avoid examples writing to non-tempfiles

Author: cboettig

R/nexml_write.R

@@ -20,7 +20,8 @@
 #' @examples
 #'  ## Write an ape tree to nexml, analgous to write.nexus:
 #'  library(ape); data(bird.orders)
-#'  write.nexml(bird.orders, file="example.xml")
+#'  ex <- tempfile(fileext=".xml")
+#'  write.nexml(bird.orders, file=ex)
 #' 
 #' \dontrun{ # takes > 5s
 #'  ## Assemble a nexml section by section and then write to file:
@@ -31,14 +32,14 @@
 #'  nexml <- add_basic_meta(title="my title", creator = "Carl Boettiger", nexml = nexml)
 #'  nexml <- add_meta(meta("prism:modificationDate", format(Sys.Date())), nexml = nexml)
 #'
-#'  write.nexml(nexml, file="example.xml")
+#'  write.nexml(nexml, file=ex)
 #'
 #'  ## As above, but in one call (except for add_meta() call).  
 #'  write.nexml(trees = geospiza$phy, 
 #'              characters = geospiza$dat, 
 #'              title = "My title", 
 #'              creator = "Carl Boettiger",
-#'              file = "example.xml")
+#'              file = ex)
 #'  
 #'  ## Mix and match: identical to the section by section: 
 #'  nexml <- add_meta(meta("prism:modificationDate", format(Sys.Date())))
@@ -47,7 +48,7 @@
 #'              characters = geospiza$dat, 
 #'              title = "My title", 
 #'              creator = "Carl Boettiger",
-#'              file = "example.xml")
+#'              file = ex)
 #' 
 #' }
 nexml_write <- function(x = nexml(),

cran-comments.md

@@ -3,7 +3,7 @@ Dear CRAN maintainers,
 This update addresses several minor issues and feature requests, as detailed in NEWS.md. 
 This package shows two notes, one indicating that I am the maintainer, the other noting that this package
 has one suggested dependency on a non-mainstream repository, which is used
-to illustrate an additional feature in one of vignettes, when available.  
+to illustrate an additional feature in one of vignettes, when available.  (This is not a new suggested dependency, it is already listed in the current CRAN version as well.)
 
 Cheers,