QuaSAR execution error Alvaro Sanchez-Bernabeu  2023-08-16 07:55
Hey there,

I was trying to run QuaSar and I have got the following error messages:

At first, I got this message at the Immediate Window:

"C:\Users\Alvaro Sanchez\Documents\R\R-3.0.1\bin\R.exe" -f "C:\Users\Alvaro Sanchez\AppData\Local\Apps\2.0\4VDK9ATE.R6G\CXV3K6ZV.VLB\skyl..tion_2e441fc3bf6adc7f_0017.0000_f621a40fd78fad56\Tools\QuaSAR-1_32\QuaSAR-Skyline.R" --slave --no-save --args "C:\Users\Alvaro Sanchez\AppData\Local\Apps\2.0\4VDK9ATE.R6G\CXV3K6ZV.VLB\skyl..tion_2e441fc3bf6adc7f_0017.0000_f621a40fd78fad56\Tools\QuaSAR-1_32\QuaSAR.R" "C:\Users\Alvaro Sanchez\AppData\Local\Apps\2.0\4VDK9ATE.R6G\CXV3K6ZV.VLB\skyl..tion_2e441fc3bf6adc7f_0017.0000_f621a40fd78fad56\Tools\QuaSAR-1_32\common.R" "C:\Users\Alvaro Sanchez\AppData\Local\Temp\QuaSAR_QuaSAR_Input.csv" NULL Trial1 "light Area" 1 "heavy Area" fmol/ul 1 1 -1 1 0 0 0 150 150 1 0,2 0 NULL Trial1 0
El sistema no puede encontrar la ruta especificada.

Then, when copy and pasting the path to the file (C:\Users\Alvaro Sanchez\AppData\Local\Temp\QuaSAR_QuaSAR_Input.csv), it would open in Excel and then when I click again at the QuaSAR execution button while keeping it open, I get the following message:

Error exporting the report, tool execution canceled.
OK More Info
System.IO.IOException: Error exporting the report, tool execution canceled.
   en pwiz.Skyline.Model.Tools.ToolMacros.GetReportTempPath(ToolMacroInfo toolMacroInfo) en C:\proj\skyline_23_1\pwiz_tools\Skyline\Model\Tools\ToolMacros.cs:línea 266
   en pwiz.Skyline.Model.Tools.ToolMacros.ReplaceMacrosHelper(SrmDocument doc, IToolMacroProvider toolMacroProvider, ToolDescription tool, IProgressMonitor progressMonitor, String replacein, Macro[] macros) en C:\proj\skyline_23_1\pwiz_tools\Skyline\Model\Tools\ToolMacros.cs:línea 206
   en pwiz.Skyline.ToolsUI.ToolDescriptionRunUI.RunExecutableBackground(ToolDescription toolDesc, SrmDocument document, IToolMacroProvider toolMacroProvider, TextWriter textWriter, IProgressMonitor progressMonitor, Control parent) en C:\proj\skyline_23_1\pwiz_tools\Skyline\ToolsUI\ToolDescriptionRunUI.cs:línea 328
   en pwiz.Skyline.ToolsUI.ToolDescriptionRunUI.<>c__DisplayClass4_0.<RunExecutable>b__0() en C:\proj\skyline_23_1\pwiz_tools\Skyline\ToolsUI\ToolDescriptionRunUI.cs:línea 164

Excuse me for the spanish lines in the error messages... Any idea what might be going wrong?

Thanks a lot!

Nick Shulman responded:  2023-08-16 08:05
The QuaSAR external tool in the tool store uses R version 3.0.1.
I think the error that you are getting is caused by that version of R no longer being in the folder that it is supposed to be.

Someone gave us a newer version of the QuaSAR external tool that works with R version 4.0.
You can find that tool zip file at the bottom of the following support request:

You can download that .zip file, and then use the "Tools > External Tools" menu item in Skyline and then press the "Add > From File" button.
-- Nick
Alvaro Sanchez-Bernabeu responded:  2023-08-17 01:30
Thanks a lot Nick!

