packages can be installed using the compiled binaries, except from sp, sf, rgdal and rgeos, which are recommended to be compiled. To do it, use the command

    install.packages(c("sp", "sf", "rgdal", "rgeos"), type = "source")

after having installed GDAL as described above.

sen 2 r can be installed from CRAN:

    install.packages("sen2r")

Alternatively, the development version can be installed from GitHub with the R package remotes. To do it:

1. install the package remotes, if missing:

       install.packages("remotes")

2. load it and install sen 2 r:

       library(remotes)
       install_github("ranghetti/sen2r")

This will install the R package along with its package dependencies, containing all the functions necessary to preprocess data.

### Installing runtime dependencies

To run the functions correctly, some external dependences are required:

- GDAL (with support for JP2OpenJPEG format): this is a mandatory dependency, needed for all the processing operations and to retrieve metadata from SAFE products. If the previous instructions were followed, it was already installed;
- Sen2Cor is used to perform atmospheric correction of Sentinel-2 Level-1C products: it is required by the package, unless you choose not to correct products locally (using only Level-1C – TOA products or downloading directly Level-2A products).
- aria2 is an alternative downloader which can be used to faster the download of SAFE archives; it can be optionally installed and used.

These dependences can be graphically checked launching the function

    library(sen2r)
    check_sen2r_deps()

This function opens a GUI which help to check that they are satisfied; if some of them are missing, the GUI allows to install them directly.

Alternatively, they can be installed individually from the command line with the three following functions (see their respective references for further details):

    check_gdal()
    install_sen2cor()
    install_aria2()