register native functions (#187)

.gitignore

@@ -8,6 +8,7 @@
 # Creates binaries
 *.o
 *.so
+*.dll
 .Rproj.user
 vignettes/abc_cache
 cran-comments.md

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: coala
-Version: 0.5.0.9001
+Version: 0.5.1
 License: MIT + file LICENSE
 Title: A Framework for Coalescent Simulation
 Authors@R: c(

NAMESPACE

@@ -153,4 +153,4 @@ importFrom(stats,rgamma)
 importFrom(stats,simulate)
 importFrom(utils,capture.output)
 importFrom(utils,suppressForeignCheck)
-useDynLib(coala)
+useDynLib(coala, .registration = TRUE)

NEWS.md

@@ -1,3 +1,12 @@
+coala 0.5.1
+===========
+
+* This is a small maintainence release
+* Fix a number of minor issues pointed out by hadley/strict (#186)
+* Register native routines to fix the new R CMD check NOTE (#187)
+
+
+
 coala 0.5.0
 ===========
 

R/RcppExports.R

@@ -1,99 +1,99 @@
-# Generated by using Rcpp::compileAttributes() -> do not edit by hand
-# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
-
-parse_ms_positions <- function(line) {
-    .Call('coala_parse_ms_positions', PACKAGE = 'coala', line)
-}
-
-parse_ms_output <- function(file_names, sample_size, loci_number) {
-    .Call('coala_parse_ms_output', PACKAGE = 'coala', file_names, sample_size, loci_number)
-}
-
-parse_seqgen_output <- function(output, individuals, locus_length, locus_number, outgroup_size, calc_segsites = TRUE) {
-    .Call('coala_parse_seqgen_output', PACKAGE = 'coala', output, individuals, locus_length, locus_number, outgroup_size, calc_segsites)
-}
-
-generate_trio_trees <- function(trees, trio_dists, file_names) {
-    .Call('coala_generate_trio_trees', PACKAGE = 'coala', trees, trio_dists, file_names)
-}
-
-#' @describeIn segsites Creates segregating sites
-#'
-#' @param snps The SNP Matrix (see Details).
-#' @param positions A numeric vector indicating the relative positions of each
-#'   SNP on the locus (see Details).
-#' @param trio_locus If the locus consists of a locus trio (see Details).
-#' @param check Whether non-segregating sites are removed from the segregating
-#'   sites (\code{TRUE}) or not (\code{FALSE}).
-#' @export
-#'
-create_segsites <- function(snps, positions, trio_locus = numeric(0), check = TRUE) {
-    .Call('coala_create_segsites', PACKAGE = 'coala', snps, positions, trio_locus, check)
-}
-
-#' @describeIn segsites Returns the SNP matrix from a segregating sites
-#'  object.
-#'
-#' @param segsites The segregating sites object
-#' @export
-get_snps <- function(segsites) {
-    .Call('coala_get_snps', PACKAGE = 'coala', segsites)
-}
-
-#' @describeIn segsites Returns the SNP's positions from a segregating
-#'   sites  object.
-#' @export
-get_positions <- function(segsites) {
-    .Call('coala_get_positions', PACKAGE = 'coala', segsites)
-}
-
-#' @describeIn segsites Sets the SNP's positions in a segregating
-#'   sites object.
-#' @export
-set_positions <- function(segsites, positions) {
-    .Call('coala_set_positions', PACKAGE = 'coala', segsites, positions)
-}
-
-#' @describeIn segsites Returns the trio locus positions from a
-#'   segregating sites  object.
-#' @export
-get_trio_locus <- function(segsites) {
-    .Call('coala_get_trio_locus', PACKAGE = 'coala', segsites)
-}
-
-#' @describeIn segsites Sets the trio locus in a segregating sites
-#'   object.
-#' @export
-set_trio_locus <- function(segsites, trio_locus) {
-    .Call('coala_set_trio_locus', PACKAGE = 'coala', segsites, trio_locus)
-}
-
-calc_four_gamete_stat <- function(seg_sites_list, individuals, locus_length, ploidy = 1L) {
-    .Call('coala_calc_four_gamete_stat', PACKAGE = 'coala', seg_sites_list, individuals, locus_length, ploidy)
-}
-
-#' Calculates the Joint Site Frequency Spectrum
-#'
-#' @param segsites_list List of segregating sites
-#' @param ind_per_pop A list of integer vector, where each entry gives the
-#'   index of the haploids that belong the corresponding population.
-#'
-#' @author Paul Staab & Dirk Metzler
-#' @return The Joint Site Frequency Spectrum, as a matrix.
-#' @keywords internal
-calc_jsfs <- function(segsites_list, ind_per_pop) {
-    .Call('coala_calc_jsfs', PACKAGE = 'coala', segsites_list, ind_per_pop)
-}
-
