Nothing
# filename does not begin with `test` so not run by `testthat::test_dir()`
# This test assumes the working directory contains all the XML files provided
# here: https://github.com/rvosa/supertreebase/tree/master/data/treebase
files <- system("ls *.xml", intern=TRUE)
print("testing parsing only")
parses <- sapply(files, function(x){
out <- try(xmlParse(x))
if(is(out, "try-error"))
out <- x
else {
free(out)
out = "success"
}
out
})
fails <- parses[parses!="success"]
works <- files[parses == "success"]
writeLines(fails, "unparseable.txt")
print("testing parsing only")
treebase <- sapply(works,
function(x){
print(x)
tree <- try(nexml_read(x, "nexml"))
if(is(tree, "try-error"))
out = "read failed:"
else {
tree <- try(as(tree, "phylo"))
if(is(tree, "try-error"))
out = "conversion failed:"
else
out = "success"
}
rm(tree)
out
})
save(list=ls(), file = "RNeXML_test_results.rda")
table(treebase)
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