R Session Aborted

[JosephCrispell]

I think the R Session Aborted error is caused by homoplasyFinder hanging after an error has been introduced. See the image below, I introduced an error by sending the wrong file name, it sends error and the next time I try runHomoplasyFinderInJava() I get the R Session Aborted error.

Maybe I could add an rJava close all function at the start of runHomoplasyFinderInJava()?

[hofskatr]

Hi, I'm running into this problem whenever I try to load in a tree. I've tried both the annotated trees made in R and Java, and get the same results.

If I try and use quotes around the tree file name instead of pointing to the working directory I get an error that the file doesn't exist. tree <- readAnnotatedTree("annotatedNewickTree_29-04-22.tree") Error in file(file, "r") : cannot open the connection In addition: Warning message: In file(file, "r") : cannot open file 'annotatedNewickTree_29-04-22.treeannotatedNewickTree_29-04-22.tree': No such file or directory I don't understand why it's duplicating the tree name though.

If I try to use the working directory the R session crashes.

Do you have any advice or can I provide any files to help troubleshoot this?

Thanks!

[JosephCrispell]

Hi @hofskatr,

Sorry for responding so slowly on this. The readAnnotatedTree() function is a really simple one: https://github.com/JosephCrispell/homoplasyFinder/blob/faed16f2ff1602a2a939663a942e0b8640b9bc50/R/homoplasyFinder.R#L270-L279

The issue you have is that this function only wants the path to the file and then it will read in a file with file name structured: "path/to/file/annotatedNewickTree_%d-%m-%y.tree"

Note the %d-%m-%y is a formatted date set through the date parameter, which defaults to today's date (the date you are running script).

In your case to avoid the error you might run something like:

readAnnotatedTree(path=".", date="29-04-22")

Sorry again for not replying sooner and let me know if the above makes sense and helps!

Joe