@@ -1,6 +1,6 @@

 Package: fenr

 Title: Fast functional enrichment for interactive applications

-Version: 1.3.1

+Version: 1.5.1

 Authors@R: person(

     given = "Marek",

     family = "Gierlinski",

@@ -53,6 +53,6 @@ Suggests:

     knitr,

     rmarkdown,

     topGO

-RoxygenNote: 7.3.1

+RoxygenNote: 7.3.2

 VignetteBuilder: knitr

 LazyData: false

@@ -171,3 +171,6 @@

  - Go term namespace added to the information extracted by `fetch_go`.

+## Version 1.4.1

+

+ - Attempted to fix a bizarre error message on Bioconductor's test machines with older version of MacOS. Windows and Linux are not affected; my laptop running Sequoia 5.2 does not show show errors. I suspect a memory leak in older systems. The error `vector memory limit of 64.0 Gb reached, see mem.maxVSize()` happened in the function parse_kegg_genes(), a flat-file parser for KEGG. It occurred around the call tidyr::separate(), which I replaced with an alternative approach. Will see if the error is fixed.

\ No newline at end of file

@@ -96,16 +96,20 @@ parse_kegg_genes <- function(s) {

       i <- i + 1

     }

-    # create final tibble, attempt to extract gene symbols when semicolon is found

-    genes |>

-      tibble::as_tibble_col(column_name = "data") |>

-      tidyr::separate(data, c("gene_id", "gene_symbol"), sep = "\\s+", extra = "merge") |>

-      dplyr::mutate(gene_symbol = dplyr::if_else(

-        stringr::str_detect(gene_symbol, ";"),

-        stringr::str_remove(gene_symbol, ";.+$"),

-        gene_id

-      )) |>

-      tibble::add_column(term_id = pathway)

+    purrr::map(genes, function(gene) {

+      # First element - gene ID, second - gene symbol, if contains semicolon

+      v <- stringr::str_split_1(gene, "\\s+")

+      tibble::tibble(

+        gene_id = v[1],

+        gene_symbol = ifelse(

+          stringr::str_detect(v[2], ";"),

+          stringr::str_remove(v[2], ";.*$"),

+          v[1]

+        ),

+        term_id = pathway

+      )

+    }) |> 

+      purrr::list_rbind()

   }) |>

     purrr::list_rbind()

 }