r-phylo2vec/scripts/install-package.R:13

• [nitpick] The cleanup code that removed temporary files was removed. If those files are no longer needed, consider documenting why the cleanup step is dropped or restoring it to avoid leaving artifacts.

devtools::install(args[1], build = FALSE)

r-phylo2vec/R/io.R:60

• load_newick() is not marked with @export, so it won't be available to package users. Add #' @export above its definition and include it in NAMESPACE.

load_newick <- function(filepath_or_buffer) {

r-phylo2vec/R/io.R:76

• save_newick() is not marked with @export and is missing from NAMESPACE. Add #' @export and export it so users can call it.

save_newick <- function(vector_or_matrix, filepath, labels = NULL) {

r-phylo2vec/NAMESPACE:16

• The new functions save_newick and load_newick are not exported; they should be added here to expose the I/O API.

export(load_p2v)

py-phylo2vec/phylo2vec/io/reader.py:34

• dtype=None can yield an object dtype for mixed int/float rows, leading to downstream errors. Consider explicitly handling numeric conversions or specifying dtype=float then casting integers afterwards.

arr = np.genfromtxt(filepath, delimiter=delimiter, dtype=None)

r-phylo2vec/src/rust/src/lib.rs:2

• [nitpick] Importing HashMap from extendr_api may be ambiguous. Use std::collections::HashMap for clarity unless extendr_api specifically re-exports it.

use extendr_api::HashMap;

r-phylo2vec/src/rust/src/lib.rs:288

• Calling unwrap() can panic on bad input. Consider propagating an error back to R with map_err or returning a Result instead of unwrapping.

ops::newick::apply_label_mapping(newick, &label_mapping_hash).unwrap()