From 9dfb1cd22e847f0cbaf412799a1981a529637c37 Mon Sep 17 00:00:00 2001
From: Jeffrey Endelman <j.endelman@gmail.com>
Date: Tue, 3 Apr 2012 00:00:00 +0000
Subject: [PATCH] version 3.6

---
 DESCRIPTION     |  6 +++---
 MD5             |  6 +++---
 NEWS            |  4 ++++
 R/mixed.solve.R | 13 ++++++++++---
 4 files changed, 20 insertions(+), 9 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 7dcb9af..f2f68f8 100755
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: rrBLUP
 Title: Ridge regression and other kernels for genomic selection
-Version: 3.5
+Version: 3.6
 Author: Jeffrey Endelman
 Maintainer: Jeffrey Endelman <j.endelman@gmail.com>
 Description: One application is to estimate marker effects by ridge
@@ -11,6 +11,6 @@ Description: One application is to estimate marker effects by ridge
 Suggests: multicore
 License: GPL-3
 LazyLoad: yes
-Packaged: 2012-02-10 20:05:57 UTC; jeffendelman
+Packaged: 2012-04-03 15:31:52 UTC; jeffendelman
 Repository: CRAN
-Date/Publication: 2012-02-14 07:20:59
+Date/Publication: 2012-04-03 21:02:09
diff --git a/MD5 b/MD5
index 102e087..6495072 100644
--- a/MD5
+++ b/MD5
@@ -1,10 +1,10 @@
-06639f9b86d7b7d138f356c360e8ed3a *DESCRIPTION
+909f5f0706ea232931f64ee54eccdd1f *DESCRIPTION
 9983baa53027ec7ecc5c44dc94318515 *NAMESPACE
-c5119304691b321449950ff08d841a98 *NEWS
+76fb9f9fdc5f599f1e738375331e9fc1 *NEWS
 3426a5afa2b38e987e53b354c267f488 *R/A.mat.R
 48dcf02533fd05c528f6c6ea2cd022fb *R/GWA.R
 f9b894abb6a3158ebfabe61486dccd94 *R/kinship.BLUP.R
-b02c08fda6a873bb6a221650e7547a96 *R/mixed.solve.R
+0d21c26c501e27b2d61363e369edb57c *R/mixed.solve.R
 b74e4e9e2c643e550a83c5ee4eb7e905 *inst/CITATION
 fbaf1e01452ed907bdb412ff35f3b067 *man/A.mat.Rd
 89ab7c69f6c5dbfca37b5220dd14525b *man/GWA.Rd
diff --git a/NEWS b/NEWS
index 4ed1c08..555cc83 100755
--- a/NEWS
+++ b/NEWS
@@ -1,3 +1,7 @@
+Changes in 3.6:
+
+* Improved error handling in mixed.solve.
+
 Changes in 3.5:
 
 * Labels now transfer from input to output with mixed.solve.
diff --git a/R/mixed.solve.R b/R/mixed.solve.R
index 26df3dd..378d9c9 100755
--- a/R/mixed.solve.R
+++ b/R/mixed.solve.R
@@ -75,9 +75,15 @@ svd.SZBt <- svd(SZBt)
 QR <- qr(cbind(X,svd.SZBt$u))
 Q <- qr.Q(QR,complete=TRUE)[,(p+1):n]
 R <- qr.R(QR)[p+1:m,p+1:m]
-theta <- c(forwardsolve(t(R^2),svd.SZBt$d^2),rep(0,n-p-m))
+ans <- try(solve(t(R^2), svd.SZBt$d^2),silent=TRUE)
+if (class(ans)=="try-error") {
+    spectral.method <- "eigen"
 } else {
-# spectral.method is "eigen"
+    theta <- c(ans,rep(0, n - p - m))
+}
+}
+
+if (spectral.method=="eigen") {
 offset <- sqrt(n)
 if (is.null(K)) {
 	Hb <- tcrossprod(Z,Z) + offset*diag(n)
@@ -92,7 +98,8 @@ SHbS <- S %*% Hb %*% S
 SHbS.system <- eigen(SHbS, symmetric = TRUE)
 theta <- SHbS.system$values[1:(n - p)] - offset
 Q <- SHbS.system$vectors[, 1:(n - p)]
-}  #if (n > m)
+}  
+    
 omega <- crossprod(Q, y)
 omega.sq <- omega^2
 if (method == "ML") {