CRAN patch

.Rbuildignore

@@ -12,3 +12,5 @@
 (^|/)\.DS\_Store$
 ^\.git($|/)
 ^CRAN-SUBMISSION$
+^\.positai$
+^\.claude$

.gitignore

@@ -41,3 +41,4 @@ inst/doc
 inst/R.ignore
 cran-comments.md
 CRAN-SUBMISSION
+.positai

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: dsROCrate
 Title: 'DataSHIELD' RO-Crate Governance Functions
-Version: 0.0.1
+Version: 0.0.2
 Authors@R: c(
     person(given = "Roberto",
            family = "Villegas-Diaz",

NEWS.md

@@ -1,3 +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.

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

README.Rmd

@@ -20,7 +20,6 @@ knitr::opts_chunk$set(
 <!-- badges: start -->
 [![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)
-<!-- [![Codecov test coverage](https://codecov.io/gh/FederatedMethods/dsROCrate/graph/badge.svg)](https://app.codecov.io/gh/FederatedMethods/dsROCrate) -->
 [![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
 <!-- badges: end -->
 

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)
-<!-- [![Codecov test coverage](https://codecov.io/gh/FederatedMethods/dsROCrate/graph/badge.svg)](https://app.codecov.io/gh/FederatedMethods/dsROCrate) -->
 [![Lifecycle:
 experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
 <!-- badges: end -->

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)
 ```