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). 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 =========== 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 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 #include -#include -#include -#include -#include #include #include #include #include - // Include openMP if the compiler supports it #ifdef _OPENMP #include #endif +#include +#include +#include +#include + // 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 // for NULL #include #include -#include // for NULL #include /* 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 -#include -#include -#include -#include #include #include #include #include +#include +#include +#include +#include // 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 -#include -#include -#include -#include #include #include #include @@ -47,6 +43,10 @@ #ifdef _OPENMP #include #endif +#include +#include +#include +#include /*~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 -#include -#include -#include -#include #include #include #include #include +#include +#include +#include +#include int perm_count; SEXP pairwise_covar(SEXP pair_vec);