Download failed when trying to download jre-17.0.1 and crux-4.1

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Download failed when trying to download jre-17.0.1 and crux-4.1 fcyu  2021-11-24
 

When I was trying to run MSFragger in Skyline, I got errors when it was downloading jre-17.0.1 and crux-4.1 (although I am not sure why needing crux. For Percolator and FDR estimation?):

Skyline version: 21.1.1.327-f21a06b12 (64-bit)
Installation ID: 605e00a1-46d6-417c-a8a9-dfc39063ff4e
Exception type: TargetInvocationException
Error message: Download failed. Check your network connection or contact Skyline developers.

--------------------

System.Reflection.TargetInvocationException: Download failed. Check your network connection or contact Skyline developers. ---> System.Exception: Download failed. Check your network connection or contact Skyline developers.
   at pwiz.Skyline.Util.SimpleFileDownloader.DownloadRequiredFiles(IEnumerable`1 filesToDownload, ILongWaitBroker waitBroker) in C:\proj\pwiz_x64\pwiz_tools\Skyline\Util\UtilInstall.cs:line 189
   at pwiz.Skyline.Controls.LongWaitDlg.RunWork(Action`1 performWork) in C:\proj\pwiz_x64\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\pwiz_x64\pwiz_tools\Skyline\Util\Util.cs:line 1941
   at pwiz.Skyline.Controls.LongWaitDlg.PerformWork(Control parent, Int32 delayMillis, Action`1 performWork) in C:\proj\pwiz_x64\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 202
   at pwiz.Skyline.Alerts.SimpleFileDownloaderDlg.Show(Control parent, String title, IEnumerable`1 requiredFiles) in C:\proj\pwiz_x64\pwiz_tools\Skyline\Alerts\SimpleFileDownloaderDlg.cs:line 124
   at pwiz.Skyline.FileUI.PeptideSearch.SearchSettingsControl.EnsureRequiredFilesDownloaded(IEnumerable`1 requiredFiles, Func`1 extraDownloadAction) in C:\proj\pwiz_x64\pwiz_tools\Skyline\FileUI\PeptideSearch\SearchSettingsControl.cs:line 106
   at pwiz.Skyline.FileUI.PeptideSearch.SearchSettingsControl.InitSelectedSearchEngine() in C:\proj\pwiz_x64\pwiz_tools\Skyline\FileUI\PeptideSearch\SearchSettingsControl.cs:line 125
   at pwiz.Skyline.FileUI.PeptideSearch.SearchSettingsControl.SearchEngineComboBox_SelectedIndexChanged(Object sender, EventArgs e) in C:\proj\pwiz_x64\pwiz_tools\Skyline\FileUI\PeptideSearch\SearchSettingsControl.cs:line 55
   at System.Windows.Forms.ComboBox.OnSelectedIndexChanged(EventArgs e)
   at System.Windows.Forms.ComboBox.WmReflectCommand(Message& m)
   at System.Windows.Forms.ComboBox.WndProc(Message& m)
   at System.Windows.Forms.NativeWindow.Callback(IntPtr hWnd, Int32 msg, IntPtr wparam, IntPtr lparam)
Exception caught at: 
   at System.Windows.Forms.Application.ThreadContext.OnThreadException(Exception t)
   at System.Windows.Forms.Control.WndProcException(Exception e)
   at System.Windows.Forms.NativeWindow.Callback(IntPtr hWnd, Int32 msg, IntPtr wparam, IntPtr lparam)
   at System.Windows.Forms.UnsafeNativeMethods.SendMessage(HandleRef hWnd, Int32 msg, IntPtr wParam, IntPtr lParam)
   at System.Windows.Forms.UnsafeNativeMethods.SendMessage(HandleRef hWnd, Int32 msg, IntPtr wParam, IntPtr lParam)
   at System.Windows.Forms.Control.SendMessage(Int32 msg, IntPtr wparam, IntPtr lparam)
   at System.Windows.Forms.Control.ReflectMessageInternal(IntPtr hWnd, Message& m)
   at System.Windows.Forms.Control.WmCommand(Message& m)
   at System.Windows.Forms.Control.WndProc(Message& m)
   at System.Windows.Forms.UserControl.WndProc(Message& m)
   at System.Windows.Forms.NativeWindow.Callback(IntPtr hWnd, Int32 msg, IntPtr wparam, IntPtr lparam)
   at System.Windows.Forms.UnsafeNativeMethods.CallWindowProc(IntPtr wndProc, IntPtr hWnd, Int32 msg, IntPtr wParam, IntPtr lParam)
   at System.Windows.Forms.UnsafeNativeMethods.CallWindowProc(IntPtr wndProc, IntPtr hWnd, Int32 msg, IntPtr wParam, IntPtr lParam)
   at System.Windows.Forms.NativeWindow.DefWndProc(Message& m)
   at System.Windows.Forms.Control.WmCommand(Message& m)
   at System.Windows.Forms.Control.WndProc(Message& m)
   at System.Windows.Forms.ComboBox.WndProc(Message& m)
