You can install R version 3.5.0 from this URL:
http://cran.wustl.edu/bin/windows/base/old/3.5.0/R-3.5.0-win.exe

It looks like the regular R project web site (cran.r-project.org) is not working right now.

Skyline is running into that error while trying to install R from:
http://cran.r-project.org/bin/windows/base/old/3.5.0/R-3.5.0-win.exe
but that URL does not work right now. If you install R version 3.5.0 yourself from a URL that works, Skyline will not try to install R, and Skyline will go on to the next step of the MSstats install process.
-- Nick

Hello Nick,

I just installed R by myself but it shows error again.


---------------------------
Skyline
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Error: Failed to connect to the website www.r-project.org

Installing R packages requires an internet connection. Please check your connection and try again
---------------------------
OK More Info
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System.Reflection.TargetInvocationException: Error: Failed to connect to the website www.r-project.org

Installing R packages requires an internet connection. Please check your connection and try again ---> pwiz.Skyline.Model.Tools.ToolExecutionException: Error: Failed to connect to the website www.r-project.org

Installing R packages requires an internet connection. Please check your connection and try again
   at pwiz.Skyline.ToolsUI.RInstaller.InstallPackages() in C:\proj\skyline_4_2_x64\pwiz_tools\Skyline\ToolsUI\RInstaller.cs:line 239
   at pwiz.Skyline.Controls.LongWaitDlg.IndefiniteWaitBroker.PerformWork(ILongWaitBroker broker) in C:\proj\skyline_4_2_x64\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 338
   at pwiz.Skyline.Controls.LongWaitDlg.RunWork(Action`1 performWork) in C:\proj\skyline_4_2_x64\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 232
   --- End of inner exception stack trace ---
   at pwiz.Skyline.Util.Helpers.WrapAndThrowException(Exception x) in C:\proj\skyline_4_2_x64\pwiz_tools\Skyline\Util\Util.cs:line 1854
   at pwiz.Skyline.Controls.LongWaitDlg.PerformWork(Control parent, Int32 delayMillis, Action`1 performWork) in C:\proj\skyline_4_2_x64\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 180
   at pwiz.Skyline.Controls.LongWaitDlg.PerformWork(Control parent, Int32 delayMillis, Action performWork) in C:\proj\skyline_4_2_x64\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 126
   at pwiz.Skyline.ToolsUI.RInstaller.GetPackages() in C:\proj\skyline_4_2_x64\pwiz_tools\Skyline\ToolsUI\RInstaller.cs:line 205
---------------------------

That is unfortunate.

Before Skyline is willing to install the R packages for you, Skyline tries to make sure that you are connected to the internet. The URL that Skyline uses to check that is "www.r-project.org" which we have already seen is not working right now.

The easiest thing to do would be to wait for the R website to come back online.

If this problem continues to happen then we may need to release an update of Skyline that allows you to customize which R mirror to use.
Sorry about this. I hope the website comes back online soon.
-- Nick