Prep for CRAN's requested patch, #290

NEWS.md

@@ -1,3 +1,11 @@
+# EML 2.0.1
+
+* Improve error message for get_attributes (#286)
+* Avoid `ifelse()` for portability (#283)
+* Avoid edge case that can create invalid EML in `set_taxonomicNames()` (#280)
+* Add documentation regarding the use of dimensionless units (#276)
+* Avoid test errors on systems for which pandoc cannot be installed (#290)
+
 # EML 2.0.0
 
 * EML 2.0.0 is a ground-up rewrite of EML 1.x package.  The primary difference

R/set_TextType.R

@@ -1,9 +1,11 @@
-## Developer note: Some functions not fully compatible with pandoc < 2.0 
+## Developer note: Some functions not fully compatible with pandoc < 2.0
 
 #' set_TextType
 #'
-#' For any EML element of class TextType, this function can be used to generate the appropriate EML from a markdown-formatted file.
-#' @param text a plain text character string which will be used directly as the content of the node if no file is given
+#' For any EML element of class TextType, this function can be used to generate
+#'  the appropriate EML from a markdown-formatted file.
+#' @param text a plain text character string which will be used directly as the content
+#'  of the node if no file is given
 #' @param file path to a file providing formatted input text, see details.
 #' @return a TextType object that can be coerced into any element inheriting from TextType, see examples
 #' @importFrom tools file_ext
@@ -20,23 +22,23 @@
 #' ## using a simple character string
 #' a <- set_TextType(text = "This is the abstract")
 #' as(a, "abstract")
-#' 
+#'
 #' ## Using an external markdown file
 #' f <- system.file("examples/hf205-abstract.md", package = "EML")
 #' a <- set_TextType(f)
 #' as(a, "abstract")
-#' 
+#'
 #' ## Can also import from methods written in a .docx MS Word file.
 #' f <- system.file("examples/hf205-abstract.docx", package = "EML")
 #' a <- set_TextType(f)
 #' as(a, "abstract")
-#' 
+#'
 #' ## Documents with title headings use `section` instead of `para` notation
 #' f <- system.file("examples/hf205-methods.docx", package = "EML")
 #' d <- set_TextType(f)
 #' as(d, "description")
 #' }
-#' 
+#'
 set_TextType <- function(file = NULL, text = NULL) {
   if (!is.null(text)) {
     TextType <- text
@@ -92,6 +94,13 @@ to_docbook <- function(file = NULL) {
         call. = FALSE
       )
     }
+    if (!rmarkdown::pandoc_available()) {
+      stop(paste("Pandoc is required to convert to Docbook format.",
+              "Please supply input text directly"),
+              call. = FALSE
+             )
+    }
+
     pandoc_convert <-
       getExportedValue("rmarkdown", "pandoc_convert")
 

README.Rmd

@@ -30,14 +30,14 @@ has_pandoc <-  rmarkdown::pandoc_available()
 
 
 
-EML is a widely used metadata standard in the ecological and environmental sciences. We strongly recommend that interested users visit the [EML Homepage](https://knb.ecoinformatics.org/#external//emlparser/docs/index.html) for an introduction and thorough documentation of the standard. Additionally, the scientific article *[The New Bioinformatics: Integrating Ecological Data from the Gene to the Biosphere (Jones et al 2006)](http://doi.org/10.1146/annurev.ecolsys.37.091305.110031)* provides an excellent introduction into the role EML plays in building metadata-driven data repositories to address the needs of highly heterogeneous data that cannot be easily reduced to a traditional vertically integrated database. At this time, the `EML` R package provides support for the serializing and parsing of all low-level EML concepts, but still assumes some familiarity with the EML standard, particularly for users seeking to create their own EML files. We hope to add more higher-level functions which will make such familiarity less essential in future development.
+EML is a widely used metadata standard in the ecological and environmental sciences. We strongly recommend that interested users visit the [EML Homepage](https://eml.ecoinformatics.org/) for an introduction and thorough documentation of the standard. Additionally, the scientific article *[The New Bioinformatics: Integrating Ecological Data from the Gene to the Biosphere (Jones et al 2006)](http://doi.org/10.1146/annurev.ecolsys.37.091305.110031)* provides an excellent introduction into the role EML plays in building metadata-driven data repositories to address the needs of highly heterogeneous data that cannot be easily reduced to a traditional vertically integrated database. At this time, the `EML` R package provides support for the serializing and parsing of all low-level EML concepts, but still assumes some familiarity with the EML standard, particularly for users seeking to create their own EML files. We hope to add more higher-level functions which will make such familiarity less essential in future development.
 
