diff --git a/.gitignore b/.gitignore index 5b6a065..1141bfd 100644 --- a/.gitignore +++ b/.gitignore @@ -1,3 +1,4 @@ +.DS_Store .Rproj.user .Rhistory .RData diff --git a/DESCRIPTION b/DESCRIPTION index ef330a6..91d0f4a 100644 --- a/DESCRIPTION +++ b/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 = "jeffrey.grover@sevenbridges.com", role = c("aut", "cre")), + person("Jeffrey", "Grover", email = "jeffrey.grover@sevenbridges.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-6246-1767")), person("Soner", "Koc", email = "soner.koc@sevenbridges.com", 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 = "dennis.dean@sevenbridges.com", role = c("aut"), diff --git a/NEWS.md b/NEWS.md index 7086353..954d78c 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,9 @@ +# biocompute 1.0.6 + +## Improvements + +- Fixed broken links to BCO specification in documentation + # biocompute 1.0.5 ## Improvements diff --git a/R/compose-error.R b/R/compose-error.R index 1acdf9d..59c5e0d 100644 --- a/R/compose-error.R +++ b/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. diff --git a/R/compose-parametric.R b/R/compose-parametric.R index ba96036..8ebc2ba 100644 --- a/R/compose-parametric.R +++ b/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} diff --git a/R/compose-top-level-fields.R b/R/compose-top-level-fields.R index 0d937dc..bdda8dc 100644 --- a/R/compose-top-level-fields.R +++ b/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 diff --git a/R/compose-usability.R b/R/compose-usability.R index 5a729f5..3313370 100644 --- a/R/compose-usability.R +++ b/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, diff --git a/R/validate-checksum.R b/R/validate-checksum.R index ae2411d..dcc904f 100644 --- a/R/validate-checksum.R +++ b/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 diff --git a/README.md b/README.md index 3dac31b..812cd3e 100644 --- a/README.md +++ b/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) diff --git a/biocompute.Rproj b/biocompute.Rproj index 270314b..be6e327 100644 --- a/biocompute.Rproj +++ b/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 diff --git a/cran-comments.md b/cran-comments.md index 28ede07..b5079d6 100644 --- a/cran-comments.md +++ b/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 diff --git a/docs/404.html b/docs/404.html index 213432e..64ca36d 100644 --- a/docs/404.html +++ b/docs/404.html @@ -73,7 +73,7 @@ biocompute - 1.0.5 + 1.0.6 @@ -81,7 +81,7 @@