Software installation and updates.
0 – Mac OS users only: install X Quartz first https://www.xquartz.org/
1 – Install the mixOmics package from Bioconductor You may need to install the latest R version and the latest BiocManager version (follow these instructions if you use R versions <=3.5.0). Install mixOmics using the following code:
## install BiocManager if not installed if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
## install mixOmics
BiocManager::install('mixOmics')
The mixOmics package should directly import the following packages: igraph, rgl, ellipse, corpcor, RColorBrewer, plyr, parallel, dplyr, tidyr, reshape2, methods , matrixStats , rARPACK, gridExtra .
1 (alternative) – To obtain the latest update of mixOmics (as Bioconductor updates mixOmics every 6 months) you will need to pull from our gitHub page using the ‘devtools’ and ‘install_github’ libraries. Install the library ‘devtools’ in R, then load and install mixOmics from gitHub:
install.packages("devtools")
# then load
library(devtools)
install_github("mixOmicsTeam/mixOmics")
2 – Check after install that the following does not throw any error (see step 0) and that the welcome message confirms you have installed mixOmics. If this is not the case, try step 1 alternative (installation from gitHub):
>library(mixOmics)
Loaded mixOmics ?.??.?
We also advise using the software RStudio
If R throws an error, you may have to install the latest R version here: https://cran.r-project.org/