Hi Brendan,

Sorry to bother, but a few times now, I've gotten the following error when trying to open relatively large Skyline documents that I had just saved with skyline the day before. I am using Skyline-daily (64 bit) 4.1.1.18118

In each case, the main error says there is a problem with the XML document with an error of the following form:

Failure opening [path_to_skyline_doc].
The file contains an error on line [line_x_which_is_usually_a_large_number] at column 16.

When this occurred most recently (today), I saved the "more info", which is pasted below.

Thanks,
joey

--MORE INFO--
System.Reflection.TargetInvocationException: There is an error in XML document (1076681, 16). ---> System.InvalidOperationException: There is an error in XML document (1076681, 16). ---> System.Reflection.TargetInvocationException: Object reference not set to an instance of an object. ---> System.NullReferenceException: Object reference not set to an instance of an object.
   at pwiz.Skyline.Model.Lib.CachedLibrary`1.FindFileInList(MsDataFileUri sourceFile, IEnumerable`1 fileNames) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Lib\Library.cs:line 1134
   at pwiz.Skyline.Model.Lib.EncyclopeDiaLibrary.GetExplicitPeakBounds(MsDataFileUri filePath, IEnumerable`1 peptideSequences) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\Lib\EncylopeDiaLibrary.cs:line 508
   at pwiz.Skyline.Model.DocSettings.SrmSettings.GetExplicitPeakBounds(PeptideDocNode nodePep, MsDataFileUri filePath) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\DocSettings\SrmSettings.cs:line 904
   at pwiz.Skyline.Model.TransitionGroupDocNode.TransitionGroupChromInfoListCalculator.AddChromInfoList(TransitionDocNode nodeTran, IList`1 listInfo) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\TransitionGroupDocNode.cs:line 2053
   at pwiz.Skyline.Model.TransitionGroupDocNode.UpdateResults(SrmSettings settingsNew, SrmSettingsDiff diff, PeptideDocNode nodePep, TransitionGroupDocNode nodePrevious) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\TransitionGroupDocNode.cs:line 1164
   at pwiz.Skyline.Model.TransitionGroupDocNode.ChangeSettings(SrmSettings settingsNew, PeptideDocNode nodePep, ExplicitMods mods, SrmSettingsDiff diff) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\TransitionGroupDocNode.cs:line 974
   at pwiz.Skyline.Model.PeptideDocNode.ChangeSettings(SrmSettings settingsNew, SrmSettingsDiff diff, Boolean recurse) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\PeptideDocNode.cs:line 858
   at pwiz.Skyline.Model.SrmDocument.<>c__DisplayClass35.<UpdateResultsSummaries>b__34(Int32 i) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\SrmDocument.cs:line 759
   at System.Threading.Tasks.Parallel.<>c__DisplayClass17_0`1.<ForWorker>b__1()
   at System.Threading.Tasks.Task.InnerInvokeWithArg(Task childTask)
   at System.Threading.Tasks.Task.<>c__DisplayClass176_0.<ExecuteSelfReplicating>b__0(Object )
   --- 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 1846
   at pwiz.Skyline.Util.ParallelEx.LoopWithExceptionHandling(Action loop, Action`1 catchClause) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Util\Util.cs:line 2053
   at pwiz.Skyline.Model.SrmDocument.UpdateResultsSummaries(IList`1 children, IDictionary`2 dictPeptideIdPeptide) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\SrmDocument.cs:line 762
   at pwiz.Skyline.Model.SrmDocument.ReadXml(XmlReader reader) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Model\SrmDocument.cs:line 1990
   at System.Xml.Serialization.XmlSerializationReader.ReadSerializable(IXmlSerializable serializable, Boolean wrappedAny)
   at Microsoft.Xml.Serialization.GeneratedAssembly.XmlSerializationReaderSrmDocument.Read1_srm_settings()
   --- End of inner exception stack trace ---
   at System.Xml.Serialization.XmlSerializer.Deserialize(XmlReader xmlReader, String encodingStyle, XmlDeserializationEvents events)
   at System.Xml.Serialization.XmlSerializer.Deserialize(TextReader textReader)
   at pwiz.Skyline.SkylineWindow.<>c__DisplayClass12f.<OpenFile>b__12d(IProgressMonitor progressMonitor) in c:\proj\pwiz_x64\pwiz_tools\Skyline\SkylineFiles.cs:line 259
   at pwiz.Skyline.Controls.LongWaitDlg.RunWork(Action`1 performWork) in c:\proj\pwiz_x64\pwiz_tools\Skyline\Controls\LongWaitDlg.cs:line 228
   --- 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 1846
   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 176
   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 131
   at pwiz.Skyline.SkylineWindow.OpenFile(String path, FormEx parentWindow) in c:\proj\pwiz_x64\pwiz_tools\Skyline\SkylineFiles.cs:line 263

It actually looks like the problem is in getting explicit peak bounds from an EncyclopeDIA library. Probably, at least this feature should be optimized not to need to re-apply peak boundaries during a file open, but also Nick should have a look at what is going wrong here.

This bug will be fixed in the next update of Skyline-Daily.
It is also fixed in the latest Skyline-Daily administrator install if you need a fix before then:
https://skyline.ms/wiki/home/software/Skyline/daily/page.view?name=install-administrator-64