preparing for release 0.3.2

DESCRIPTION

@@ -6,7 +6,7 @@ Description: Provides taxonomic classes for
     with data. Methods provided are "taxonomically aware", in
     that they know about ordering of ranks, and methods that
     filter based on taxonomy also filter associated data.
-Version: 0.3.1.9004
+Version: 0.3.2
 Authors@R: c(
     person("Scott", "Chamberlain", role = "aut", 
        email = "myrmecocystus+r@gmail.com", comment = c(ORCID = "0000-0003-1444-9135")),

NEWS.md

@@ -1,5 +1,5 @@
-development
-===========
+taxa 0.3.1
+==========
 
 ### Bug fixes
 

R/taxmap--parsers.R

@@ -408,9 +408,6 @@ parse_tax_data <- function(tax_data, datasets = list(), class_cols = 1,
     mappings <- c("{{index}}" = "{{index}}", mappings)
   }
 
-  # Convert additional tables to tibbles
-  are_tables <- vapply(datasets, is.data.frame, logical(1))
-  datasets[are_tables] <- lapply(datasets[are_tables], dplyr::as.tbl)
 
   # Add additional data sets
   name_datset <- function(dataset, sort_var) {
@@ -434,6 +431,10 @@ parse_tax_data <- function(tax_data, datasets = list(), class_cols = 1,
                                                                   mappings[i])),
                                    names(datasets)))
 
+  # Convert additional tables to tibbles
+  are_tables <- vapply(output$data, is.data.frame, logical(1))
+  output$data[are_tables] <- lapply(output$data[are_tables], dplyr::as.tbl)
+
   # Fix incorrect taxon ids in data if a list of data.frames is given
   if (is_list_of_frames && include_tax_data) {
     output$data$tax_data <- output$data$tax_data[!duplicated(output$data[[1]]), ]
@@ -1008,7 +1009,9 @@ get_sort_var <- function(data, var) {
 #'
 #' @return Returns an object of type [taxmap()]
 #'
-#' @examples \dontrun{
+#' @examples
+#'
+#' \dontrun{
 #'
 #'   # For demonstration purposes, the following example dataset has all the
 #'   # types of data that can be used, but any one of them alone would work.

cran-comments.md

@@ -1,7 +1,7 @@
 ## Test environments
 
-* local ubuntu 16.04, R 3.4.4
-* ubuntu 14.04 (on travis-ci), R 3.5.0
+* local ubuntu 16.04, R 3.5.1
+* ubuntu 14.04 (on travis-ci), R 3.5.1
 * win-builder (devel and release)
 
 ## R CMD check results
@@ -13,45 +13,8 @@
 
 ### metacoder
 
-Metacoder passes all checks with no notes, warnings, or errors, except a few tests fail.
+I also maintain `metacoder`. The current CRAN version will have test errors with this version of `taxa`, but I will be submitting an update to `metacoder` that is compatible with this version of `taxa` and builds without errors shortly after submitting this version of `taxa`.
 
-The warning "'min' arg is deprecated. Use 'lower' instead." is due to a change in the `GA` package, where an argument was renamed, but works the same.
-It has been fixed in the development version of `metacoder` and does not affect the functionality of the CRAN version.
+### taxlist
 
-The "did not produce any warnings." errors are because `taxa` used to produce warnings in some cases, but these were removed since I found out that it was not actually a problem.
-
-This version of taxa being submitted should be fully compatible with the current CRAN version of metacoder, even though the tests fail.
-
-```
-Testing metacoder
-✔ | OK F W S | Context
-✔ | 40       | Calculations [35.1 s]
-✔ |  3   2   | Tree plotting [6.0 s]
-─────────────────────────────────────────────────────────────────────────────
-test--heat_tree.R:12: warning: basic tree plotting works
-'min' arg is deprecated. Use 'lower' instead.
-
-test--heat_tree.R:12: warning: basic tree plotting works
-'max' arg is deprecated. Use 'upper' instead.
-─────────────────────────────────────────────────────────────────────────────
-✖ | 51 3     | Input parsing [4.1 s]
-─────────────────────────────────────────────────────────────────────────────
-test--parsers_and_writers.R:78: failure: Mothur classify.seqs *.tax.summary  detailed parsing
-`result <- parse_mothur_tax_summary(text = raw_data)` did not produce any warnings.
-
-test--parsers_and_writers.R:79: failure: Mothur classify.seqs *.tax.summary  detailed parsing
-`result_from_file <- parse_mothur_tax_summary(file = "example_data/mothur_summary.txt")` did not produce any warnings.
-
-test--parsers_and_writers.R:97: failure: Mothur classify.seqs *.tax.summary simple parsing
-`result <- parse_mothur_tax_summary(text = raw_data)` did not produce any warnings.
-─────────────────────────────────────────────────────────────────────────────
-✔ | 19       | Simulated PCR [1.3 s]
-
-══ Results ══════════════════════════════════════════════════════════════════
-Duration: 46.9 s
-
-OK:       113
-Failed:   3
-Warnings: 2
-Skipped:  0
-```
+`taxa` is in the suggests and no code from `taxa` is actually used.

tests/testthat/test--taxmap.R

@@ -694,8 +694,6 @@ test_that("New tables and vectors can be made",  {
   expect_equal(length(result$data$new_table), 0)
 
  # Invlaid: inputs of mixed lengths
-  expect_error(mutate_obs(test_obj, "new_table", a = 1, b = character(0)),
-               "must be length 1, not 0")
   expect_error(mutate_obs(test_obj, "new_table", a = 1:3, b = 2:8),
                "Cannot make a new table out of multiple values of unequal length")