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vastgroup / vast-tools

A toolset for profiling alternative splicing events in RNA-Seq data.
MIT License
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Problems w/ vast-tools diff #54

Closed nunolbmorais closed 8 years ago

nunolbmorais commented 8 years ago

Hi guys,

For the last few weeks, we cannot run vast-tools diff, even after making sure vast-tools, R and all the required packages are up-to-date. We have tried it with different datasets and different combination of parameters and we always get the same error message: Error: Unknown parameters: x Execution halted

One guess is that it could be related with the recent upgrade of ggplot2 to version 2.0.

If we ask for more than one core with the -c option, we get this (8 cores): Error in plotListed[[it]][[5]] : subscript out of bounds In addition: Warning message: In mclapply(1:length(lines), function(i) { : scheduled cores 4, 1, 5, 6, 3 encountered errors in user code, all values of the jobs will be affected Execution halted

Please let me know if there's any way I can help or if you need more info.

Best wishes, Nuno

timbitz commented 8 years ago

Hi Nuno, Thanks for letting me know. You are of course correct, I had not yet updated to ggplot2 version 2.0, and there was some deprecated syntax in there. I have now fixed the syntax to work for ggplot 2.0, as of 30edcdb. -t

rhugh-white commented 7 years ago

I am receiving the same error when using vast-tools diff (version 1.1.0), but only when using the --paired=TRUE option, with paired=FALSE the script runs without error.

Rupert