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GarrettLab-UF / LipidMatch

R script using rule based feature identification for lipids
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Error in file(file, "rt") : cannot open the connection (LipidMatch-3.0.0) #10

Open AlbertThommen opened 3 years ago

AlbertThommen commented 3 years ago

Hi Jeremy and Nick,

I am trying to run the updated script from LipidMatch-3.0.0 but it gets stuck with the following error message (example shown uses the provided example data):

From Directory: \Mac\Home\Desktop\LipidMatch-3.0.0\ExampleData\dd_pos.ms2 Read 564955 items [1] "Finished Positive by class ddMS analysis" [1] "Creating Identifications for Positive Mode" Error in file(file, "rt") : cannot open the connection Called from: file(file, "rt")

I am aware that this issue has already been raised for the previous LipidMatch version (2.0.2), but I cannot tell whether the current issue is related. I'd be glad if you could have a look at this or give some hints what could be the underlying problem.

I am running R studio (R version 3.3.3) using Windows 10 on my Mac (using Parallels Desktop) and LipidMatch-2.0.2 works fine.

Thank you very much for your help and please keep up your excellent work!

Kind regards,

Albert

jeremykoelmel commented 3 years ago

This can happen if the R script is trying to access a file which either has been renamed (by you) or is open (for example in excel). So make sure all files are closed and that you don't rename any files as they are being processed. Sometime shutting down and restarting can ensure that all files are accessible. Also please use the latest version of LipidMatch (3.4) and let me know if you still have the same issue.

http://innovativeomics.com/software/lipidmatch-flow-covers-entire-lipidomics-workflow/