Download and installation¶

Download¶

The latest stable release of alakazam can be downloaded from CRAN or GitHub.

Installing Released Versions¶

The simplest way to install alakazam is via CRAN:

install.packages("alakazam")

Downloaded source builds from GitHub may be installed in the usual way:

install.packages("alakazam_x.y.z.tar.gz", repos = NULL, type = "source")

If you have any trouble installing the package, it may be due to the Bioconductor dependencies. You can run the following command to see what other packages may be needed:

available.packages()["alakazam", "Imports"]

Alternatively, you can use Bioconductor’s install function:

install.packages("BiocManager")
BiocManager::install("alakazam")

Building Development Versions¶

To build from the source code, first install the build dependencies:

install.packages(c("devtools", "roxygen2", "testthat", "knitr", "rmarkdown", "Rcpp"))

To install the latest development code via devtools:

library(devtools)
install_github("immcantation/alakazam@master")

Note, using install_github will not build the documentation. To generate the documentation, clone the repository and build as normal using devtools, roxygen and knitr:

library(devtools)
install_deps()
document()
build()
install()

Some users might experience issues with alakazam if certain dependencies are not installed correctly. One straightforward way to ensure all required packages are available is to install alakazam via Bioconductor:

install.packages("BiocManager")
BiocManager::install("alakazam")

If you still encounter issues with missing dependencies, you can use the Posit Public Package Manager to identify and install them manually.

If problems persist while installing alakazam, feel free to contact us here for support.