Minor changes for Bioconductor release.

bartongroup · Oct 11, 2023 · 6bd0a7a · 6bd0a7a
1 parent d1e672d
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Showing 9 changed files with 33 additions and 8 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: fenr
 Title: Fast functional enrichment for interactive applications
-Version: 0.99.6
+Version: 0.99.7
 Authors@R: person(
     given = "Marek",
     family = "Gierlinski",

diff --git a/NEWS.md b/NEWS.md
@@ -111,4 +111,7 @@
  - Replaced yeast with simpler organisms in Wiki and KEGG tests to speed up testing
  - Replaced yeast with simpler organisms in Wiki and KEGG examples to speed up checking
 
-
+## Version 0.99.7
+
+ - Minor changes to prepare for Bioconductor release
+ - Reverting temporarily to *readr* version 1 to circumvent a *vroom* 1.6.4 bug
diff --git a/R/go.R b/R/go.R
@@ -48,6 +48,9 @@ fetch_go_terms <- function(obo_file = "http://purl.obolibrary.org/obo/go.obo",
   # Binding variables from non-standard evaluation locally
   key <- term_id <- value <- term_name <- NULL
 
+  # Temporary patch to circumvent vroom 1.6.4 bug
+  readr::local_edition(1)
+
   lpath <- cached_url_path("obo", obo_file, use_cache)
   parsed <- readr::read_lines(lpath) |>
     parse_obo_file()
@@ -122,6 +125,9 @@ fetch_go_genes_go <- function(species, use_cache) {
   gene_synonym <- db_object_synonym <- symbol <- NULL
   db_id <- go_term <- NULL
 
+  # Temporary patch to circumvent vroom 1.6.4 bug
+  readr::local_edition(1)
+
   gaf_file <- stringr::str_glue("http://current.geneontology.org/annotations/{species}.gaf.gz")
   assert_url_path(gaf_file)
 

diff --git a/R/iteractive_example.R → R/interactive_example.R b/R/iteractive_example.R → R/interactive_example.R
@@ -173,10 +173,10 @@ main_plot <- function(de, input) {
 #' @importFrom assertthat assert_that
 #' @export
 #' @examples
-#' \dontrun{
 #' data(yeast_de)
 #' term_data <- fetch_terms_for_example(yeast_de)
-#' enrichment_interactive(yeast_de, term_data)
+#' if(interactive()) {
+#'   enrichment_interactive(yeast_de, term_data)
 #' }
 enrichment_interactive <- function(de, term_data) {
   assert_that(is.data.frame(de))

diff --git a/R/kegg.R b/R/kegg.R
@@ -22,6 +22,10 @@ fetch_kegg_data <- function(path) {
 #' @examples
 #' spe <- fetch_kegg_species()
 fetch_kegg_species <- function() {
+
+  # Temporary patch to circumvent vroom 1.6.4 bug
+  readr::local_edition(1)
+
   s <- fetch_kegg_data("list/organism")
   readr::read_tsv(I(s), col_names = c("id", "designation", "species", "phylogeny"), show_col_types = FALSE)
 }
@@ -37,6 +41,9 @@ fetch_kegg_pathways <- function(species) {
   # Binding variables from non-standard evaluation locally
   term_id <- NULL
 
+  # Temporary patch to circumvent vroom 1.6.4 bug
+  readr::local_edition(1)
+
   query <- stringr::str_glue("list/pathway/{species}")
   url <- file.path(KEGG_BASE_URL, query)
   if(!assert_url_path(url, stop_if_error = FALSE))

diff --git a/R/reactome.R b/R/reactome.R
@@ -65,6 +65,9 @@ fetch_reactome_ensembl_genes <- function(spec, use_cache = TRUE) {
   # Binding variables from non-standard evaluation locally
   species <- gene_id <- term_id <- NULL
 
+  # Temporary patch to circumvent vroom 1.6.4 bug
+  readr::local_edition(1)
+
   url <- "https://reactome.org/download/current/Ensembl2Reactome.txt"
   assert_url_path(url)
 
@@ -87,6 +90,9 @@ fetch_reactome_gene_association <- function(tax_id, use_cache = TRUE) {
   # Binding variables from non-standard evaluation locally
   symbol <- taxon <- db_ref <- db_id <- NULL
 
+  # Temporary patch to circumvent vroom 1.6.4 bug
+  readr::local_edition(1)
+
   gaf_file <- "https://reactome.org/download/current/gene_association.reactome.gz"
   assert_url_path(gaf_file)
 

diff --git a/man/enrichment_interactive.Rd b/man/enrichment_interactive.Rd
diff --git a/man/fetch_terms_for_example.Rd b/man/fetch_terms_for_example.Rd
diff --git a/tests/testthat/test_kegg.R b/tests/testthat/test_kegg.R
@@ -13,6 +13,9 @@ test_that("Incorrect batch size in fetch_kegg", {
 
 
 test_that("Parsing KEGG flat file", {
+  # Temporary patch to circumvent vroom 1.6.4 bug
+  readr::local_edition(1)
+
   flat <- readr::read_file("../test_data/kegg_test.txt")
   expected <- readr::read_rds("../test_data/kegg_parseing_result.rds")
   parsed <- parse_kegg_genes(flat)