Rollback installation

support
Rollback installation Joakim Bygdell  2018-01-26 03:36
 
Hi,
I need to get my hands on an installer for Skyline 3.7.0.11317

//Joakim
 
 
Nick Shulman responded:  2018-01-26 04:30
 
Brendan MacLean responded:  2018-01-26 09:33
Is this just for compatibility or reproducing a prior result, or is there some reason you found that Skyline 4.1 wasn't working for you? If the latter, we would like to hear about any issues to give us the opportunity to fix them.

Thanks for using Skyline.

--Brendan
 
Joakim Bygdell responded:  2018-01-29 00:58
We hit a snag with one of our instruments.

1# Our current QC method (generated on 3.6) was not compatible with 4.1 due to the changes in how skyline handles small molecules in 4.1.

2# 4.1 was not able to upload to our Panorama server, "Uncaught exception in PipelineJob: Missing attribute mass_monoisotopic for element molecule"

Getting the Instrument QC back into working order was higher priority than debugging the cause of the error. Something I have to do before we do any further upgrades to both Skyline and Panaorama.

 
Vagisha Sharma responded:  2018-01-29 11:00
Hi Joakim,

Which version of LabKey Server (Panorama) do you have installed? We recently fixed a bug in Panorama that was causing the error you reported ("....Missing attribute mass_monoisotopic for element molecule"). An updated installer for LabKey Server 17.3 will be available in the next few days.

Thanks, Vagisha

 
Joakim Bygdell responded:  2018-01-29 23:02
Hi Vagisha,

We are still on an older version of panorama, since the update is coming I will hold of the upgrade until it is released.

 
Vagisha Sharma responded:  2018-01-30 13:27
Hi Joakim,

Just wanted to let you know that the installer for LabKey Server 17.3 has been updated. This should fix the Panorama issue you reported.

We still need to understand your first problem: 1# Our current QC method (generated on 3.6) was not compatible with 4.1 due to the changes in how skyline handles small molecules in 4.1.

Can you please give us some more details? It would also help if you could upload your Skyline document here https://skyline.ms/files.url? so that we can try to reproduce the problems you are seeing.

Thanks, Vagisha

 
Joakim Bygdell responded:  2018-02-01 00:16
Hi, The Skyline file where created pre 3.6 and then updated due to changes in 3.6. This method is for small molecules in both positive and negative mode.

Error message when opening the file in 4.1

System.Reflection.TargetInvocationException: There is an error in XML document (1962, 10). ---> System.InvalidOperationException: There is an error in XML document (1962, 10). ---> pwiz.Skyline.Util.AssumptionException: error reading mz values - declared mz value 378.203445 does not match calculated value 380.219094779909
at pwiz.Skyline.Model.Serialization.DocumentReader.ValidateSerializedVsCalculatedProductMz(Nullable`1 declaredProductMz, TransitionDocNode node) in c:projskyline_4_1_x64pwiz_toolsSkylineModelSerializationDocumentReader.cs:line 1493
at pwiz.Skyline.Model.Serialization.DocumentReader.ReadTransitionXml(XmlReader reader, TransitionGroup group, ExplicitMods mods, IsotopeDistInfo isotopeDist) in c:projskyline_4_1_x64pwiz_toolsSkylineModelSerializationDocumentReader.cs:line 1476
at pwiz.Skyline.Model.Serialization.DocumentReader.ReadTransitionListXml(XmlReader reader, TransitionGroupDocNode nodeGroup, ExplicitMods mods) in c:projskyline_4_1_x64pwiz_toolsSkylineModelSerializationDocumentReader.cs:line 1365
at pwiz.Skyline.Model.Serialization.DocumentReader.ReadTransitionGroupXml(XmlReader reader, Peptide peptide, ExplicitMods mods, Double deltaMass) in c:projskyline_4_1_x64pwiz_toolsSkylineModelSerializationDocumentReader.cs:line 1237
at pwiz.Skyline.Model.Serialization.DocumentReader.ReadTransitionGroupListXml(XmlReader reader, Peptide peptide, ExplicitMods mods, Double deltaMass) in c:projskyline_4_1_x64pwiz_toolsSkylineModelSerializationDocumentReader.cs:line 1042
at pwiz.Skyline.Model.Serialization.DocumentReader.ReadPeptideXml(XmlReader reader, PeptideGroup group, Boolean isCustomMolecule) in c:projskyline_4_1_x64pwiz_toolsSkylineModelSerializationDocumentReader.cs:line 873
at pwiz.Skyline.Model.Serialization.DocumentReader.ReadPeptideListXml(XmlReader reader, PeptideGroup group) in c:projskyline_4_1_x64pwiz_toolsSkylineModelSerializationDocumentReader.cs:line 756
at pwiz.Skyline.Model.Serialization.DocumentReader.ReadPeptideGroupXml(XmlReader reader) in c:projskyline_4_1_x64pwiz_toolsSkylineModelSerializationDocumentReader.cs:line 726
at pwiz.Skyline.Model.Serialization.DocumentReader.ReadPeptideGroupListXml(XmlReader reader) in c:projskyline_4_1_x64pwiz_toolsSkylineModelSerializationDocumentReader.cs:line 568
at pwiz.Skyline.Model.Serialization.DocumentReader.ReadXml(XmlReader reader) in c:projskyline_4_1_x64pwiz_toolsSkylineModelSerializationDocumentReader.cs:line 536
at pwiz.Skyline.Model.SrmDocument.ReadXml(XmlReader reader) in c:projskyline_4_1_x64pwiz_toolsSkylineModelSrmDocument.cs:line 1947
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__DisplayClass12b.<OpenFile>b__129(IProgressMonitor progressMonitor) in c:projskyline_4_1_x64pwiz_toolsSkylineSkylineFiles.cs:line 258
at pwiz.Skyline.Controls.LongWaitDlg.RunWork(Action`1 performWork) in c:projskyline_4_1_x64pwiz_toolsSkylineControlsLongWaitDlg.cs:line 228
--- End of inner exception stack trace ---
at pwiz.Skyline.Util.Helpers.WrapAndThrowException(Exception x) in c:projskyline_4_1_x64pwiz_toolsSkylineUtilUtil.cs:line 1837
at pwiz.Skyline.Controls.LongWaitDlg.PerformWork(Control parent, Int32 delayMillis, Action`1 performWork) in c:projskyline_4_1_x64pwiz_toolsSkylineControlsLongWaitDlg.cs:line 176
at pwiz.Skyline.Controls.LongWaitDlg.PerformWork(Control parent, Int32 delayMillis, Action`1 performWork) in c:projskyline_4_1_x64pwiz_toolsSkylineControlsLongWaitDlg.cs:line 131
at pwiz.Skyline.SkylineWindow.OpenFile(String path, FormEx parentWindow) in c:projskyline_4_1_x64pwiz_toolsSkylineSkylineFiles.cs:line 262
 
Brian Pratt responded:  2018-02-01 09:16
Hi Joakim,

Thanks for providing the file. I can confirm that our upcoming Skyline 4.1 patch release will handle this just fine. Sorry for the bother!

Skyline is built with community support, and part of that is reporting problems with Skyline - we really do want to know about any issues anyone might be having, and we sincerely welcome the feedback. Backward compatibility is extremely important - we always want everyone using the current version of Skyline.

Thanks,

Brian Pratt