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Showing content from https://github.com/green-striped-gecko/dartR/wiki/Installation-tutorial below:

Installation tutorial · green-striped-gecko/dartR Wiki · GitHub

1. Download and install R from here.

2. Download and install RStudio from here.

3. Download and install the latest version of Rtools from here. Rtools is a toolchain bundle used for building R packages from source (those that need compilation of C/C++ or Fortran code).

4. Install dartRverse; see the specific section for this step below.

1. Download and run the R installer from here.

2. Download and open the RStudio app from here. You must drag the application to the Applications folder to install it.

3. Install Command-Line tools. Open the Terminal app and type:

1. Install Homebrew by typing in the Terminal app the code below. Homebrew is a management system that simplifies software installation on macOS and Linux.

/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"

1. Add Homebrew to your PATH if prompted. After installing Homebrew, you might see that the last message, "==> Next steps:" describes further instructions. Follow these instructions and type them in the Terminal app. These instructions should be something similar to the following:

echo 'eval "$(/opt/homebrew/bin/brew shellenv)"' >> /Users/m1/.zprofile
eval "$(/opt/homebrew/bin/brew shellenv)"

1. Install GNU Compiler Collection (GCC) by typing in the Terminal app:

1. Check the version of GCC you installed in the previous step by typing in the Terminal app:

1. Make a symlink (a symbolic link that points to another file or folder on your computer) from your GCC version to gcc using the Terminal app. Replace the X in the code below with the GCC version you checked in the previous step.

1. Install GDAL using Homebrew. GDAL is a translator library for raster and vector geospatial data. In the first command, we install the headers files first to avoid GDAL fail.

brew install gdal --HEAD
brew install gdal

1. Open RStudio. If you get warning messages such as Setting LC_CTYPE failed, using "C" or the error: tar: Failed to set default locale. Type the command below in the R console and then restart your RStudio session. Find more information here.

system('defaults write org.R-project.R force.LANG en_US.UTF-8')

1. Create a makevars file and put the path to libgfortran into FLIBS. Open RStudio and type in the R console:

dir.create('~/.R')
write.table("FLIBS=`gfortran -print-search-dirs | grep '^libraries:' | sed 's|libraries: =||' | sed 's|:| -L|g' | sed 's|^|-L|'`", file='~/.R/Makevars', col.names = FALSE, row.names = FALSE, quote = FALSE)

1. Install dartRverse; see the specific section for this step below.

1. Install R by following these instructions.

2. Install the r-base-dev package. Open Terminal and type the code below. This package compiles R packages from source (those that need compilation of C/C++ or Fortran code).

sudo apt-get install r-base-dev

1. Install the various packages that are required in LINUX by typing in Terminal:

sudo apt install libcurl4-openssl-dev libssl-dev libfontconfig1-dev libxml2-dev libharfbuzz-dev libfribidi-dev libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev gdal-bin proj-bin libgdal-dev libproj-dev libgmp3-dev jags

1. Download RStudio from here.

2. Install RStudio using the code below in Terminal specifying the location of the file that you downloaded in the previous step, for example:

sudo gdebi '/home/vdiuser/Downloads/rstudio-2022.07.1-554-amd64.deb' 

1. Indicate where RStudio should search for the R executable. Locate the R executable first, then use the environment variable RSTUDIO_WHICH_R to specify the executable location and add it to the profile file (the shell script file that gets executed after login). Enter the following command in Terminal after updating the location of your specific R executable. Note that ~ is a shortcut to the current user's home directory.

echo 'export RSTUDIO_WHICH_R=/opt/R/4.1.3/bin/R' >> ~/.profile

1. Source the profile file to update the change from the previous step. Type in Terminal:

1. Open RStudio by typing in Terminal (not from the desktop Applications menu):

1. Install dartRverse; see the specific section for this step below.

We have developed a new suite of packages called dartRverse that will replace the previous dartR package, which will no longer be supported. The dartRverse is meant to be a 1:1 replacement of dartR, and only in very few instances will minor changes be needed to update previous code. For example, we reworked the "output" of all functions, now being able to save figures in specified folders, which can be quickly recovered and manipulated for further tweaking. The main reasons for splitting dartR into several packages and developing the dartRverse suit of packages was the difficulty of maintaining dartR because of limits imposed by CRAN, but also limits due to the long time to test new functions when compiling the package. Therefore, we were forced to split the package into several smaller packages. This has several advantages and no disadvantages in the best of all cases.

• Easier maintenance.
• Faster development.
• Less dependencies on other packages.
• Easier to become a contributor.
• Have your own package developed that can be branded as part of the dartRverse.

The main paradigm was also that for our users, nothing (or at as little as possible) needs to change, and all existing code and scripts should still work. Also, the installation process was meant to be straightforward, and finally, the coexistence between dartR and dartRverse packages should be possible (for the interim until dartR will no longer be supported).

# Install the necessary Bioconductor packages
install.packages("devtools")
install.packages("BiocManager")
BiocManager::install("SNPRelate")

# Install dartRverse (dartRverse) & core (dartR.base, dartR.data)
install.packages("dartRverse")

The dartRverse package is the first package to be installed, and its only purpose is to support the installation of the other dartRverse packages. It will also be the first port of call to provide links to tutorials and other documentation.

