more cran check fixes

Author: zachary-foster

DESCRIPTION

@@ -20,7 +20,7 @@ Authors@R:
              family = "Gilmore",
              role = "ctb"))
 Maintainer: Zachary Foster <zacharyfoster1989@gmail.com>
-Description: 'Metacoder' is a package for reading, plotting, and manipulating large
+Description: This package is for reading, plotting, and manipulating large
     taxonomic data sets, like those generated from modern high-throughput
     sequencing, like metabarcoding (i.e. amplification metagenomics, 16S
     metagenomics, etc). It provides a tree-based visualization called "heat

R/calculations.R

@@ -801,6 +801,7 @@ calc_taxon_abund <- function(obj, data, cols = NULL, groups = NULL,
 #' @family calculations
 #'
 #' @examples
+#' \donttest{
 #' # Parse data for example
 #' x = parse_tax_data(hmp_otus, class_cols = "lineage", class_sep = ";",
 #'                    class_key = c(tax_rank = "taxon_rank", tax_name = "taxon_name"),
@@ -829,6 +830,7 @@ calc_taxon_abund <- function(obj, data, cols = NULL, groups = NULL,
 #' calc_n_samples(x, data = "tax_data", other_cols = TRUE)
 #' calc_n_samples(x, data = "tax_data", other_cols = 2)
 #' calc_n_samples(x, data = "tax_data", other_cols = "otu_id")
+#' }
 #' @export
 calc_n_samples <- function(obj, data, cols = NULL, groups = "n_samples",
                            other_cols = FALSE, out_names = NULL, drop = FALSE,
@@ -889,6 +891,7 @@ calc_n_samples <- function(obj, data, cols = NULL, groups = "n_samples",
 #' @family calculations
 #'
 #' @examples
+#' \donttest{
 #' # Parse data for example
 #' x = parse_tax_data(hmp_otus, class_cols = "lineage", class_sep = ";",
 #'                    class_key = c(tax_rank = "taxon_rank", tax_name = "taxon_name"),
@@ -917,6 +920,7 @@ calc_n_samples <- function(obj, data, cols = NULL, groups = "n_samples",
 #' calc_prop_samples(x, data = "tax_data", other_cols = TRUE)
 #' calc_prop_samples(x, data = "tax_data", other_cols = 2)
 #' calc_prop_samples(x, data = "tax_data", other_cols = "otu_id")
+#' }
 #' @export
 calc_prop_samples <- function(obj, data, cols = NULL, groups = "prop_samples",
                               other_cols = FALSE, out_names = NULL, drop = FALSE,

cran-comments.md

@@ -29,6 +29,14 @@ CRAN repository db overrides:
   X-CRAN-Comment: Archived on 2024-10-01 as issues were not corrected
     in time.
 
+Possibly misspelled words in DESCRIPTION:
+  al (32:18)
+  bioinformatics (30:16)
+  et (32:15)
+  metabarcoding (26:22)
+  metagenomics (26:56, 27:5)
+  microbiome (30:5)
+  
 Suggests or Enhances not in mainstream repositories:
   traits
 ```
@@ -38,6 +46,7 @@ Suggests or Enhances not in mainstream repositories:
 The package `traits` was also removed from CRAN because it depends on `taxize` as well.
 It is only a suggested package for `metacoder` used for one function and I expect `traits` will be returned to CRAN as well soon.
 I am not sure if it is required for all packages in "Suggests" to be on CRAN or not.
+The "Possibly misspelled words" are all real words.
 
 
 ### Response to CRAN review