-calc_mcmf <- function(seg_sites, individuals, has_trios = TRUE, expand_mcmf = FALSE, type_expand = 1L, ploidy = 1L, locus_length = matrix(0)) {
-    .Call('coala_calc_mcmf', PACKAGE = 'coala', seg_sites, individuals, has_trios, expand_mcmf, type_expand, ploidy, locus_length)
-}
-
-calc_nucleotide_div <- function(segsites_list, individuals) {
-    .Call('coala_calc_nucleotide_div', PACKAGE = 'coala', segsites_list, individuals)
-}
-
-unphase_segsites <- function(seg_sites_list, ploidy, samples_per_ind) {
-    .Call('coala_unphase_segsites', PACKAGE = 'coala', seg_sites_list, ploidy, samples_per_ind)
-}
-
+# Generated by using Rcpp::compileAttributes() -> do not edit by hand
+# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
+
+parse_ms_positions <- function(line) {
+    .Call(coala_parse_ms_positions, line)
+}
+
+parse_ms_output <- function(file_names, sample_size, loci_number) {
+    .Call(coala_parse_ms_output, file_names, sample_size, loci_number)
+}
+
+parse_seqgen_output <- function(output, individuals, locus_length, locus_number, outgroup_size, calc_segsites = TRUE) {
+    .Call(coala_parse_seqgen_output, output, individuals, locus_length, locus_number, outgroup_size, calc_segsites)
+}
+
+generate_trio_trees <- function(trees, trio_dists, file_names) {
+    .Call(coala_generate_trio_trees, trees, trio_dists, file_names)
+}
+
+#' @describeIn segsites Creates segregating sites
+#'
+#' @param snps The SNP Matrix (see Details).
+#' @param positions A numeric vector indicating the relative positions of each
+#'   SNP on the locus (see Details).
+#' @param trio_locus If the locus consists of a locus trio (see Details).
+#' @param check Whether non-segregating sites are removed from the segregating
+#'   sites (\code{TRUE}) or not (\code{FALSE}).
+#' @export
+#'
+create_segsites <- function(snps, positions, trio_locus = numeric(0), check = TRUE) {
+    .Call(coala_create_segsites, snps, positions, trio_locus, check)
+}
+
+#' @describeIn segsites Returns the SNP matrix from a segregating sites
+#'  object.
+#'
+#' @param segsites The segregating sites object
+#' @export
+get_snps <- function(segsites) {
+    .Call(coala_get_snps, segsites)
+}
+
+#' @describeIn segsites Returns the SNP's positions from a segregating
+#'   sites  object.
+#' @export
+get_positions <- function(segsites) {
+    .Call(coala_get_positions, segsites)
+}
+
+#' @describeIn segsites Sets the SNP's positions in a segregating
+#'   sites object.
+#' @export
+set_positions <- function(segsites, positions) {
+    .Call(coala_set_positions, segsites, positions)
+}
+
+#' @describeIn segsites Returns the trio locus positions from a
+#'   segregating sites  object.
+#' @export
+get_trio_locus <- function(segsites) {
+    .Call(coala_get_trio_locus, segsites)
+}
+
+#' @describeIn segsites Sets the trio locus in a segregating sites
+#'   object.
+#' @export
+set_trio_locus <- function(segsites, trio_locus) {
+    .Call(coala_set_trio_locus, segsites, trio_locus)
+}
+
+calc_four_gamete_stat <- function(seg_sites_list, individuals, locus_length, ploidy = 1L) {
+    .Call(coala_calc_four_gamete_stat, seg_sites_list, individuals, locus_length, ploidy)
+}
+
+#' Calculates the Joint Site Frequency Spectrum
+#'
+#' @param segsites_list List of segregating sites
+#' @param ind_per_pop A list of integer vector, where each entry gives the
+#'   index of the haploids that belong the corresponding population.
+#'
+#' @author Paul Staab & Dirk Metzler
+#' @return The Joint Site Frequency Spectrum, as a matrix.
+#' @keywords internal
+calc_jsfs <- function(segsites_list, ind_per_pop) {
+    .Call(coala_calc_jsfs, segsites_list, ind_per_pop)
+}
+
+calc_mcmf <- function(seg_sites, individuals, has_trios = TRUE, expand_mcmf = FALSE, type_expand = 1L, ploidy = 1L, locus_length = matrix(0)) {
+    .Call(coala_calc_mcmf, seg_sites, individuals, has_trios, expand_mcmf, type_expand, ploidy, locus_length)
+}
+
+calc_nucleotide_div <- function(segsites_list, individuals) {
+    .Call(coala_calc_nucleotide_div, segsites_list, individuals)
+}
+
+unphase_segsites <- function(seg_sites_list, ploidy, samples_per_ind) {
+    .Call(coala_unphase_segsites, seg_sites_list, ploidy, samples_per_ind)
+}
+

