Merge pull request #89 from stitam/gbif

Fix checks on macOS
ropensci · Feb 4, 2025 · 83488da · 83488da
2 parents e0d74e6 + 36953a9
commit 83488da
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Showing 2 changed files with 8 additions and 7 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -29,7 +29,8 @@ Imports:
     dbplyr (>= 1.0.0),
     magrittr (>= 1.5),
     hoardr (>= 0.1.0),
-    taxize
+    taxize,
+    vroom
 Suggests:
     testthat
 Remotes: ropensci/bold, ropensci/taxize

diff --git a/R/db_download.R b/R/db_download.R
@@ -485,15 +485,15 @@ db_download_gbif <- function(verbose = TRUE, overwrite = FALSE) {
   mssg(verbose, 'building SQLite database...')
   db <- RSQLite::dbConnect(RSQLite::SQLite(), dbname = db_path)
 
-  out <- readr::read_tsv_chunked(
+  out <- vroom::vroom(
     paste0(tdb_cache$cache_path_get(), "/gbif/Taxon.tsv"),
-    callback = function(chunk, dummy) {
-      DBI::dbWriteTable(db, "gbif", chunk, append = T)
-    },
-    chunk_size = 10000,
-    col_types = "icccccccccccccccccccccc"
+    delim = "\t",
+    col_types = "icccccccccccccccccccccc",
+    progress = FALSE
   )
 
+  DBI::dbWriteTable(db, "gbif", out, append = TRUE, batch_rows = 10000)
+
   # create indices
   RSQLite::dbExecute(db, 'CREATE UNIQUE INDEX id on gbif (taxonID)')
   RSQLite::dbExecute(db, 'CREATE INDEX conname on gbif (canonicalName)')