From 6e26dd50831e408540d78efbfa5751963a2d045e Mon Sep 17 00:00:00 2001
From: "Martin R. Smith" <1695515+ms609@users.noreply.github.com>
Date: Thu, 5 Sep 2024 14:00:56 +0100
Subject: [PATCH] MKL testing

---
 .github/workflows/rhub.yaml               | 2 +-
 DESCRIPTION                               | 2 +-
 NEWS.md                                   | 5 +++++
 cran-comments.md                          | 4 ++--
 tests/testthat/test-spectral_clustering.R | 3 ++-
 5 files changed, 11 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/rhub.yaml b/.github/workflows/rhub.yaml
index de92657f..1383a3ff 100644
--- a/.github/workflows/rhub.yaml
+++ b/.github/workflows/rhub.yaml
@@ -15,7 +15,7 @@ on:
       config:
         description: 'A comma separated list of R-hub platforms to use.'
         type: string
-        default: 'linux,macos,macos-arm64,windows,atlas,clang-asan,valgrind'
+        default: 'linux,macos,macos-arm64,windows,atlas,mkl,clang-asan,valgrind'
       name:
         description: 'Run name (optional)'
         type: string
diff --git a/DESCRIPTION b/DESCRIPTION
index d2dd615d..a9d5caf4 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: TreeDist
 Type: Package
 Title: Calculate and Map Distances Between Phylogenetic Trees
-Version: 2.9.0
+Version: 2.9.1
 Authors@R: c(person("Martin R.", "Smith",
                     email = "martin.smith@durham.ac.uk", 
                     role = c("aut", "cre", "cph", "prg"), 
diff --git a/NEWS.md b/NEWS.md
index bd94a8f9..315e7e5d 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,8 @@
+# TreeDist 2.9.1 (2024-09-05)
+
+- Avoid false positive in MKL testing environment.
+
+
 # TreeDist 2.9.0 (2024-09-03)
 
 - `VisualizeMatching()` allows more control over output format, and returns
diff --git a/cran-comments.md b/cran-comments.md
index 3c921e5d..d17cbc82 100644
--- a/cran-comments.md
+++ b/cran-comments.md
@@ -1,5 +1,5 @@
 ## Test environments
-* Local machine, Windows 10, R 4.4.1 (2024-06-14 ucrt)
+* Local machine, Windows 10, R devel (2024-09-02 r87090 ucrt)
 
 * `devtools::check_win_devel()`
 
@@ -11,7 +11,7 @@
 * [valgrind mem-check](https://github.com/ms609/TreeDist/actions/workflows/memcheck.yml)
 
 * [R-hub](https://github.com/ms609/TreeDist/actions/workflows/rhub.yaml):
-  - linux,macos,macos-arm64,windows,atlas,clang-asan,valgrind
+  - linux,macos,macos-arm64,windows,atlas,mkl,clang-asan,valgrind
 
 
 ## Downstream dependencies
diff --git a/tests/testthat/test-spectral_clustering.R b/tests/testthat/test-spectral_clustering.R
index 5d3952bf..89ceed48 100644
--- a/tests/testthat/test-spectral_clustering.R
+++ b/tests/testthat/test-spectral_clustering.R
@@ -7,5 +7,6 @@ test_that("Spectral clustering fails gracefully", {
 test_that("Spectral clustering works", {
   allEig <- SpectralEigens(d, nEig = Inf)
   expect_equal(dim(allEig), c(40, 40))
-  expect_equal(SpectralEigens(d, nEig = 2), allEig[, 40:39])
+  expect_equal(SpectralEigens(d, nEig = 2), allEig[, 40:39],
+               tolerance = sqrt(.Machine[["double.eps"]]))
 })