Skip to content

Commit

Permalink
v1.0.2 fixes
Browse files Browse the repository at this point in the history
  • Loading branch information
nanxstats committed Nov 18, 2019
1 parent db0afa2 commit 89b1902
Show file tree
Hide file tree
Showing 55 changed files with 478 additions and 205 deletions.
6 changes: 3 additions & 3 deletions DESCRIPTION
Original file line number Diff line number Diff line change
@@ -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")),
Expand All @@ -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
Expand All @@ -40,4 +40,4 @@ Imports:
rmarkdown
Suggests:
knitr
RoxygenNote: 6.1.1
RoxygenNote: 7.0.0
6 changes: 6 additions & 0 deletions NEWS.md
Original file line number Diff line number Diff line change
@@ -1,3 +1,9 @@
# biocompute 1.0.2

## Improvements

- Minor improvements in description text and example code.

# biocompute 1.0.1

## Improvements
Expand Down
21 changes: 9 additions & 12 deletions R/export-docs.R
Original file line number Diff line number Diff line change
Expand Up @@ -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, ...) {
Expand All @@ -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, ...) {
Expand All @@ -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, ...) {
Expand Down
7 changes: 3 additions & 4 deletions R/export-sevenbridges.R
Original file line number Diff line number Diff line change
Expand Up @@ -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(
Expand Down
4 changes: 3 additions & 1 deletion README.md
Original file line number Diff line number Diff line change
Expand Up @@ -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.

Expand Down
24 changes: 24 additions & 0 deletions cran-comments.md
Original file line number Diff line number Diff line change
@@ -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
Expand Down
2 changes: 1 addition & 1 deletion docs/404.html

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

2 changes: 1 addition & 1 deletion docs/LICENSE-text.html

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

8 changes: 4 additions & 4 deletions docs/articles/case-study.html

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

2 changes: 1 addition & 1 deletion docs/articles/index.html

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

30 changes: 15 additions & 15 deletions docs/articles/intro.html

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

2 changes: 1 addition & 1 deletion docs/authors.html

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

Loading

0 comments on commit 89b1902

Please sign in to comment.