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Fixed broken links to BCO specification, generated documentation, inc…
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…remented version to 1.0.6
groverj3 committed Sep 28, 2021

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1 change: 1 addition & 0 deletions .gitignore
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.DS_Store
.Rproj.user
.Rhistory
.RData
4 changes: 2 additions & 2 deletions DESCRIPTION
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Package: biocompute
Type: Package
Title: Create and Manipulate BioCompute Objects
Version: 1.0.5
Version: 1.0.6
Authors@R: c(
person("Jeffrey", "Grover", email = "[email protected]", role = c("aut", "cre")),
person("Jeffrey", "Grover", email = "[email protected]", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-6246-1767")),
person("Soner", "Koc", email = "[email protected]", role = c("aut"), comment = c(ORCID = "0000-0002-0772-6600")),
person("Nan", "Xiao", role = c("aut"), comment = c(ORCID = "0000-0002-0250-5673")),
person("Dennis", "Dean", email = "[email protected]", role = c("aut"),
6 changes: 6 additions & 0 deletions NEWS.md
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# biocompute 1.0.6

## Improvements

- Fixed broken links to BCO specification in documentation

# biocompute 1.0.5

## Improvements
2 changes: 1 addition & 1 deletion R/compose-error.R
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#' The error domain can be used to determine what range of input
#' returns outputs that are within the tolerance level defined
#' in this subdomain and therefore can be used to optimize algorithm
#' (\href{https://github.com/biocompute-objects/BCO_Specification/blob/main/docs/error-domain.md}{domain definition}).
#' (\href{https://github.com/biocompute-objects/BCO_Specification/blob/1.3.0/error-domain.md}{domain definition}).
#'
#' @param empirical Data frame. Variables include \code{key} and \code{value}.
#' Each row is one item in the empirical error subdomain.
2 changes: 1 addition & 1 deletion R/compose-parametric.R
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#'
#' Non-default parameters customizing the computational flow
#' which can affect the output of the calculations
#' (\href{https://github.com/biocompute-objects/BCO_Specification/blob/main/docs/parametric-domain.md}{domain definition}).
#' (\href{https://github.com/biocompute-objects/BCO_Specification/blob/1.3.0/parametric-domain.md}{domain definition}).
#'
#' @param df Data frame. Variables include \code{param} (parameter names),
#' \code{value} (value of the parameters), and \code{step}
2 changes: 1 addition & 1 deletion R/compose-top-level-fields.R
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#' @param io I/O domain
#' @param error Error domain
#' @param bco_id BioCompute Object identifier
#' (\href{https://github.com/biocompute-objects/BCO_Specification/blob/main/docs/top-level.md#202-biocompute-object-identifier-object_id}{definition}).
#' (\href{https://github.com/biocompute-objects/BCO_Specification/blob/1.3.0/top-level.md#202-biocompute-object-identifier-bco_id}{definition}).
#' If \code{NULL}, will use a UUID generated by \code{\link{generate_id}}.
#'
#' @return A vector of top level fields
2 changes: 1 addition & 1 deletion R/compose-usability.R
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#' Compose BioCompute Object - Usability Domain (v1.3.0)
#'
#' The usability domain
#' (\href{https://github.com/biocompute-objects/BCO_Specification/blob/main/docs/usability-domain.md}{domain definition}).
#' (\href{https://github.com/biocompute-objects/BCO_Specification/blob/1.3.0/usability-domain.md}{domain definition}).
#'
#' @param text A character vector of free text values that could
#' improves search-ability, provide specific scientific use cases,
2 changes: 1 addition & 1 deletion R/validate-checksum.R
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#' @export validate_checksum_v1.3.0
#'
#' @note An SHA-256 checksum is
#' \href{https://github.com/biocompute-objects/BCO_Specification/blob/main/docs/top-level.md#203-etag-etag}{calculated and stored}
#' \href{https://github.com/biocompute-objects/BCO_Specification/blob/1.3.0/top-level.md#203-checksum-checksum}{calculated and stored}
#' in the top level fields when a BioCompute Object is created. In reality,
#' due to the delicate differences in how the data in JSON is represented,
#' parsed, and handled in different languages, there could be false positives
2 changes: 1 addition & 1 deletion README.md
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# biocompute

