From ef1ab5587b8a5c0e9b17036905bd8618fa02c5a8 Mon Sep 17 00:00:00 2001 From: Roberto Villegas-Diaz Date: Wed, 22 Apr 2026 12:00:20 +0100 Subject: [PATCH 1/5] Increment version number to 0.0.1.9000 --- DESCRIPTION | 2 +- NEWS.md | 2 ++ 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index f8707ec..3fcf3ba 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: dsROCrate Title: 'DataSHIELD' RO-Crate Governance Functions -Version: 0.0.1 +Version: 0.0.1.9000 Authors@R: c( person(given = "Roberto", family = "Villegas-Diaz", diff --git a/NEWS.md b/NEWS.md index 56ef97b..0a87f0f 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,5 @@ +# dsROCrate (development version) + # dsROCrate 0.0.1 * Initial CRAN submission. From 3b97e5da430665c56c27975a406d788169460e50 Mon Sep 17 00:00:00 2001 From: Roberto Villegas-Diaz Date: Mon, 27 Apr 2026 09:54:36 +0100 Subject: [PATCH 2/5] Set overwrite to TRUE when updating root entity in the safe_output.opal S3 generic --- .Rbuildignore | 2 ++ .gitignore | 1 + R/safe_output.R | 3 ++- 3 files changed, 5 insertions(+), 1 deletion(-) diff --git a/.Rbuildignore b/.Rbuildignore index cf0abdd..7217209 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -12,3 +12,5 @@ (^|/)\.DS\_Store$ ^\.git($|/) ^CRAN-SUBMISSION$ +^\.positai$ +^\.claude$ diff --git a/.gitignore b/.gitignore index 2b827fe..6899798 100644 --- a/.gitignore +++ b/.gitignore @@ -41,3 +41,4 @@ inst/doc inst/R.ignore cran-comments.md CRAN-SUBMISSION +.positai diff --git a/R/safe_output.R b/R/safe_output.R index c8548fb..7a8a9cc 100644 --- a/R/safe_output.R +++ b/R/safe_output.R @@ -395,7 +395,8 @@ safe_output.opal <- function( list(`@id` = log_entity$`@id`), list(`@id` = log_maps_entity$`@id`) ) - ) + ), + overwrite = TRUE ) # attach input arguments as attributes From b55292bb3d0ab83f8685e6c0b7f0b35047e0a764 Mon Sep 17 00:00:00 2001 From: Roberto Villegas-Diaz Date: Mon, 27 Apr 2026 09:55:04 +0100 Subject: [PATCH 3/5] Update options to display all contents of RO-Crates in vignette --- vignettes/getting-started.Rmd | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/vignettes/getting-started.Rmd b/vignettes/getting-started.Rmd index d97ad2e..e680850 100644 --- a/vignettes/getting-started.Rmd +++ b/vignettes/getting-started.Rmd @@ -73,6 +73,10 @@ rocrate_txt <- function(rocrate) { ```{r setup} library(dsROCrate) + +# show all the lines in the RO-Crate +oopt <- options(max_lines = Inf) +on.exit(options(oopt), add = TRUE) ``` This tutorial assumes that you have an internet connection and can access @@ -503,4 +507,6 @@ study_crate_v1 |> unlink(safe_people_crate_v1_rmd, TRUE, TRUE) unlink(safe_project_crate_v1_rmd, TRUE, TRUE) unlink(study_crate_v1_rmd, TRUE, TRUE) +# reverse options +options(oopt) ``` From b0d1a21ea8e9355082a33b39816cfbfaf8b6f49c Mon Sep 17 00:00:00 2001 From: Roberto Villegas-Diaz Date: Mon, 27 Apr 2026 09:57:14 +0100 Subject: [PATCH 4/5] Update badges --- README.Rmd | 1 - README.md | 1 - 2 files changed, 2 deletions(-) diff --git a/README.Rmd b/README.Rmd index 526c123..9cb45fe 100644 --- a/README.Rmd +++ b/README.Rmd @@ -20,7 +20,6 @@ knitr::opts_chunk$set( [![CRAN status](https://www.r-pkg.org/badges/version/dsROCrate)](https://CRAN.R-project.org/package=dsROCrate) [![R-CMD-check](https://github.com/FederatedMethods/dsROCrate/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/FederatedMethods/dsROCrate/actions/workflows/R-CMD-check.yaml) - [![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental) diff --git a/README.md b/README.md index ce66b20..d10b58a 100644 --- a/README.md +++ b/README.md @@ -8,7 +8,6 @@ [![CRAN status](https://www.r-pkg.org/badges/version/dsROCrate)](https://CRAN.R-project.org/package=dsROCrate) [![R-CMD-check](https://github.com/FederatedMethods/dsROCrate/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/FederatedMethods/dsROCrate/actions/workflows/R-CMD-check.yaml) - [![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental) From fb7b5828ab83f13ae31aa9d0febfb50c7b26e080 Mon Sep 17 00:00:00 2001 From: Roberto Villegas-Diaz Date: Mon, 27 Apr 2026 10:23:57 +0100 Subject: [PATCH 5/5] Bump version to 0.0.2 --- DESCRIPTION | 2 +- NEWS.md | 5 +++++ 2 files changed, 6 insertions(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 3fcf3ba..832cc87 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: dsROCrate Title: 'DataSHIELD' RO-Crate Governance Functions -Version: 0.0.1.9000 +Version: 0.0.2 Authors@R: c( person(given = "Roberto", family = "Villegas-Diaz", diff --git a/NEWS.md b/NEWS.md index 0a87f0f..bc7280e 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,10 @@ # dsROCrate (development version) +# dsROCrate 0.0.2 + +* This patch addresses an issue with the vignettes. The `safe_output.opal()` S3 +generic now uses `overwrite = TRUE` to update the root (`./`) entity. + # dsROCrate 0.0.1 * Initial CRAN submission.