 
 ## Notes on the EML v2.0 Release
 
 `EML` v2.0 is a complete re-write which aims to provide both a drop-in replacement for the higher-level functions of the existing EML package while also providing additional functionality.  This new `EML` version uses only simple and familiar list structures (S3 classes) instead of the more cumbersome use of S4 found in the original `EML`.  While the higher-level functions are identical, this makes it easier to for most users and developers to work with `eml` objects and also to write their own functions for creating and manipulating EML objects.  Under the hood, `EML` relies on the [emld](https://github.com/cboettig/emld) package, which uses a Linked Data representation for EML.  It is this approach which lets us combine the simplicity of lists with the specificity required by the XML schema.    
 
-This revision also supports the upcoming release of the EML 2.2 specification.  
+This revision also supports the **[recently released EML 2.2.0 specification](https://eml.ecoinformatics.org/whats-new-in-eml-2-2-0.html)**.  
 
 # Creating EML
 

README.md

@@ -16,11 +16,10 @@ status](https://www.r-pkg.org/badges/version/EML)](https://cran.r-project.org/pa
 
 EML is a widely used metadata standard in the ecological and
 environmental sciences. We strongly recommend that interested users
-visit the [EML
-Homepage](https://knb.ecoinformatics.org/#external//emlparser/docs/index.html)
-for an introduction and thorough documentation of the standard.
-Additionally, the scientific article *[The New Bioinformatics:
-Integrating Ecological Data from the Gene to the Biosphere (Jones et
+visit the [EML Homepage](https://eml.ecoinformatics.org/) for an
+introduction and thorough documentation of the standard. Additionally,
+the scientific article *[The New Bioinformatics: Integrating Ecological
+Data from the Gene to the Biosphere (Jones et
 al 2006)](http://doi.org/10.1146/annurev.ecolsys.37.091305.110031)*
 provides an excellent introduction into the role EML plays in building
 metadata-driven data repositories to address the needs of highly
@@ -47,8 +46,8 @@ which uses a Linked Data representation for EML. It is this approach
 which lets us combine the simplicity of lists with the specificity
 required by the XML schema.
 
-This revision also supports the upcoming release of the EML 2.2
-specification.
+This revision also supports the **[recently released EML 2.2.0
+specification](https://eml.ecoinformatics.org/whats-new-in-eml-2-2-0.html)**.
 
 # Creating EML
 
@@ -76,7 +75,7 @@ eml_validate("ex.xml")
 
 ## A Richer Example
 
-Here we show a the creation of a relatively complete EML document using
+Here we show the creation of a relatively complete EML document using
 `EML`. This closely parallels the function calls shown in the original
 EML [R-package
 vignette](https://docs.ropensci.org/EML/articles/creating-EML.html).

codemeta.json

@@ -14,10 +14,10 @@
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
-    "version": "3.5.3",
+    "version": "3.6.1",
     "url": "https://r-project.org"
   },
-  "runtimePlatform": "R version 3.5.3 (2019-03-11)",
+  "runtimePlatform": "R version 3.6.1 (2019-07-05)",
   "provider": {
     "@id": "https://cran.r-project.org",
     "@type": "Organization",
@@ -336,7 +336,7 @@
     }
   ],
   "readme": "https://github.com/ropensci/EML/blob/master/README.md",
-  "fileSize": "490.911KB",
+  "fileSize": "491.462KB",
   "contIntegration": [
     "https://travis-ci.org/ropensci/EML",
     "https://ci.appveyor.com/project/cboettig/eml",

cran-comments.md

@@ -1,10 +1,6 @@
-This is a thorough re-write of the EML package based on S3 instead of S4
-object system. 
+This release provides the requested changes to avoid errors in testing on systems 
+for which pandoc is not or cannot be installed.
 
-## Test environments
-* local OS X install, R 3.5.3
-* ubuntu 14.04 (on travis-ci), R 3.5.3
-* win-builder (devel and release)
 
 ## R CMD check results
 

tests/testthat/test-additional-tests.R

@@ -24,10 +24,10 @@ test_that("set_physical can compute file size automatically", {
 })
 
 test_that("set_method with additional input files", {
-  
+
   skip_on_appveyor()
-
-  
+  skip_on_cran()
+
   coverage <-
     set_coverage(
       date = c("2012-06-01", "2013-12-31"),

tests/testthat/test-eml2.R

@@ -5,6 +5,8 @@ test_that("we can do a complete eml construction", {
   ## Appveyor cannot even evaluate rmarkdown::pandoc_version() ?
   skip_on_appveyor()
   skip_on_os("solaris")
+  skip_on_cran()
+
 
 ## ------------------------------------------------------------------------
 geographicDescription <-