fix imports from base packages

statgenlmu · Sep 5, 2015 · 644194e · 644194e
1 parent d8d9925
commit 644194e
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Showing 5 changed files with 12 additions and 3 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: jaatha
-Version: 2.99.0.9210
-Date: 2015-09-04
+Version: 2.99.0.9211
+Date: 2015-09-05
 License: GPL (>= 3)
 Title: Simulation Based Parameter Estimation in a Frequentistic Framework
 Authors@R: c(
@@ -20,7 +20,9 @@ Imports:
     assertthat (>= 0.1),
     R6 (>= 2.0.1),
     reshape2 (>= 1.4),
-    parallel
+    parallel,
+    stats,
+    utils
 Suggests:
     coala (>= 0.1.1),
     testthat (>= 0.10.0),

diff --git a/NAMESPACE b/NAMESPACE
@@ -23,3 +23,6 @@ importFrom(stats,glm.fit)
 importFrom(stats,optim)
 importFrom(stats,poisson)
 importFrom(stats,predict.glm)
+importFrom(stats,rpois)
+importFrom(stats,simulate)
+importFrom(utils,capture.output)
diff --git a/R/coala_interface.R b/R/coala_interface.R
@@ -24,6 +24,7 @@
 #' @param mcmf_breaks Quantiles of the real data that will be used as breaks
 #'   for binning the MCMF statistic if present in the model.
 #' @inheritParams create_jaatha_model
+#' @importFrom stats simulate
 #' @export
 create_jaatha_model.coalmodel <- function(x, 
                                           jsfs_summary = c("sums",
@@ -37,6 +38,7 @@ create_jaatha_model.coalmodel <- function(x,
                                           test = TRUE) {
 
   require_package("coala")
+
   if (length(jsfs_summary) > 1) jsfs_summary <- jsfs_summary[1]
 
   sim_func <- function(pars, opts = NULL) simulate(x, pars = pars)

diff --git a/R/jaatha_model.R b/R/jaatha_model.R
@@ -114,6 +114,7 @@ create_jaatha_model.function <- function(x, par_ranges, sum_stats,
 is_jaatha_model <- function(x) inherits(x, "jaatha_model")
 
 
+#' @importFrom stats rpois
 create_test_model <- function() {
   create_jaatha_model(function(x, y) rpois(10, x),
                       par_ranges = matrix(c(0.1, 0.1, 10, 10), 2, 2),

diff --git a/R/popgenome_interface.R b/R/popgenome_interface.R
@@ -128,6 +128,7 @@ get_popgenome_locus <- function(data, locus_number, only_synonymous) {
 }
 
 
+#' @importFrom utils capture.output
 create_popgenome_test_data <- function() {
   require_package("PopGenome")