R/coala.R

@@ -4,7 +4,7 @@
 #' within R. The `introduction` vignette is a good place to start.
 #'
 #' @importFrom Rcpp evalCpp
-#' @useDynLib coala
+#' @useDynLib coala, .registration = TRUE
 #' @importFrom assertthat assert_that
 "_PACKAGE"
 

src/R_init_pkg.c

@@ -0,0 +1,46 @@
+#include <R.h>
+#include <Rinternals.h>
+#include <stdlib.h> // for NULL
+#include <R_ext/Rdynload.h>
+
+/* .Call calls */
+extern SEXP coala_calc_four_gamete_stat(SEXP, SEXP, SEXP, SEXP);
+extern SEXP coala_calc_jsfs(SEXP, SEXP);
+extern SEXP coala_calc_mcmf(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
+extern SEXP coala_calc_nucleotide_div(SEXP, SEXP);
+extern SEXP coala_create_segsites(SEXP, SEXP, SEXP, SEXP);
+extern SEXP coala_generate_trio_trees(SEXP, SEXP, SEXP);
+extern SEXP coala_get_positions(SEXP);
+extern SEXP coala_get_snps(SEXP);
+extern SEXP coala_get_trio_locus(SEXP);
+extern SEXP coala_parse_ms_output(SEXP, SEXP, SEXP);
+extern SEXP coala_parse_ms_positions(SEXP);
+extern SEXP coala_parse_seqgen_output(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);
+extern SEXP coala_set_positions(SEXP, SEXP);
+extern SEXP coala_set_trio_locus(SEXP, SEXP);
+extern SEXP coala_unphase_segsites(SEXP, SEXP, SEXP);
+
+static const R_CallMethodDef CallEntries[] = {
+  {"coala_calc_four_gamete_stat", (DL_FUNC) &coala_calc_four_gamete_stat, 4},
+  {"coala_calc_jsfs",             (DL_FUNC) &coala_calc_jsfs,             2},
+  {"coala_calc_mcmf",             (DL_FUNC) &coala_calc_mcmf,             7},
+  {"coala_calc_nucleotide_div",   (DL_FUNC) &coala_calc_nucleotide_div,   2},
+  {"coala_create_segsites",       (DL_FUNC) &coala_create_segsites,       4},
+  {"coala_generate_trio_trees",   (DL_FUNC) &coala_generate_trio_trees,   3},
+  {"coala_get_positions",         (DL_FUNC) &coala_get_positions,         1},
+  {"coala_get_snps",              (DL_FUNC) &coala_get_snps,              1},
+  {"coala_get_trio_locus",        (DL_FUNC) &coala_get_trio_locus,        1},
+  {"coala_parse_ms_output",       (DL_FUNC) &coala_parse_ms_output,       3},
+  {"coala_parse_ms_positions",    (DL_FUNC) &coala_parse_ms_positions,    1},
+  {"coala_parse_seqgen_output",   (DL_FUNC) &coala_parse_seqgen_output,   6},
+  {"coala_set_positions",         (DL_FUNC) &coala_set_positions,         2},
+  {"coala_set_trio_locus",        (DL_FUNC) &coala_set_trio_locus,        2},
+  {"coala_unphase_segsites",      (DL_FUNC) &coala_unphase_segsites,      3},
+  {NULL, NULL, 0}
+};
+
+void R_init_coala(DllInfo *dll)
+{
+  R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);
+  R_useDynamicSymbols(dll, FALSE);
+}

src/RcppExports.cpp

@@ -199,27 +199,3 @@ BEGIN_RCPP
     return rcpp_result_gen;
 END_RCPP
 }
-
-static const R_CallMethodDef CallEntries[] = {
-    {"coala_parse_ms_positions", (DL_FUNC) &coala_parse_ms_positions, 1},
-    {"coala_parse_ms_output", (DL_FUNC) &coala_parse_ms_output, 3},
-    {"coala_parse_seqgen_output", (DL_FUNC) &coala_parse_seqgen_output, 6},
-    {"coala_generate_trio_trees", (DL_FUNC) &coala_generate_trio_trees, 3},
-    {"coala_create_segsites", (DL_FUNC) &coala_create_segsites, 4},
-    {"coala_get_snps", (DL_FUNC) &coala_get_snps, 1},
-    {"coala_get_positions", (DL_FUNC) &coala_get_positions, 1},
-    {"coala_set_positions", (DL_FUNC) &coala_set_positions, 2},
-    {"coala_get_trio_locus", (DL_FUNC) &coala_get_trio_locus, 1},
-    {"coala_set_trio_locus", (DL_FUNC) &coala_set_trio_locus, 2},
-    {"coala_calc_four_gamete_stat", (DL_FUNC) &coala_calc_four_gamete_stat, 4},
-    {"coala_calc_jsfs", (DL_FUNC) &coala_calc_jsfs, 2},
-    {"coala_calc_mcmf", (DL_FUNC) &coala_calc_mcmf, 7},
-    {"coala_calc_nucleotide_div", (DL_FUNC) &coala_calc_nucleotide_div, 2},
-    {"coala_unphase_segsites", (DL_FUNC) &coala_unphase_segsites, 3},
-    {NULL, NULL, 0}
-};
-
-RcppExport void R_init_coala(DllInfo *dll) {
-    R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);
-    R_useDynamicSymbols(dll, FALSE);
-}