Fixed broken links to BCO specification, generated documentation, inc…

…remented version to 1.0.6

.gitignore

@@ -1,3 +1,4 @@
+.DS_Store
 .Rproj.user
 .Rhistory
 .RData

DESCRIPTION

@@ -1,9 +1,9 @@
 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"),

NEWS.md

@@ -1,3 +1,9 @@
+# biocompute 1.0.6
+
+## Improvements
+
+- Fixed broken links to BCO specification in documentation
+
 # biocompute 1.0.5
 
 ## Improvements

R/compose-error.R

@@ -3,7 +3,7 @@
 #' 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.

R/compose-parametric.R

@@ -2,7 +2,7 @@
 #'
 #' 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}

R/compose-top-level-fields.R

@@ -9,7 +9,7 @@
 #' @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

R/compose-usability.R

@@ -1,7 +1,7 @@
 #' 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,

R/validate-checksum.R

@@ -10,7 +10,7 @@
 #' @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

README.md

@@ -1,6 +1,6 @@
 # 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)

biocompute.Rproj

@@ -18,4 +18,5 @@ StripTrailingWhitespace: Yes
 BuildType: Package
 PackageUseDevtools: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source
+PackageCheckArgs: --as-cran
 PackageRoxygenize: rd,collate,namespace

cran-comments.md

@@ -1,3 +1,14 @@
+# 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