thank you for quick response! It looks like R.4.1.2 misses the required package of 'BiocManager'. Here are what I did this morning:
1. uninstalled all R-versions (including rTools, R-studio) from control panel
2. deleted R-folder in documents
3. Skyline (version: 21.2.0536)-->tools-->Tool store-->MSstats
4. computer tried to install R-4.1.2 with warning of "A full R installation requires administrative privileges, and it appears that those are not available. if you continue with this installation, you will not be able to associate R with .RData files. Installation must be made to a directory where you have write permission".
5. So I cancelled the installation and installed R.4.1.2 as administrator
6.R.4.1.2 was successfully installed
7. back to Skyline -->tools---> tool store-->MSstats
8. it run for a few seconds and stopped with error message (see attached screenshot) and message below:
on error message (more information) panel:
System.Reflection.TargetInvocationException: Unknown Error installing packages. Output logged to the Immediate Window. ---> pwiz.Skyline.Model.Tools.ToolExecutionException: Unknown Error installing packages. Output logged to the Immediate Window.
at pwiz.Skyline.ToolsUI.RInstaller.InstallPackages() in C:\proj\skyline_21_2\pwiz_tools\Skyline\ToolsUI\RInstaller.cs:line 254
at pwiz.Skyline.Controls.LongWaitDlg.RunWork(Action`1 performWork) in C:\proj\skyline_21_2\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 254
--- End of inner exception stack trace ---
at pwiz.Skyline.Util.Helpers.WrapAndThrowException(Exception x) in C:\proj\skyline_21_2\pwiz_tools\Skyline\Util\Util.cs:line 1941
at pwiz.Skyline.Controls.LongWaitDlg.PerformWork(Control parent, Int32 delayMillis, Action`1 performWork) in C:\proj\skyline_21_2\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 202
at pwiz.Skyline.ToolsUI.RInstaller.GetPackages() in C:\proj\skyline_21_2\pwiz_tools\Skyline\ToolsUI\RInstaller.cs:line 205
In Immediate Window:
package 'BiocManager' is not available for this version of R
A version of this package for your version of R might be available elsewhere,
see the ideas at
Error in loadNamespace(x) : there is no package called 'BiocManager'
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart