From 2875cfa149260264819dc696791645e3b747b852 Mon Sep 17 00:00:00 2001
From: Tuomas Borman <tvborm@utu.fi>
Date: Wed, 29 Jul 2026 13:58:42 +0300
Subject: [PATCH 1/3] fix formula parsing

---
 R/runCCA.R | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/R/runCCA.R b/R/runCCA.R
index 5e9f47d32..6aadbb2a7 100644
--- a/R/runCCA.R
+++ b/R/runCCA.R
@@ -480,8 +480,7 @@ setMethod("addRDA", "SingleCellExperiment",
             "'col.var' and leave 'formula' unspecified.", call. = FALSE)
     }
     # Get variables from formula
-    terms <- rownames(attr(terms(formula), "factors"))
-    terms <- terms[terms != as.character(formula)[2L]]
+    terms <- formula |> terms() |> delete.response() |> all.vars()
     terms <- .remove_special_functions_from_terms(terms)
     # Check that all variables specify a column from colData
     if( !all(terms %in% colnames(colData(x))) ){

From ecefa0049f565d785a10960f04775599d8a151dd Mon Sep 17 00:00:00 2001
From: Tuomas Borman <tvborm@utu.fi>
Date: Wed, 29 Jul 2026 14:02:34 +0300
Subject: [PATCH 2/3] up

---
 R/runCCA.R                 |  1 -
 tests/testthat/test-6cca.R | 12 ------------
 2 files changed, 13 deletions(-)

diff --git a/R/runCCA.R b/R/runCCA.R
index 6aadbb2a7..29ff9217d 100644
--- a/R/runCCA.R
+++ b/R/runCCA.R
@@ -481,7 +481,6 @@ setMethod("addRDA", "SingleCellExperiment",
     }
     # Get variables from formula
     terms <- formula |> terms() |> delete.response() |> all.vars()
-    terms <- .remove_special_functions_from_terms(terms)
     # Check that all variables specify a column from colData
     if( !all(terms %in% colnames(colData(x))) ){
         stop("All variables on the right hand side of 'formula' must be ",
diff --git a/tests/testthat/test-6cca.R b/tests/testthat/test-6cca.R
index 470968be4..db9878a0a 100644
--- a/tests/testthat/test-6cca.R
+++ b/tests/testthat/test-6cca.R
@@ -1,17 +1,5 @@
 context("CCA")
 test_that("CCA", {
-    # .remove_special_functions_from_terms
-    expect_error(mia:::.remove_special_functions_from_terms(),
-                 'argument "terms" is missing, with no default')
-    expect_equal(mia:::.remove_special_functions_from_terms("abc"),
-                 c(abc = "abc"))
-    expect_equal(mia:::.remove_special_functions_from_terms("Condition(abc)"),
-                 c("Condition(abc)" = "abc"))
-    expect_equal(mia:::.remove_special_functions_from_terms(c("abc","def")),
-                 c(abc = "abc", def = "def"))
-    expect_equal(mia:::.remove_special_functions_from_terms(c("Condition(abc)","def")),
-                 c("Condition(abc)" = "abc", def = "def"))
-    #
     skip_if_not(requireNamespace("vegan", quietly = TRUE))
     data(dune, dune.env, package = "vegan")
     sce <- SingleCellExperiment(assays = list(counts = t(dune)),

From 868ec2da00ac1647695880ad6c2e332430cc13d6 Mon Sep 17 00:00:00 2001
From: Tuomas Borman <tvborm@utu.fi>
Date: Wed, 29 Jul 2026 14:03:45 +0300
Subject: [PATCH 3/3] up

---
 R/runCCA.R | 14 --------------
 1 file changed, 14 deletions(-)

diff --git a/R/runCCA.R b/R/runCCA.R
index 29ff9217d..af2ba2446 100644
--- a/R/runCCA.R
+++ b/R/runCCA.R
@@ -491,20 +491,6 @@ setMethod("addRDA", "SingleCellExperiment",
     return(df)
 }
 
-# This function parses right-hand side formula so that it now includes only
-# the covariates.
-.remove_special_functions_from_terms <- function(terms){
-    names(terms) <- terms
-    m <- regexec("^Condition\\(([^\\(\\)]*)\\)$|^([^\\(\\)]*)$", terms)
-    m <- regmatches(terms, m)
-    terms <- vapply(m, function(n){
-        n <- n[seq.int(2L,length(n))]
-        n <- n[n != ""]
-        return(n)
-        }, character(1))
-    return(terms)
-}
-
 # This function performs dbRDA or CCA. It returns side scores with other
 # information scores in attributes.
 #' @importFrom stats as.formula na.fail