   at System.Windows.Forms.NativeWindow.Callback(IntPtr hWnd, Int32 msg, IntPtr wparam, IntPtr lparam)
   at System.Windows.Forms.UnsafeNativeMethods.DispatchMessageW(MSG& msg)
   at System.Windows.Forms.UnsafeNativeMethods.DispatchMessageW(MSG& msg)
   at System.Windows.Forms.Application.ComponentManager.System.Windows.Forms.UnsafeNativeMethods.IMsoComponentManager.FPushMessageLoop(IntPtr dwComponentID, Int32 reason, Int32 pvLoopData)
   at System.Windows.Forms.Application.ThreadContext.RunMessageLoopInner(Int32 reason, ApplicationContext context)
   at System.Windows.Forms.Application.ThreadContext.RunMessageLoop(Int32 reason, ApplicationContext context)
   at System.Windows.Forms.Form.ShowDialog(IWin32Window owner)
   at pwiz.Skyline.SkylineWindow.ShowImportPeptideSearchDlg(Nullable`1 workflowType) in C:\proj\pwiz_x64\pwiz_tools\Skyline\SkylineFiles.cs:line 3139
   at pwiz.Skyline.Controls.Startup.ActionImport.OpenSkylineStartupSettingsUI(SkylineWindow skylineWindow) in C:\proj\pwiz_x64\pwiz_tools\Skyline\Controls\Startup\StartupActions.cs:line 111
   at System.Windows.Forms.Form.OnShown(EventArgs e)
   at pwiz.Skyline.SkylineWindow.OnShown(EventArgs e) in C:\proj\pwiz_x64\pwiz_tools\Skyline\Skyline.cs:line 261
   at System.Windows.Forms.Control.InvokeMarshaledCallbackHelper(Object obj)
   at System.Threading.ExecutionContext.RunInternal(ExecutionContext executionContext, ContextCallback callback, Object state, Boolean preserveSyncCtx)
   at System.Threading.ExecutionContext.Run(ExecutionContext executionContext, ContextCallback callback, Object state, Boolean preserveSyncCtx)
   at System.Threading.ExecutionContext.Run(ExecutionContext executionContext, ContextCallback callback, Object state)
   at System.Windows.Forms.Control.InvokeMarshaledCallback(ThreadMethodEntry tme)
   at System.Windows.Forms.Control.InvokeMarshaledCallbacks()
   at System.Windows.Forms.Control.WndProc(Message& m)
   at System.Windows.Forms.Form.WndProc(Message& m)
   at System.Windows.Forms.NativeWindow.Callback(IntPtr hWnd, Int32 msg, IntPtr wparam, IntPtr lparam)
   at System.Windows.Forms.UnsafeNativeMethods.DispatchMessageW(MSG& msg)
   at System.Windows.Forms.UnsafeNativeMethods.DispatchMessageW(MSG& msg)
   at System.Windows.Forms.Application.ComponentManager.System.Windows.Forms.UnsafeNativeMethods.IMsoComponentManager.FPushMessageLoop(IntPtr dwComponentID, Int32 reason, Int32 pvLoopData)
   at System.Windows.Forms.Application.ThreadContext.RunMessageLoopInner(Int32 reason, ApplicationContext context)
   at System.Windows.Forms.Application.ThreadContext.RunMessageLoop(Int32 reason, ApplicationContext context)
   at pwiz.Skyline.Program.Main(String[] args) in C:\proj\pwiz_x64\pwiz_tools\Skyline\Program.cs:line 307

Any clue?

Thanks,

Fengchao

 
 
Nick Shulman responded:  2021-11-27
Oops! Thank you for reporting this bug.

In the latest release of Skyline-Daily we made a mistake in the URL that it tries to download Java from.

We will try to fix this in the next update of Skyline-Daily which will hopefully happen Monday or Tuesday.

I do not believe there is any way to work around this problem so you will have to wait until the next Skyline-Daily update to try out these new search engines on Skyline.

--Nick
 
matt.chambers42 responded:  2021-11-30
Yes, will be fixed in next release. Broken URL due to insufficient testing after a last minute S3 reorganization. :(

I just realized I could simply duplicate the file in S3 at the old location, so the current Skyline-daily should work now as well.

Crux is used right now just for Percolator for MSFragger (with pepXML output, which the bare Percolator sadly doesn't have), but in the near future I'll add Comet, Diameter, and possibly Tide as search engine options as well; all are included in Crux.

I guess the MSFragger download dialog looks familiar to you! :D
 
fcyu responded:  2021-11-30
Thank you both for your prompt replies.

The downloading works for the current Skyline-daily now. Thanks.

And yes, the MSFragger download dialog looks so familiar.

Best,

Fengchao