closes #110

MicrobialGenomics-IrsicaixaOrg · Dec 14, 2023 · 45f83d8 · 45f83d8
1 parent b1afac6
commit 45f83d8
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Showing 2 changed files with 34 additions and 20 deletions.
diff --git a/R/corncob.R b/R/corncob.R
@@ -128,25 +128,37 @@ methods::setMethod(
                         rarefy,
                         id) {
 
-    recipes_pkg_check(required_pkgs_corncob(), "step_croncob()")
-    add_step(
-      rec,
-      step_corncob_new(
-        phi.formula = phi.formula,
-        formula_null = formula_null,
-        phi.formula_null = phi.formula_null,
-        link = link,
-        phi.link = phi.link,
-        test = test,
-        boot = boot,
-        B = B,
-        filter_discriminant = filter_discriminant,
-        fdr_cutoff = fdr_cutoff,
-        fdr = fdr,
-        log2FC = log2FC,
-        rarefy = rarefy,
-        id = id
-      ))
+    check <- recipes_pkg_check(required_pkgs_corncob(), "step_croncob()")
+    if (check) {
+      rec <- add_step(
+        rec,
+        step_corncob_new(
+          phi.formula = phi.formula,
+          formula_null = formula_null,
+          phi.formula_null = phi.formula_null,
+          link = link,
+          phi.link = phi.link,
+          test = test,
+          boot = boot,
+          B = B,
+          filter_discriminant = filter_discriminant,
+          fdr_cutoff = fdr_cutoff,
+          fdr = fdr,
+          log2FC = log2FC,
+          rarefy = rarefy,
+          id = id
+        ))
+    } else {
+      rlang::inform(c(
+        "i" = glue::glue(
+          "The {crayon::blue('corncob')} package is currently unavailable on ",
+          "CRAN due to dependency issues. The functionality of this function ",
+          "that requires {crayon::blue('corncob')} has been temporarily ",
+          "disabled."
+        )
+      ), use_cli_format = TRUE)
+    }
+  rec
   }
 )
 

diff --git a/R/pkg_check.R b/R/pkg_check.R
@@ -37,6 +37,7 @@ recipes_pkg_check <- function(pkg = NULL, step_name, ...) {
     }
   }
 
+  res <- TRUE
   if (any(!good)) {
     pkList <- paste(
       stringr::str_remove_all(pkg[!good], ".*[/]|.*[:]") , collapse = ", "
@@ -73,9 +74,10 @@ recipes_pkg_check <- function(pkg = NULL, step_name, ...) {
       '{crayon::blue(inst)}' 
     )
     cat(c(msg, "\n"))
+    res <- FALSE
   }
 
-  invisible()
+  invisible(res)
 }
 
 #' @noRd