Fix three URLs to satisfy CRAN checks

Note that this breaks the DOI in the creating-EML vignette because the PNAS DOI 503s without either JS or cookies enabled (not sure which) due to that URL being fronted with Cloudflare and probably some sort of anti-abuse config PNAS has with them. This is regrettable but being on CRAN is better than making DOIs URLs.

Author: amoeba

NEWS.md

@@ -6,7 +6,7 @@
 * Fixed a minor typographical issue in the Working with Units vignette (See https://github.com/ropensci/EML/commit/eb1604817809d2cbea5405ed6909c0e046e31a3e)
 * Modified how `set_attributes` sets storageType on numeric columns so it will accept `integer` when provided by the user while still defaulting to `float` (See https://github.com/ropensci/EML/issues/324)
 * Extends `get_attributes`, `set_attributes`, and `shiny_attributes` to support attribute-level semantic annotations (See https://github.com/ropensci/EML/issues/318)
-* The test suite will now skip tests dependent on [taxadb](https://cran.r-project.org/web/packages/taxadb/index.html) when it's not installed (See https://github.com/ropensci/EML/issues/320)
+* The test suite will now skip tests dependent on [taxadb](https://cran.r-project.org/package=taxadb) when it's not installed (See https://github.com/ropensci/EML/issues/320)
 
 # EML 2.0.5
 

README.Rmd

@@ -7,7 +7,7 @@ output: github_document
 [![lifecycle](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://lifecycle.r-lib.org/articles/stages.html)
 [![Build Status](https://travis-ci.org/ropensci/EML.svg?branch=master)](https://travis-ci.org/ropensci/EML)
 [![Windows build status](https://ci.appveyor.com/api/projects/status/u2gw24yfkvxgny96?svg=true)](https://ci.appveyor.com/project/cboettig/eml)
-[![codecov](https://codecov.io/gh/ropensci/EML/branch/master/graph/badge.svg)](https://codecov.io/gh/ropensci/EML)
+[![codecov](https://codecov.io/gh/ropensci/EML/branch/master/graph/badge.svg)](https://app.codecov.io/gh/ropensci/EML)
 [![CRAN status](https://www.r-pkg.org/badges/version/EML)](https://cran.r-project.org/package=EML)
 ![downloads](http://cranlogs.r-pkg.org/badges/grand-total/RNeXML)
 [![DOI](https://zenodo.org/badge/10894022.svg)](https://zenodo.org/badge/latestdoi/10894022)

README.md

@@ -6,7 +6,7 @@
 Status](https://travis-ci.org/ropensci/EML.svg?branch=master)](https://travis-ci.org/ropensci/EML)
 [![Windows build
 status](https://ci.appveyor.com/api/projects/status/u2gw24yfkvxgny96?svg=true)](https://ci.appveyor.com/project/cboettig/eml)
-[![codecov](https://codecov.io/gh/ropensci/EML/branch/master/graph/badge.svg)](https://codecov.io/gh/ropensci/EML)
+[![codecov](https://codecov.io/gh/ropensci/EML/branch/master/graph/badge.svg)](https://app.codecov.io/gh/ropensci/EML)
 [![CRAN
 status](https://www.r-pkg.org/badges/version/EML)](https://cran.r-project.org/package=EML)
 ![downloads](http://cranlogs.r-pkg.org/badges/grand-total/RNeXML)

vignettes/creating-EML.Rmd

@@ -68,10 +68,10 @@ In this example, we will use R to re-generate
 the EML metadata originally published by [Ellison _et al_
 (2012), HF205](https://harvardforest.fas.harvard.edu/harvard-forest-data-archive)
 through the Harvard Forest Long Term Ecological Research
-Center, accompanying the PNAS paper [Sirota _et al_
-(2013)](https://doi.org/10.1073/pnas.1221037110). We have made only
-a few modifications to simplify the presentation of this tutorial, 
-so our resulting EML will not be perfectly identical to the original.
+Center, accompanying the PNAS paper (Sirota _et al_. 2013;
+doi:10.1073/pnas.1221037110). We have made only a few modifications to
+simplify the presentation of this tutorial, so our resulting EML will not
+be perfectly identical to the original.
 
 
 ### Our strategy