Skip scanning of gzipped file if zgrep is not detected

R/gb-setup-tools.R

@@ -168,8 +168,9 @@ gb_sql_add <- function(df) {
 #' @param dpth Download path (where seq_files are stored)
 #' @param seq_files .seq.tar seq file names
 #' @param scan Logical vector of length 1; should the sequence file be scanned
-#' for accessions in `acc_filter` prior to processing? Only used if
-#' `acc_filter` is not NULL and `invert` is FALSE. Default FALSE.
+#' for accessions in `acc_filter` prior to processing?
+#' Requires zgrep to be installed (so does not work on Windows).
+#' Only used if `acc_filter` is not NULL and `invert` is FALSE. Default FALSE.
 #' @return Logical
 #' @family private
 gb_build <- function(
@@ -221,6 +222,11 @@ gb_build <- function(
 #' @return Logical
 #' @family private
 search_gz <- function(terms, path) {
+  # Skip scan if no zgrep
+  if (nchar(Sys.which("zgrep")) == 0) {
+    warning("Cannot scan gzipped file without zgrep; skipping scan")
+    return(TRUE)
+  }
   # There are a potentially large number of terms,
   # so grepping works best with external files
   temp_file <- tempfile()