From a370f6bd07375b5b62952b88d60b189694593d8b Mon Sep 17 00:00:00 2001
From: "Zhian N. Kamvar" <zkamvar@gmail.com>
Date: Sat, 4 Sep 2021 07:15:56 -0700
Subject: [PATCH 1/4] move all headers to the top of the file

This will fix #245
---
 src/bitwise_distance.c | 10 +++++-----
 src/init.c             |  2 +-
 src/mlg_clustering.c   |  8 ++++----
 src/msn.c              |  8 ++++----
 src/poppr_distance.c   |  8 ++++----
 5 files changed, 18 insertions(+), 18 deletions(-)

diff --git a/src/bitwise_distance.c b/src/bitwise_distance.c
index 9b2ee7bd..625301f7 100644
--- a/src/bitwise_distance.c
+++ b/src/bitwise_distance.c
@@ -36,19 +36,19 @@
 
 #include <stdio.h>
 #include <stdint.h>
-#include <Rinternals.h>
-#include <R_ext/Utils.h>
-#include <Rdefines.h>
-#include <R.h>
 #include <math.h>
 #include <time.h>
 #include <string.h>
 #include <stdlib.h>
-
 // Include openMP if the compiler supports it
 #ifdef _OPENMP
 #include <omp.h>
 #endif
+#include <Rinternals.h>
+#include <R_ext/Utils.h>
+#include <Rdefines.h>
+#include <R.h>
+
 
 // Assumptions:
 //  All genotypes have the same number of SNPs available.
diff --git a/src/init.c b/src/init.c
index e0fc5e26..46ec08a5 100644
--- a/src/init.c
+++ b/src/init.c
@@ -1,6 +1,6 @@
+#include <stdlib.h> // for NULL
 #include <R.h>
 #include <Rinternals.h>
-#include <stdlib.h> // for NULL
 #include <R_ext/Rdynload.h>
 
 /* FIXME: 
diff --git a/src/mlg_clustering.c b/src/mlg_clustering.c
index 59effca4..5bae3cf9 100644
--- a/src/mlg_clustering.c
+++ b/src/mlg_clustering.c
@@ -35,14 +35,14 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~*/
 
 #include <stdio.h>
-#include <Rinternals.h>
-#include <R_ext/Utils.h>
-#include <Rdefines.h>
-#include <R.h>
 #include <math.h>
 #include <time.h>
 #include <string.h>
 #include <stdlib.h>
+#include <Rinternals.h>
+#include <R_ext/Utils.h>
+#include <Rdefines.h>
+#include <R.h>
 
 // Thu Apr 13 08:42:12 2017 ------------------------------
 // This code produces bugs when run on Fedora with multiple threads. Because of
diff --git a/src/msn.c b/src/msn.c
index 5fd8dce4..4a51694f 100644
--- a/src/msn.c
+++ b/src/msn.c
@@ -35,10 +35,6 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~*/
 
 #include <stdio.h>
-#include <Rinternals.h>
-#include <R_ext/Utils.h>
-#include <Rdefines.h>
-#include <R.h>
 #include <math.h>
 #include <time.h>
 #include <string.h>
@@ -47,6 +43,10 @@
 #ifdef _OPENMP
 #include <omp.h>
 #endif
+#include <Rinternals.h>
+#include <R_ext/Utils.h>
+#include <Rdefines.h>
+#include <R.h>
 
 
 /*~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
diff --git a/src/poppr_distance.c b/src/poppr_distance.c
index 2f139d7b..ad0e3e8d 100755
--- a/src/poppr_distance.c
+++ b/src/poppr_distance.c
@@ -34,14 +34,14 @@
 #
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~*/
 #include <stdio.h>
-#include <Rinternals.h>
-#include <Rdefines.h>
-#include <R.h>
-#include <R_ext/Utils.h>
 #include <math.h>
 #include <time.h>
 #include <string.h>
 #include <stdlib.h>
+#include <Rinternals.h>
+#include <Rdefines.h>
+#include <R.h>
+#include <R_ext/Utils.h>
 int perm_count;
 
 SEXP pairwise_covar(SEXP pair_vec);

From 46faacc6378799e79cb7a05173e10974562f71dc Mon Sep 17 00:00:00 2001
From: "Zhian N. Kamvar" <zkamvar@gmail.com>
Date: Sat, 4 Sep 2021 11:04:36 -0700
Subject: [PATCH 2/4] update NEWS; bump version

---
 DESCRIPTION | 2 +-
 NEWS.md     | 9 +++++++++
 2 files changed, 10 insertions(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 3c2da37a..f11b3b47 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: poppr
 Type: Package
 Title: Genetic Analysis of Populations with Mixed Reproduction
-Version: 2.9.2
+Version: 2.9.3
 Authors@R: c(person(c("Zhian", "N."), "Kamvar", role = c("cre", "aut"),
     email = "zkamvar@gmail.com", comment = c(ORCID = "0000-0003-1458-7108")),
     person(c("Javier", "F."), "Tabima", role = "aut",
diff --git a/NEWS.md b/NEWS.md
index b607b293..0245bb98 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,12 @@
+poppr 2.9.3
+===========
+
+CRAN MAINTENANCE
+----------------
+
+* C headers were re-arranged to place R-specific headers _after_ OMP headers to
+  avoid problems in clang 13 (@zkamvar, https://github.com/grunwaldlab/poppr/pull/246).
+
 poppr 2.9.2
 ===========
 

From 4013eba7d88c2b7211647cb542764f6f5c9289f7 Mon Sep 17 00:00:00 2001
From: "Zhian N. Kamvar" <zkamvar@gmail.com>
Date: Mon, 6 Sep 2021 17:12:38 -0700
Subject: [PATCH 3/4] update cran comments

---
 cran-comments.md | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/cran-comments.md b/cran-comments.md
index 8bdf973d..3dc773c8 100644
--- a/cran-comments.md
+++ b/cran-comments.md
@@ -1,11 +1,11 @@
-# Poppr version 2.9.2
+# Poppr version 2.9.3
 
-This update fixes a test failure pointed out by CRAN on 2021-05-21
+This update rearranges the C files to declare all non-R headers before R headers to address the openmp failures in clang13 as pointed out by Prof. Ripley. 
 
 ## Test environments
 
-* local macOS install, R 4.1.0
-* local ubuntu 20.04 install, R 4.1.0
+* local macOS install, R 4.1.1
+* local ubuntu 20.04 install, R 4.1.1, R devel
 * windows R Under development (unstable) 
 
 ## R CMD check results

From 000c00f987a83fe4c5db67ff142ee33ef3e502a5 Mon Sep 17 00:00:00 2001
From: "Zhian N. Kamvar" <zkamvar@gmail.com>
Date: Tue, 7 Sep 2021 07:36:59 -0700
Subject: [PATCH 4/4] release to CRAN (yesterday)

---
 CRAN-RELEASE | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/CRAN-RELEASE b/CRAN-RELEASE
index b134f242..ab1088bf 100644
--- a/CRAN-RELEASE
+++ b/CRAN-RELEASE
@@ -1,2 +1,2 @@
-This package was submitted to CRAN on 2021-05-22.
-Once it is accepted, delete this file and tag the release (commit f0601677).
+This package was submitted to CRAN on 2021-09-06.
+Once it is accepted, delete this file and tag the release (commit 4013eba7).