created test_001_vcfR.R

knausb · Sep 8, 2017 · a34298b · a34298b
1 parent 0c44ea4
commit a34298b
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Showing 4 changed files with 53 additions and 38 deletions.
diff --git a/R/RcppExports.R b/R/RcppExports.R
@@ -2,6 +2,6 @@
 # Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
 
 timesTwo <- function(x) {
-    .Call('vcfR_timesTwo', PACKAGE = 'vcfR', x)
+    .Call('_vcfR_timesTwo', PACKAGE = 'vcfR', x)
 }
 
diff --git a/src/RcppExports.cpp b/src/RcppExports.cpp
@@ -7,7 +7,7 @@ using namespace Rcpp;
 
 // timesTwo
 NumericVector timesTwo(NumericVector x);
-RcppExport SEXP vcfR_timesTwo(SEXP xSEXP) {
+RcppExport SEXP _vcfR_timesTwo(SEXP xSEXP) {
 BEGIN_RCPP
     Rcpp::RObject rcpp_result_gen;
     Rcpp::RNGScope rcpp_rngScope_gen;
@@ -18,7 +18,7 @@ END_RCPP
 }
 
 static const R_CallMethodDef CallEntries[] = {
-    {"vcfR_timesTwo", (DL_FUNC) &vcfR_timesTwo, 1},
+    {"_vcfR_timesTwo", (DL_FUNC) &_vcfR_timesTwo, 1},
     {NULL, NULL, 0}
 };
 

diff --git a/tests/testthat/test_001_vcfR.R b/tests/testthat/test_001_vcfR.R
@@ -0,0 +1,49 @@
+
+#
+library(testthat)
+#detach(package:vcfR, unload=TRUE)
+#
+library(vcfR)
+
+#
+context("vcfR functions")
+
+
+##### ##### ##### ##### #####
+#
+# vcfR class.
+#
+##### ##### ##### ##### #####
+
+
+test_that("We can create an empty vcfR object",{
+  myvcf <- methods::new("vcfR")
+
+  expect_is(myvcf@meta, "character")
+  expect_equal(length(myvcf@meta), 0)
+
+  expect_is(myvcf@fix, "matrix")
+  expect_equal(nrow(myvcf@fix), 0)
+  expect_equal(ncol(myvcf@fix), 8)
+
+  expect_is(myvcf@gt, "matrix")
+  expect_equal(nrow(myvcf@gt), 0)
+  expect_equal(ncol(myvcf@gt), 0)
+
+})
+
+
+test_that("vcfR subsetters works",{
+  data(vcfR_example)
+  # Rows
+  vcf2 <- vcf[1:10,]
+  expect_equal(nrow(vcf2@fix), 10)
+  expect_equal(nrow(vcf2@gt), 10)
+
+  # Columns
+  vcf2 <- vcf[,1:4]
+  expect_equal(ncol(vcf2@fix), 8)
+  expect_equal(ncol(vcf2@gt), 4)
+})
+
+
diff --git a/tests/testthat/test_1_vcf.R b/tests/testthat/test_1_vcf.R
@@ -27,31 +27,9 @@ setwd( test_dir )
 #ex_file <- paste(test_dir, "/test.vcf.gz", sep="")
 ex_file <- "test.vcf.gz"
 
-write.vcf(vcf, file=ex_file)
+#write.vcf(vcf, file=ex_file)
 
 
-##### ##### ##### ##### #####
-#
-# vcfR class.
-#
-##### ##### ##### ##### #####
-
-
-test_that("We can create an empty vcfR object",{
-  myvcf <- methods::new("vcfR")
-
-  expect_is(myvcf@meta, "character")
-  expect_equal(length(myvcf@meta), 0)
-
-  expect_is(myvcf@fix, "matrix")
-  expect_equal(nrow(myvcf@fix), 0)
-  expect_equal(ncol(myvcf@fix), 8)
-
-  expect_is(myvcf@gt, "matrix")
-  expect_equal(nrow(myvcf@gt), 0)
-  expect_equal(ncol(myvcf@gt), 0)
-
-})
 
 
 ##### ##### ##### ##### #####
@@ -349,17 +327,6 @@ test_that("read.vcfR verbose works",{
 ##### ##### ##### ##### #####
 
 
-test_that("vcfR subsetters works",{
-  # Rows
-  vcf2 <- vcf[1:10,]
-  expect_equal(nrow(vcf2@fix), 10)
-  expect_equal(nrow(vcf2@gt), 10)
-
-  # Columns
-  vcf2 <- vcf[,1:4]
-  expect_equal(ncol(vcf2@fix), 8)
-  expect_equal(ncol(vcf2@gt), 4)
-})
 
 
 #debug(read.vcfR)
@@ -427,4 +394,3 @@ setwd(original_dir)
 
 ##### ##### ##### ##### #####
 # EOF.
-