I have managed to reinstall the new QuaSAR after some hiccups with R packages, however when running QuaSAR now I get the following message:

"C:\Users\Alvaro Sanchez\Documents\R\R-4.0.0\bin\R.exe" -f "C:\Users\Alvaro Sanchez\AppData\Local\Apps\2.0\4VDK9ATE.R6G\CXV3K6ZV.VLB\skyl..tion_2e441fc3bf6adc7f_0017.0000_f621a40fd78fad56\Tools\QuaSAR-2020.1\QuaSAR-Skyline.R" --slave --no-save --args "C:\Users\Alvaro Sanchez\AppData\Local\Apps\2.0\4VDK9ATE.R6G\CXV3K6ZV.VLB\skyl..tion_2e441fc3bf6adc7f_0017.0000_f621a40fd78fad56\Tools\QuaSAR-2020.1\QuaSAR.R" "C:\Users\Alvaro Sanchez\AppData\Local\Apps\2.0\4VDK9ATE.R6G\CXV3K6ZV.VLB\skyl..tion_2e441fc3bf6adc7f_0017.0000_f621a40fd78fad56\Tools\QuaSAR-2020.1\common.R" "C:\Users\Alvaro Sanchez\AppData\Local\Temp\QuaSAR_QuaSAR_Input.csv" NULL Trial1 "light Area" 1 "heavy Area" fmol/ul 1 1 -1 0 0 0 0 150 150 0 NULL 0 NULL Trial1 0
[1] $Id: QuaSAR-Skyline.R 149 2014-10-23 13:56:13Z manidr $
[1] $Id: QuaSAR.R 149 2014-10-23 13:56:13Z manidr $

Attaching package: 'boot'

The following object is masked from 'package:lattice':


The following objects are masked from 'package:gtools':

    inv.logit, logit

Attaching package: 'gplots'

The following object is masked from 'package:stats':


[1] Processing arguments ...
[1] >>> Processing part 1 of 1
[1] Initializing ...
Error in calculate(data.subset, concentrationFile, output.prefix = outputPrefix, :
   No data for LOD calculation -- disable LOD calculation
Calls: tryCatch -> tryCatchList -> parse.cmdline -> calculate
Ejecuci�n interrumpida


Any ideas how to troubleshoot this one?

Much appreciated
Nick Shulman responded:  2023-08-17 08:01

I don't know what to do about the error "No data for LOD calculation".
I have an email in my inbox from eight years ago where some other people started to look into that error and in the end it turned out that our problem had something to do with multi-sample .wiff files, but I cannot tell from reading these emails whether "No data for LOD calculation" was the real error that was being investigated or whether that was just the first thing that they noticed.

If you want to troubleshoot this, you could run this tool inside of RStudio.
When you run the tool inside of Skyline, the first line of text that is written to the Immediate Window is the commandline that was used to invoke R.exe.
You can use that commandline to figure out how to run the script "QuaSAR-Skyline.R" that is in the .zip file that you can download from the QuaSAR tool store page.

By the way, the QuaSAR external tool was written a very long time ago before Skyline had its own way of doing calibration curves.
You might find the calibration curve features in Skyline are good enough for what you are trying to do.
You can learn about calibration curves in Skyline with the Absolute Quantification tutorial:
-- Nick

Alvaro Sanchez-Bernabeu responded:  2023-08-18 00:29

Hey Nick!

Thank you for your thorought answer.

I looked into the Abs Quant tutorial and it is greatly explained, it was very useful. However, I was looking for the calculation of %CV and precision as well.

Is there a way to do it within Skyline that I am missing?

Thank you,


Nick Shulman responded:  2023-08-18 00:42
One way to see the CVs in your document is to use the "View > Peak Areas > CV Histogram" menu item.
There is some documentation about how to use the CV Histogram graph in a PowerPoint (.pptx) file on this page:

A different way to see CVs is by using the Pivot Editor in the Document Grid. There is a description of how to calculate CVs using the Pivot Editor here:

-- Nick