Difficulty installing MSstats as an external tool in Skyline - related to ggplot2

[jwinget]

Software version:
Skyline 26.1.0.057

When attempting to install MSstats as an external tool using the Skyline interface, the R version is set to 4.2.2.
The ggplot2 package fails to install, with an error related to "<element_geom} object properties are invalid".

I have confirmed that ggplot2 and MSstats (through bioconductor) will install fine under R 4.6.1, however it's unclear how to force the Skyline external tool to use this verison of R. Any help is appreciated.

[tonywu1999]

Hi,

Thanks for the detailed writeup. Unfortunately, this is a Skyline-specific issue (how the external tool installer selects/forces an R version) that's outside what we're able to troubleshoot on our end.

I'd recommend reaching out directly to the Skyline team/support. They maintain the external tool integration and R version handling. I'd advise asking them if you could override the R version requested by an installed external tool like MSstats, or request if the external tool could be repackaged to request 4.6.1