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:

homoplasyFinder/R/homoplasyFinder.R

Lines 270 to 279 in faed16f

	#' Read in the annotated Newick tree
	#'
	#' This function runs reads in the annotated Newick formatted phylogenetic tree file produced by HomoplasyFinder. Node labels of tree report where changes occured for inconsistent positions ("-" separated)
	#' @param path The full path to the directory where the output files were created (must match what was used for \code{runHomoplasyFinderInJava()})
	#' @param date Date \code{runHomoplasyFinderInJava()} was ran. Format: "\%d-\%m-\%y". Defaults to today.
	#' @keywords tree newick annotated
	#' @export
	readAnnotatedTree <- function(path, date=format(Sys.Date(), "%d-%m-%y")){
	return(ape::read.tree(paste0(path, "annotatedNewickTree_", date, ".tree")))
	}

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

[ankeetkumar]

I generated the files using GUI HomoplasyFinder and then tried to make a tree in R. But as soon as I load the file the session gets terminated.

Kindly help me sort the issue

library(homoplasyFinder)
workingDirectory<- paste0(getwd(), "/") Set directory to the folder where files are saved, but I remove the original tree file and fasta file used to generate the ouput

date <- format(Sys.Date(), "%d-%m-%y")
resultsFile <- paste0(workingDirectory, "consistencyIndexReport_27-02-25", ".txt")
results <- read.table(resultsFile, header=TRUE, sep="\t", stringsAsFactors=FALSE)

Read in the annotated tree

tree <- readAnnotatedTree(workingDirectory) R crashes at this step

Plot the annotated tree

plotAnnotatedTree(tree, inconsistentPositions, fastaFile)