v1.0.2 fixes

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: biocompute
 Type: Package
 Title: Create and Manipulate BioCompute Objects
-Version: 1.0.1
+Version: 1.0.2
 Authors@R: c(
     person("Nan", "Xiao", email = "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-0250-5673")),
@@ -17,7 +17,7 @@ Description: Tools to create, validate, and export BioCompute Objects
     BioCompute Objects from the domains defined by the standard.
     A checksum validator and a JSON schema validator are provided.
     This package also supports exporting BioCompute Objects as JSON,
-    PDF, HTML, or Word documents, and exporting to cloud-based platforms.
+    PDF, HTML, or 'Word' documents, and exporting to cloud-based platforms.
 License: AGPL-3 | file LICENSE
 VignetteBuilder: knitr
 URL: https://sbg.github.io/biocompute/, https://github.com/sbg/biocompute
@@ -40,4 +40,4 @@ Imports:
     rmarkdown
 Suggests:
     knitr
-RoxygenNote: 6.1.1
+RoxygenNote: 7.0.0

NEWS.md

@@ -1,3 +1,9 @@
+# biocompute 1.0.2
+
+## Improvements
+
+- Minor improvements in description text and example code.
+
 # biocompute 1.0.1
 
 ## Improvements

R/export-docs.R

@@ -13,11 +13,10 @@
 #' @export export_pdf
 #'
 #' @examples
-#' \dontrun{
-#'
+#' \donttest{
 #' file_pdf <- tempfile(fileext = ".pdf")
-#' generate_example("HCV1a") %>%
-#'   convert_json() %>%
+#' generate_example("HCV1a") \%>\%
+#'   convert_json() \%>\%
 #'   export_pdf(file_pdf)
 #' }
 export_pdf <- function(x, file, wrap = FALSE, linewidth = 80, ...) {
@@ -44,11 +43,10 @@ export_pdf <- function(x, file, wrap = FALSE, linewidth = 80, ...) {
 #' @export export_html
 #'
 #' @examples
-#' \dontrun{
-#'
+#' \donttest{
 #' file_html <- tempfile(fileext = ".html")
-#' generate_example("HCV1a") %>%
-#'   convert_json() %>%
+#' generate_example("HCV1a") \%>\%
+#'   convert_json() \%>\%
 #'   export_html(file_html)
 #' }
 export_html <- function(x, file, wrap = FALSE, linewidth = 80, ...) {
@@ -75,11 +73,10 @@ export_html <- function(x, file, wrap = FALSE, linewidth = 80, ...) {
 #' @export export_word
 #'
 #' @examples
-#' \dontrun{
-#'
+#' \donttest{
 #' file_docx <- tempfile(fileext = ".docx")
-#' generate_example("HCV1a") %>%
-#'   convert_json() %>%
+#' generate_example("HCV1a") \%>\%
+#'   convert_json() \%>\%
 #'   export_word(file_docx)
 #' }
 export_word <- function(x, file, wrap = FALSE, linewidth = 80, ...) {

R/export-sevenbridges.R

@@ -18,11 +18,10 @@
 #' @export export_sevenbridges
 #'
 #' @examples
-#' \dontrun{
-#'
+#' \donttest{
 #' file_json <- tempfile(fileext = ".json")
-#' generate_example("HCV1a") %>%
-#'   convert_json() %>%
+#' generate_example("HCV1a") \%>\%
+#'   convert_json() \%>\%
 #'   export_json(file_json)
 #'
 #' export_sevenbridges(

README.md

@@ -3,7 +3,9 @@
 [![Travis build status](https://travis-ci.org/sbg/biocompute.svg?branch=master)](https://travis-ci.org/sbg/biocompute)
 [![AppVeyor build status](https://ci.appveyor.com/api/projects/status/2owpw6m61bnihetf/branch/master?svg=true)](https://ci.appveyor.com/project/nanxstats/biocompute)
 
-Seven Bridges implementation of the BioCompute Object (BCO) specification. It offers the capabilities to compose, validate, and convert BioCompute Objects with R.
+Seven Bridges implementation of the BioCompute Object (BCO) specification. Offers the capabilities to compose, validate, and convert BioCompute Objects with R.
+
+Users can encode information in data frames, and compose BioCompute Objects from the domains defined by the standard. A checksum validator and a JSON schema validator are provided. This package also supports exporting BioCompute Objects as JSON, PDF, HTML, or Word documents, and exporting to cloud-based platforms.
 
 Check out the [introduction vignette](https://sbg.github.io/biocompute/articles/intro.html) or the [case study vignette](https://sbg.github.io/biocompute/articles/case-study.html) to get started.
 

cran-comments.md

@@ -1,3 +1,27 @@
+# biocompute 1.0.2
+
+## Test environments
+
+- Local macOS install, R 3.6.1
+- Ubuntu 16.04.6 LTS (on Travis-CI), R 3.6.1
+- win-builder (release, devel, and oldrelease)
+
+## R CMD check results
+
+There were no ERRORs or WARNINGs.
+
+## Explanation for the stylized names
+
+A 'BioCompute Object' ('BCO') is an instance of the 'BioCompute' standard (https://en.wikipedia.org/wiki/BioCompute_Object). To follow the convention, we stylized it as 'BioCompute Object' instead of 'BioCompute object' in the Description text.
+
+## Single quotes
+
+Added single quotes to the Description section as suggested ('Word').
+
+## Use \donttest
+
+Replaced \dontrun{} by \donttest{} in the Rd files as suggested.
+
 # biocompute 1.0.1
 
 ## Test environments