small change to test_toplevel to plot phylos at same time, added tidy…

…ing in test_parsing and test_serializing

inst/tests/test_parsing.R

@@ -9,4 +9,5 @@ test_that("We can parse a NeXML file to an S4 RNeXML::tree object", {
   doc <- xmlParse(f)
   root <- xmlRoot(doc)
   nexml <- as(root, "nexml")  ## parse the XML into S4
+  expect_is(nexml,"nexml")
 })

inst/tests/test_serializing.R

@@ -32,6 +32,8 @@ test_that("We can serialize parsed NeXML to S4 RNeXML into valid NeXML",{
   tree <- as(root, "nexml")
   nexml_write(tree, "test.xml")
 
+#! change directory to something that will work across machines if possible
+
 # results <- xmlSchemaValidate("http://www.nexml.org/2009/nexml.xsd", "test.xml")
   results <- xmlSchemaValidate("~/Documents/code/thirdparty/nexml/xsd/nexml.xsd", "test.xml")
   expect_equal(results$status, 0)

inst/tests/test_toplevel_api.R

@@ -9,7 +9,9 @@ test_that("read.nexml works (to ape::phylo)", {
   f <- system.file("examples", "trees.xml", package="RNeXML")
   phy <- nexml_read(f, type="phylo")
 #  phy <- read.nexml(f, type="phylo")
-  plot(phy)
+  layout(matrix(1:2, 1, 2), c(5, 4))
+  plot(phy[[1]])
+  plot(phy[[2]])
 })
 
 test_that("write.nexml works (from ape::phylo)", {