Frequently asked questions (FAQ)
General questions
Where to start
This Glotaran screencast - getting started with Glotaran video from 2012 may answer your question.
How to connect two components
To connect two components/containers together in the analysis scheme editor: press CTRL, click on the name of the container and drag towards another (on the Mac: CMD+CTRL). In this way, a model container can be linked to a dataset container and a dataset container can be linked to an output container.
How to change a model
From the Palette (App Menu -> Window -> Glotaran Tools -> Palette) modelling components can be dragged onto the model contains (inside the Parameters container). From there the aspects of each properties can be edited using the property editor (App Menu -> Window -> Glotaran Tools -> Properties). At minimum you need a Kinetic Parameter component with one rate specified and/or a IRF Parameter (Gaussian).
How to run an analysis
Once an analysis scheme is fully connected and a valid model is specified. Right click the analysis file from the project explorer and select ‘Run analysis’ from the pop-up menu.
No valid results
If you are getting an error “the analysis did not return valid results, try again with different parameters” when you try to run an analysis with more than 0 iterations, there are two primary reasons.
- The starting values for your parameters are way off
- There is too much freedom in your model for the fitting algorithm to function and you need to simplify your model or introduce constraints in the model somehow
Constraints can be imposed by fixing certain parameters, or by imposing additional spectral constraints - what is best depends on your specific situation. You are more likely to encounter this problem when using target models (KMatrix component), in which you try to estimate more parameters than was possible in global analysis.
I am getting an error message “Unable to connect to the Glotaran Update Center because of Zero sized file reported at”
- A: If your network setting are correct, this is most likely due to a mis-configured update center. The easiest solution to this problem is to go to http://glotaran.org/downloads and download the latest version of Glotaran in which this problem has been fixed.
My question about Glotaran is not answered by this FAQ
Browse through the list of known technical issues, or reach out by e-mail.
Technical issues
How to fix tcl/tk errors in Mac OS X
-
Download and install: http://xquartz.macosforge.org/landing/
- Download Xcode for your version of Mac OS X and install
- Download Command line Tools for Xcode. You will need an Apple ID to sign in.
For instance, if you are running OS X 10.7 (Lion) then you would need
- Xcode 4.6.3
- Command Line Tools (OS X Lion) for Xcode - April 2013
If you are running OS X 10.8 (Mountain Lion) then you would need
- Xcode 5.1.1
- Command Line Tools (OS X Mountain Lion) for Xcode - April 2013
If you are running OS X 10.9 (Mavericks) then you would need
- Xcode 6.1.1
- Command Line Tools (OS X 10.9) for Xcode - Xcode 6.1.1
If you are running OS X 10.10 (Yosemite) then you would need
- Xcode 6.1.1
- Command Line Tools (OS X 10.10) for Xcode - Xcode 6.1.1
etc …
How to fix result overview not opening
Glotaran uses the R package TIMP as a fitting backend. The fit progression is reported by nls.lm.
Something changed in R version R 4.1.0 in the way the output of NLS is formatted (as described here).
This results in an “Unexpected Exception” with the text:
A java.util.NoSuchElementException exception has occurred.
Click Show Details or see the messages.log file located in your ... .glotaran\1.5\var\log folder.
If you expand it further you will see:
java.util.NoSuchElementException
at java.util.Scanner.throwFor(Scanner.java:862)
at java.util.Scanner.next(Scanner.java:1371)
at org.glotaran.core.resultdisplayers.overview.AnalysisResultFileViewerTopComponent.parseNlsProgress(AnalysisResultFileViewerTopComponent.java:310)
at org.glotaran.core.resultdisplayers.overview.AnalysisResultFileViewerTopComponent.<init>(AnalysisResultFileViewerTopComponent.java:82)
at org.glotaran.core.resultdisplayers.overview.AnalyisResultFileViewer.getCloneableTopComponent(AnalyisResultFileViewer.java:12)
at org.glotaran.analysisoverviewfilesupport.AnalysisResultFileOpenSupport.createCloneableTopComponent(AnalysisResultFileOpenSupport.java:18)
... etc etc ...
The issue is described in detail in this issue
A workaround is to use R version 4.0.5 or earlier, until version 1.5.2 is released which patches this issues.
Apologies for this inconvenience. It was not forseen back in 2015 that this change might happen in 2021.