Merge pull request #246 from grunwaldlab/fix-clang-13

move all headers to the top of the file

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).

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 = "[email protected]", comment = c(ORCID = "0000-0003-1458-7108")),
     person(c("Javier", "F."), "Tabima", role = "aut",

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
 ===========
 

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

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.

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: 

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

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>
 
 
 /*~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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);