[![Lifecycle: maturing](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://www.tidyverse.org/lifecycle/#maturing)
[![Lifecycle: maturing](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://lifecycle.r-lib.org/articles/stages.html#maturing)
[![CRAN Version](https://www.r-pkg.org/badges/version/biocompute)](https://cran.r-project.org/package=biocompute)
[![Travis build status](https://travis-ci.org/sbg/biocompute.svg?branch=master)](https://travis-ci.org/sbg/biocompute)
[![Downloads from the RStudio CRAN mirror](https://cranlogs.r-pkg.org/badges/grand-total/biocompute)](https://cran.r-project.org/package=biocompute)
1 change: 1 addition & 0 deletions biocompute.Rproj
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@@ -18,4 +18,5 @@ StripTrailingWhitespace: Yes
BuildType: Package
PackageUseDevtools: Yes
PackageInstallArgs: --no-multiarch --with-keep.source
PackageCheckArgs: --as-cran
PackageRoxygenize: rd,collate,namespace
11 changes: 11 additions & 0 deletions cran-comments.md
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# biocompute 1.0.6

## Test environments

- Local macOS install, R 4.1.1
- Ubuntu 20.04.1 LTS (on R-hub), R 4.1.1
- win-builder (release, devel, and oldrelease)

## R CMD check results

There were no ERRORs or WARNINGs.
# biocompute 1.0.3

## Test environments
6 changes: 3 additions & 3 deletions docs/404.html

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96 changes: 48 additions & 48 deletions docs/articles/case-study.html
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// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
// be compatible with the behavior of Pandoc < 2.8).
document.addEventListener('DOMContentLoaded', function(e) {
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
var i, h, a;
for (i = 0; i < hs.length; i++) {
h = hs[i];
if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
a = h.attributes;
while (a.length > 0) h.removeAttribute(a[0].name);
}
});
6 changes: 3 additions & 3 deletions docs/articles/index.html
42 changes: 21 additions & 21 deletions docs/articles/intro.html
12 changes: 12 additions & 0 deletions docs/articles/intro_files/header-attrs-2.10/header-attrs.js
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// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
// be compatible with the behavior of Pandoc < 2.8).
document.addEventListener('DOMContentLoaded', function(e) {
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
var i, h, a;
for (i = 0; i < hs.length; i++) {
h = hs[i];
if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
a = h.attributes;
while (a.length > 0) h.removeAttribute(a[0].name);
}
});
8 changes: 4 additions & 4 deletions docs/authors.html
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38 changes: 25 additions & 13 deletions docs/news/index.html
4 changes: 2 additions & 2 deletions docs/pkgdown.yml
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pandoc: 2.7.3
pandoc: 2.14.0.3
pkgdown: 1.6.1
pkgdown_sha: ~
articles:
case-study: case-study.html
intro: intro.html
last_built: 2021-09-21T20:19Z
last_built: 2021-09-28T21:02Z

8 changes: 4 additions & 4 deletions docs/reference/biocompute-package.html
8 changes: 4 additions & 4 deletions docs/reference/compose.html
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6 changes: 3 additions & 3 deletions docs/reference/compose_fhir.html
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8 changes: 4 additions & 4 deletions docs/reference/compose_parametric.html
8 changes: 4 additions & 4 deletions docs/reference/compose_provenance.html
6 changes: 3 additions & 3 deletions docs/reference/compose_scm.html
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8 changes: 4 additions & 4 deletions docs/reference/compose_usability.html
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6 changes: 3 additions & 3 deletions docs/reference/generate_example.html
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6 changes: 3 additions & 3 deletions docs/reference/is_bco.html
6 changes: 3 additions & 3 deletions docs/reference/is_domain.html
6 changes: 3 additions & 3 deletions docs/reference/pipe.html
18 changes: 9 additions & 9 deletions docs/reference/validate_checksum.html
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