Issues with SpectronauttoMSstatsFormat function

[Emilio Cirri]

Dear MSStats team,

I am having issues with the SpectronauttoMSstatsFormat function, as when I run it it says " Error in toString(missing.col) : object 'missing.col' not found"
I check within the function and indeed there is a small typo:

if (!all(requiredinput.general %in% colnames(input))) { misssing.col <- requiredinput.general[!requiredinput.general %in% colnames(input)] stop(paste0("** Please check the required input. The required input needs : ", toString(missing.col))) }

I haven't had this problem before, therefore I am sking you if you had changed the package recently (I have version 3.22.1). Is there any repository to install prior versions?

Best regards

Emilio Cirri

Proteomics Core Facility
Leibniz Institut on Aging

FLI Jena

[Anthony Wu]

Hi Emilio,

It sounds like you're using an old version of MSstats (our latest version if 4.18.0).  I haven't been able to reproduce the issue on my side, which makes me think we resolved this problem after upgrading MSstats.  

Would you be able to upgrade MSstats to the latest version?  Here's a command to do so:

if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install(version = "3.22")

BiocManager::install("MSstats")  

This would also require upgrading R to version 4.5.0

Thanks,

Anthony