From 68eca2d39c4a4276bc37f514347b1323b4e7ea4c Mon Sep 17 00:00:00 2001
From: ms609-agent <313734811+ms609-agent@users.noreply.github.com>
Date: Fri, 16 Oct 2026 13:04:58 +0100
Subject: [PATCH 1/3] Suggest parallelly::availableCores() in mc.cores docs

parallel::detectCores() reports the hardware count; availableCores()
respects scheduler and cgroup allocations, R CMD check's core limit and
MC_CORES, so "use all cores" no longer oversubscribes a shared machine
or HPC job. Prose snippets only; no new dependency.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
---
 R/parallel.R           | 4 ++--
 R/tree_distance_info.R | 4 ++--
 man/StartParallel.Rd   | 4 ++--
 man/TreeDistance.Rd    | 4 ++--
 4 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/R/parallel.R b/R/parallel.R
index 9c835b064..5f81d2e16 100644
--- a/R/parallel.R
+++ b/R/parallel.R
@@ -22,8 +22,8 @@
 #' `"mc.cores"` option:
 #' 
 #' ```r
-#' options(mc.cores = parallel::detectCores())  # use all available cores
-#' options(mc.cores = 4L)                        # or a fixed number
+#' options(mc.cores = parallelly::availableCores())  # use all available cores
+#' options(mc.cores = 4L)                             # or a fixed number
 #' ```
 #' 
 #' The default is `1` (single-threaded).
diff --git a/R/tree_distance_info.R b/R/tree_distance_info.R
index 3cfe8c69f..a6ad95d47 100644
--- a/R/tree_distance_info.R
+++ b/R/tree_distance_info.R
@@ -128,8 +128,8 @@
 #' automatically.  Control the number of threads with the `"mc.cores"` option:
 #' 
 #' ```r
-#' options(mc.cores = parallel::detectCores())  # use all cores
-#' options(mc.cores = 4L)                        # or a fixed number
+#' options(mc.cores = parallelly::availableCores())  # use all cores
+#' options(mc.cores = 4L)                             # or a fixed number
 #' ```
 #' 
 #' Do **not** call [`StartParallel()`] for these functions: a registered
diff --git a/man/StartParallel.Rd b/man/StartParallel.Rd
index 1a918897e..0cbf7a106 100644
--- a/man/StartParallel.Rd
+++ b/man/StartParallel.Rd
@@ -54,8 +54,8 @@ no cluster setup is required.  The affected functions are:
 The number of \acronym{OpenMP} threads is controlled by the standard
 \code{"mc.cores"} option:
 
-\if{html}{\out{<div class="sourceCode r">}}\preformatted{options(mc.cores = parallel::detectCores())  # use all available cores
-options(mc.cores = 4L)                        # or a fixed number
+\if{html}{\out{<div class="sourceCode r">}}\preformatted{options(mc.cores = parallelly::availableCores())  # use all available cores
+options(mc.cores = 4L)                             # or a fixed number
 }\if{html}{\out{</div>}}
 
 The default is \code{1} (single-threaded).
diff --git a/man/TreeDistance.Rd b/man/TreeDistance.Rd
index f753909c9..dd0fdce5b 100644
--- a/man/TreeDistance.Rd
+++ b/man/TreeDistance.Rd
@@ -263,8 +263,8 @@ When \code{tree2 = NULL} and all trees share the same tip labels, pairwise
 distance calculation uses a multi-threaded \acronym{OpenMP} batch path
 automatically.  Control the number of threads with the \code{"mc.cores"} option:
 
-\if{html}{\out{<div class="sourceCode r">}}\preformatted{options(mc.cores = parallel::detectCores())  # use all cores
-options(mc.cores = 4L)                        # or a fixed number
+\if{html}{\out{<div class="sourceCode r">}}\preformatted{options(mc.cores = parallelly::availableCores())  # use all cores
+options(mc.cores = 4L)                             # or a fixed number
 }\if{html}{\out{</div>}}
 
 Do \strong{not} call \code{\link[=StartParallel]{StartParallel()}} for these functions: a registered

From a5ff64fa9f8138706efa9fbf39c65c252a579da6 Mon Sep 17 00:00:00 2001
From: "Martin R. Smith" <1695515+ms609@users.noreply.github.com>
Date: Mon, 19 Oct 2026 10:19:27 +0100
Subject: [PATCH 2/3] alignment

---
 R/parallel.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/parallel.R b/R/parallel.R
index 5f81d2e16..c36ef7983 100644
--- a/R/parallel.R
+++ b/R/parallel.R
@@ -23,7 +23,7 @@
 #' 
 #' ```r
 #' options(mc.cores = parallelly::availableCores())  # use all available cores
-#' options(mc.cores = 4L)                             # or a fixed number
+#' options(mc.cores = 4L)                            # or a fixed number
 #' ```
 #' 
 #' The default is `1` (single-threaded).

From a6a119901662592885b9197559dd9eb0cafc930d Mon Sep 17 00:00:00 2001
From: "Martin R. Smith" <1695515+ms609@users.noreply.github.com>
Date: Mon, 19 Oct 2026 10:19:51 +0100
Subject: [PATCH 3/3] Alignment

---
 R/tree_distance_info.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/tree_distance_info.R b/R/tree_distance_info.R
index a6ad95d47..296be5419 100644
--- a/R/tree_distance_info.R
+++ b/R/tree_distance_info.R
@@ -129,7 +129,7 @@
 #' 
 #' ```r
 #' options(mc.cores = parallelly::availableCores())  # use all cores
-#' options(mc.cores = 4L)                             # or a fixed number
+#' options(mc.cores = 4L)                            # or a fixed number
 #' ```
 #' 
 #' Do **not** call [`StartParallel()`] for these functions: a registered