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