Dear all,

I have been trying to run a few examples using proteomics data and I have been getting the follow error message below. Could anyone help me to understand this problem?

Thanks in advance!

Version Info
R version: R version 3.5.3 (2018-12-20) 
RStudio version 1.1.463
Bioconductor version: 3.8 

>install.packages("BiocManager")
BiocManager::install("colorspace", dependencies = TRUE)
BiocManager::install("RforProteomics")
BiocManager::install("MSnbase", dependencies = TRUE)

>library("RforProteomics")
Loading required package: MSnbase
Loading required package: mzR
Error: package or namespace load failed for ‘mzR’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called ‘ncdf4’
Error: package ‘mzR’ could not be loaded

The mzR package is missing. The lines that tried to installed RforProteomics and MSnbase must have failed, as both depend on mzR.

To install mzR you will first have to install a system dependency, ncdf4, using your package manager. On ubuntu/debian, it should be sudo apt install libnetcdf-dev. Then, run BiocManager::install("mzR").