If everything works well, this should install two more packages from the core version of dartRverse, namely dartR.base and dartR.data. Those core packages have all the main functions of the old dartR package that deals with input, conversion, reporting and data filtering. Also, some base functions to analyse data (e.g., PCoA and Fst) are included.

Once the dartRverse package has been installed, we can load the package to check which part of the dartRverse has been installed.

Now, we can install the additional packages that are part of the dartRverse. You can install all or only the one you want, depending on your needs.

For example, if you are interested in additional functions to analyse population structure (e.g. run STRUCTURE or FastStructure) you can install the dartR.popgen package. If you are interested in functions that support data simulation, you can install the dartR.sim package.

You can check which packages are available and which of them you have installed by typing:

dartRverse::dartRverse_install()

The currently available packages are:

• dartR.sim (simulate SNP data).
• dartR.popgen (run population genetic analysis).
• dartR.spatial (run landscape genetic analysis).
• dartR.captive (estimate relatedness, support captive breeding).
• dartR.sexlinked (identify sex-linked markers, not ready yet).

So, to install the dartR.sim simply type:

install.packages("dartR.sim")

We make all of our packages available via CRAN. This is because CRAN packages follow stringent testing before they are allowed to be uploaded to CRAN and, therefore, are more likely to contain fewer errors than packages available on other repositories. Nevertheless, we also make our packages available during development via GitHub.

You can find the repositories under: https://github.com/green-striped-gecko/dartR.base [for the dartR.base package] and equivalent for the other packages.

You might want to install a package from GitHub because you want to use the latest version of the package. However, you should be aware that the packages on GitHub are not tested and, therefore, might contain errors. Also, the packages on GitHub might be updated daily and, therefore, might change without notice.

We use different branches, reflecting different stages of development and maturity.

• main (the main branch, which is equivalent to the current CRAN version)
• dev (development branch, which has the latest functions that might be in the next CRAN version but have not been tested yet)
• dev_name (These are branches of our leading developers used for testing and developing new functions. Installing functions from here might cause problems and should only be done if you know what you are doing)

dartRverse supports the installation of the GitHub version of the packages using the following syntax:

dartRverse_install(package = "dartR.base", rep = "github", branch = "dev")

This installs the dev branch of dartR.base from GitHub. All main and dev branches are tested to see if they can be installed (and some additional error checks via): https://github.com/green-striped-gecko/dartRverse

Please note that you should provide the package repository (github/cran), the branch (main, dev, dev_name) and version number in case you want to report a bug. You can use the GitHub methods to report issues or our Google Groups Forum: https://groups.google.com/d/forum/dartr.

NOTE

Due to CRAN requirements, even after installing the dartRverse using this approach, some of the functions require additional installation of packages. This is not to tease users; we want to ensure the packages do not fall over because of an incompatibility of one function (often, users do not use all functions anyway). We are working on a command that installs all packages in one go for those users who want to have all functions available. However, this is not a priority at the moment. If you want to use a function that is unavailable, please install the required package. If you are unsure which package is required, please check the function's documentation or ask on our Google Groups Forum. We are happy to help. ;-)

Important

For the Kioloa workshop, we had quite a few last-minute changes. Hence, we will use the packages as installed on the RStudio Cloud. If you want to run the workshop on your own machine, please install the latest R [ >=4.3], the latest Rstudio [>=2023.12] and the dev branch GitHub version of the packages dartR.base, dartR.data, dartR.sim, dartR.popgen, dartR.spatial, dartR.captive, dartR.sexlinked. [e.g. installing via: dartRverse_install(package = "dartR.base", rep = "github", branch = "dev")

For whatever reason, you might want to use legacy dartR instead of the dartRverse packages [e.g. for initial testing]. The good news is that both packages can be installed next to each other, but you must ensure you detach the other package. This can be done in Rstudio via the package tab by unticking the packages. Please note that the order in which you untick the packages is essential. So, first the non-core packages (dartR.sim, dartR.popgen, dartR.captive, dartR.spatial), then dartRverse followed by the core packages dartR.base and finally dartR.data. If you do not follow the correct order, you get a warning message, and it will not detach the package. If you want to use code, type:

detach("package:dartR.sim", unload = TRUE)
detach("package:dartR.sexlinked", unload = TRUE)
detach("package:dartR.spatial", unload = TRUE)
detach("package:dartR.captive", unload = TRUE)
detach("package:dartR.popgen", unload = TRUE)
detach("package:dartRverse", unload = TRUE)
detach("package:dartR.base", unload = TRUE)
detach("package:dartR.data", unload = TRUE)

Now, you can load and use the legacy dartR package as before.

To unload dartR, you can use the Packages tab as described before or the following code:

detach("package:dartR", unload = TRUE)
detach("package:dartR.data", unload = TRUE)

To use dartRverse, you can load the package and use it as before.

We hope you have fun in the dartRverse ;-)

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