Merge pull request #299 from alexmccreight/master

Matrix symmetry check with mismatching row/col names bug fix

Author: gaow

DESCRIPTION

@@ -16,7 +16,7 @@ Description: Implements methods for variable selection in linear
     and fast, allowing the SuSiE model be fit to large data sets
     (thousands of samples and hundreds of thousands of variables).
 Date: 2026-03-09
-Version: 0.15.56
+Version: 0.15.57
 Authors@R: c(person("Gao","Wang",role="aut",email="wang.gao@columbia.edu"),
              person("Yuxin","Zou",role="aut"),
              person("Alexander","McCreight",role="aut"),

R/susie_constructors.R

@@ -950,8 +950,9 @@ rss_lambda_constructor <- function(z, R = NULL, X = NULL, n = NULL,
         length(z), ")."
       ))
     }
-    if (!isSymmetric(R)) {
-      stop("R is not a symmetric matrix.")
+    if (!is_symmetric_matrix(R)) {
+      warning_message("R not symmetric; using (R + t(R))/2.")
+      R <- (R + t(R)) / 2
     }
     if (!(is.double(R) & is.matrix(R)) & !inherits(R, "sparseMatrix")) {
       stop("Input R must be a double-precision matrix or a sparse matrix.")

R/susie_utils.R

@@ -116,7 +116,7 @@ is_symmetric_matrix <- function(x) {
       requireNamespace("Rfast", quietly = TRUE)) {
     return(Rfast::is.symmetric(x))
   } else {
-    return(Matrix::isSymmetric(x))
+    return(Matrix::isSymmetric(x, check.attributes = FALSE))
   }
 }
 

tests/testthat/test_susie_constructors.R

@@ -1137,6 +1137,41 @@ test_that("rss_lambda_constructor rejects non-symmetric R", {
   )
 })
 
+test_that("rss_lambda_constructor accepts R with mismatched rownames and colnames", {
+  p <- 10
+  z <- rnorm(p)
+  R <- diag(p)
+  rownames(R) <- paste0("row_", 1:p)
+  colnames(R) <- paste0("col_", 1:p)
+
+  # Should succeed despite mismatched dimnames (values are symmetric)
+  result <- rss_lambda_constructor(z, R, lambda = 0.5)
+  expect_equal(result$data$p, p)
+  expect_s3_class(result$data, "rss_lambda")
+})
+
+test_that("rss_lambda_constructor accepts R with matching rownames and colnames", {
+  p <- 10
+  z <- rnorm(p)
+  R <- diag(p)
+  rownames(R) <- paste0("SNP", 1:p)
+  colnames(R) <- paste0("SNP", 1:p)
+
+  result <- rss_lambda_constructor(z, R, lambda = 0.5)
+  expect_equal(result$data$p, p)
+  expect_s3_class(result$data, "rss_lambda")
+})
+
+test_that("rss_lambda_constructor accepts R with no dimnames", {
+  p <- 10
+  z <- rnorm(p)
+  R <- diag(p)
+
+  result <- rss_lambda_constructor(z, R, lambda = 0.5)
+  expect_equal(result$data$p, p)
+  expect_s3_class(result$data, "rss_lambda")
+})
+
 test_that("rss_lambda_constructor rejects integer matrix R", {
   R <- matrix(1:25, 5, 5)
   R <- R + t(R)  # Make it symmetric