Parentheses error importing tree with R version 4.1.1

[jrede]

Hi @jbisanz ,

I recently updated R to 4.1.1 because of compatibility issues. However, now when I try to import a .qza tree file I get the following error:

Error in FUN(X[[i]], ...) :
numbers of left and right parentheses in Newick string not equal

Any idea how to fix this without running two versions of R?

Thanks!
Jordan

[roxanacoras]

Hi, I have the exact same problem!
I would appreciate your help with fixing this.

Thanks a lot,
Roxana

[mestaki]

I believe this is the same as #33 resulting from something with newest version of "ape".
If ape is just being used for reading the tree then phytools::read.newick("tree.nwk") could be an easy replacement? Worked fine for me from an extract Q2 tree.

[jbisanz]

@mestaki That sounds like a great idea. Could you test this and do a pull request? You would add phytools to DESCRIPTION, add in the import of read.newick to NAMESPACE and change line 48 of R/read_qza.R,

[mestaki]

Sounds good @jbisanz, hopefully I'll have some time next week to test this properly.