update CRAN comments

.Rbuildignore

@@ -17,3 +17,5 @@ cran-comments.md
 ^codecov\.yml$
 ^RNeXML_.*\.tar\.gz$
 cache
+.circleci
+

cran-comments.md

@@ -1,8 +1,15 @@
 Dear CRAN maintainers,
 
-As requested by CRAN, this update addresses the occassional failing tests introduced by
-a recent release of taxize and crul packages.
+This update addresses several minor bugs in the handling of ploymorphic 
+characters, as detailed in NEWS.md.
 
 Cheers,
 
 Carl
+
+
+## Test environments
+
+* local OS X install, R 3.5.1
+* ubuntu 14.04 (on travis-ci), R 3.5.1
+* win-builder (devel and release)

tests/testthat/test_taxonomy.R

@@ -4,7 +4,6 @@ context("taxonomy")
 data(bird.orders)
 birdorders_small <- drop.tip(bird.orders, tip = 1:10)
 birds <- add_trees(birdorders_small)
-birds <- taxize_nexml(birds, "NCBI")
 
 data(chiroptera)
 chiroptera_small <- drop.tip(chiroptera, tip = 1:906)
@@ -20,6 +19,7 @@ test_that("taxize_nexml correctly collects ncbi identifiers", {
 
   testthat::skip_on_cran()
 
+  birds <- taxize_nexml(birds, "NCBI")
 
   chir <- taxize_nexml(chir, "NCBI")
   chir_super_small <- taxize_nexml(chir_super_small, "NCBI")
@@ -43,8 +43,8 @@ test_that("taxize_nexml correctly collects ncbi identifiers", {
 })
 
 test_that("we can extract taxonomy data from the object", {
+
   expect_is(get_metadata(birds, "otus/otu"), "data.frame")
-
   expect_is(get_metadata(chir_super_small, 'otus/otu'), "data.frame")
 })