From 0d035e586d527f75b4ddc36b851585fff4db37a3 Mon Sep 17 00:00:00 2001
From: Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>
Date: Mon, 16 Sep 2024 15:06:38 +0200
Subject: [PATCH] Possible fix for CRAN check errors on non windows systems

---
 R/f_dc_CA.R               | 16 +++++++++++-----
 inst/tinytest/test_dcca.R |  2 +-
 2 files changed, 12 insertions(+), 6 deletions(-)

diff --git a/R/f_dc_CA.R b/R/f_dc_CA.R
index bc02ce4..2ecf06c 100644
--- a/R/f_dc_CA.R
+++ b/R/f_dc_CA.R
@@ -74,18 +74,24 @@ calculate_b_se_tval <- function(X_or_qr_decomp_of_X,
     out1 <- fitted_values
   } else {
     if (any(is.na(beta_hat))) {
-      warning("collinearity detected in ", name, "-model.\n")
+      warning("collinearity detected in ", name, "-model.\n", call. = FALSE)
     }
     # Compute residual sum of squares (RSS)
     RSS <- colSums(residuals ^ 2)
     # Estimate variance of the errors
     n <- length(w)
     p <- QR$rank
-    sigma_hat_sq <- RSS / (n - p - 1 ) 
+    sigma_hat_sq <- RSS / (n - p - 1) 
     # Calculate variance-covariance matrix of the estimated regression coefficients
-    XtXinv <- chol2inv(QR$qr)
-    diagXtX_inv <- diag(chol2inv(QR$qr)) 
-    names(diagXtX_inv) <- colnames(QR$qr)
+    diagXtX_inv <- diag(chol2inv(QR$qr, size = p))
+    naBetaHat <- apply(X = beta_hat, MARGIN = 1, FUN = function(x) all(is.na(x)))
+    if (sum(naBetaHat) > 0) {
+      diagXtX_inv <- c(diagXtX_inv, rep(NA, times = sum(naBetaHat)))
+      names(diagXtX_inv) <- c(colnames(QR$qr)[!naBetaHat], 
+                              rownames(beta_hat)[naBetaHat])
+    } else {
+      names(diagXtX_inv) <- colnames(QR$qr)
+    }
     diagXtX_inv <- diagXtX_inv[rownames(beta_hat)]
     se <- matrix(nrow = nrow(beta_hat), ncol = length(sigma_hat_sq))
     for (i in seq_along(sigma_hat_sq)) {
diff --git a/inst/tinytest/test_dcca.R b/inst/tinytest/test_dcca.R
index f08dca4..956f68c 100644
--- a/inst/tinytest/test_dcca.R
+++ b/inst/tinytest/test_dcca.R
@@ -46,7 +46,7 @@ expect_message(mod_dcca3 <- dc_CA(formulaEnv = ~ A1 + Moist + Mag + Use + Manure
                                   verbose = FALSE),
                "Some constraints or conditions were aliased because they were redundant")
 
-expect_warning(scores(mod_dcca3),"collinearity detected in SNC-model")																			
+expect_warning(scores(mod_dcca3), "collinearity detected in SNC-model")																			
 expect_inherits(mod_dcca, "dcca")
 expect_equal_to_reference(mod_dcca, "mod_dcca")