MSstats error laure bastide  2021-10-22 03:32
 

Hello Skyline team,

I have a new issu when I want to use MSstats as an external tools in Skyline, when I want to start the Data Processing, i have this warning message :
"** Loading the required statistical software packages in R .....

Registered S3 methods overwritten by 'tibble':
method from
format.tbl pillar
print.tbl pillar
Error : package or namespace load failed for 'MSstats' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
namespace 'tibble' 2.1.3 is already loaded, but >= 3.0.0 is required

Can't finish analysis."

I desintall and reinstall MSstats and R files and I try to install directly the "tibble" package in R but I can't because the package 3.0.0 is not available for R version 3.6.1...
The MSstats googlegroup suggested that you may have to make an update of R/packages/MSstats.
Alternatively, I can use it outside of Skyline but it was just for you know !

Thanks a lot for your great help !

Have a good day.

Laure.

What can I do ? Thanks a lot for your answer !
 
 
Nick Shulman responded:  2021-10-22 06:36
Laure,

I have been working on a new version of the MSstats external tool that uses R version 4.1.
The .zip file is available here:

https://github.com/nickshulman/pwiz/raw/Skyline/work/20210525_MSstatsRVersion41/pwiz_tools/Skyline/Executables/Tools/MSstats/MSstats.zip

In Skyline, you can go to:
Tools > External Tools
and push the "Add > From File" button, and then paste that whole URL into the "File name" box on the Open dialog.

Can you let me know whether this new version of the tool works for you?
If it does work, I will probably upload it to the Tool Store.
-- Nick
 
laure bastide responded:  2021-10-27 05:09
Hello !

Thanks a lot for your help !
I did the first part (Dataprocessing) without trouble but when I want to do the second part (Group comparison) I receive this message :

 Error : Can't compare the groups.
Error in MSstatsConvert::MSstatsLogsSettings(use_log_file, append, verbose, :
  Assertion on 'log_file_path' failed: 'Y:\4_Skyline_Analysis\MS4MS\MSstats_GroupComparison.log' not readable.

I am not sure to understand where is the problem... If you have any idea, I will be happy to try it !

Laure.
 
Nick Shulman responded:  2021-10-27 08:57
Hmmm.

When you use the MSstats external tool, it creates and writes to a log file named "MSstats_GroupComparison.log" in the same folder as your Skyline document.
I am not sure what could cause the error that you are seeing.
If you really did not have permissions to create the log file, then you would have seen a different error ("Permission denied") so I do not know what is going wrong in this case.

I imagine this might work for you if the Skyline document was on the C: drive instead of the Y: drive, but I am not sure. I assume that Y: drive is a network share.
I will investigate whether I have any difficulties running this tool when my Skyline document is on a network share.

Thanks for testing this!
-- Nick