From 19e3728b846733eb19bfab57203c93ff4ebf898c Mon Sep 17 00:00:00 2001 From: Julien Brun Date: Mon, 31 Aug 2026 14:04:36 -0700 Subject: [PATCH 01/15] switch to tempdir and better headers --- vignettes/use02_dataset-single-dataone.Rmd | 58 ++++++---------------- 1 file changed, 15 insertions(+), 43 deletions(-) diff --git a/vignettes/use02_dataset-single-dataone.Rmd b/vignettes/use02_dataset-single-dataone.Rmd index da6bdba..7a6fcb8 100644 --- a/vignettes/use02_dataset-single-dataone.Rmd +++ b/vignettes/use02_dataset-single-dataone.Rmd @@ -18,9 +18,9 @@ knitr::opts_chunk$set(collapse = TRUE, comment = "#>") This vignette aims to showcase a use case using the 2 main functions of `metajam` - `download_d1_data` and `read_d1_files` to download one dataset from the DataOne data repository. -## Note on data url provenance when using download_d1_data.R +## Note on data url provenance when using `download_d1_data()` -There are two parameters required to run the download_d1_data.R function in metajam. One is the data url for the dataset you'd like to download.You can retrieve this by navigating to the data package of interest, right-clicking on the download data button, and selecting Copy Link Address. +There are two parameters required to run the `download_d1_data()` function in metajam. One is the data url for the dataset you'd like to download.You can retrieve this by navigating to the data package of interest, right-clicking on the download data button, and selecting "Copy Link Address". For several DataOne member nodes (Arctic Data Center, Environmental Data Initiative, and The Knowledge Network for Biocomplexity), metajam users can retrieve the data url from either the 'home' site of the member node or the from the DataOne instance of that same data package. For example, if you wanted to download this dataset: @@ -40,12 +40,12 @@ We have not tested metajam's compatibility with the home sites of all DataOne me We include two examples, one downloading a dataset with metadata in eml (ecological metadata format) and the other downloading a dataset with metadata in ISO (International Organization for Standardization) format. -## Example 1: eml +## Example 1: EML metadata For the first example, we are using Diatom Community Data from Coweeta LTER, 2005-2019: Kelsey J. Solomon, Rebecca J. Bixby, and Catherine M. Pringle. Environmental Data Initiative. . -## Libraries and constants +### Libraries and constants ```{r libraries, warning=FALSE} # devtools::install_github("NCEAS/metajam") @@ -55,7 +55,7 @@ library(metajam) ```{r constants} # Directory to save the data set -path_folder <- "Data_coweeta" +path_folder <- file.path(tempdir(),"Data_coweeta") # URL to download the dataset from DataONE data_url <- "https://cn.dataone.org/cn/v2/resolve/https%3A%2F%2Fpasta.lternet.edu%2Fpackage%2Fdata%2Feml%2Fedi%2F858%2F1%2F15ad768241d2eeed9f0ba159c2ab8fd5" @@ -63,7 +63,7 @@ data_url <- "https://cn.dataone.org/cn/v2/resolve/https%3A%2F%2Fpasta.lternet.ed ``` -## Download the dataset +### Download the dataset ```{r download, eval=FALSE} @@ -73,27 +73,21 @@ dir.create(path_folder, showWarnings = FALSE) # Download the dataset and associated metdata data_folder <- metajam::download_d1_data(data_url, path_folder) - - +data_folder ``` At this point, you should have the data and the metadata downloaded inside your main directory; `Data_coweeta` in this example. `metajam` organize the files as follow: - Each dataset is stored a sub-directory named after the package DOI and the file name - Inside this sub-directory, you will find - - the data: `my_data.csv` + - the data: `CWT_Hemlock_Diatom_Data.csv` - the raw EML with the naming convention _file name_ + `__full_metadata.xml`: `my_data__full_metadata.xml` - the package level metadata summary with the naming convention _file name_ + `__summary_metadata.csv`: `my_data__summary_metadata.csv` - If relevant, the attribute level metadata with the naming convention _file name_ + `__attribute_metadata.csv`: `my_data__attribute_metadata.csv` - If relevant, the factor level metadata with the naming convention _file name_ + `__attribute_factor_metadata.csv`: my_data`__attribute_factor_metadata.csv` - -```{r, out.width="90%", echo=FALSE, fig.align="center", fig.cap="Local file structure of a dataset downloaded by metajam"} -knitr::include_graphics("../man/figures/metajam_v1_folder.png") -``` - -## Read the data and metadata in your R environment +### Read the data and metadata in your R environment ```{r read_data, eval=FALSE} # Read all the datasets and their associated metadata in as a named list @@ -101,16 +95,17 @@ coweeta_diatom <- metajam::read_d1_files(data_folder) ``` -## Structure of the named list object +### Structure of the named list object You have now loaded in your R environment one named list object that contains the data `coweeta_diatom$data`, the general (summary) metadata `coweeta_diatom$summary_metadata` - such as title, creators, dates, locations - and the attribute level metadata information `coweeta_diatom$attribute_metadata`, allowing user to get more information, such as units and definitions of your attributes. -## Example 2: iso + +## Example 2: ISO metatdata For the second example, we are using Marine bird survey observation and density data from Northern Gulf of Alaska LTER cruises, 2018. Kathy Kuletz, Daniel Cushing, and Elizabeth Labunski. Research Workspace. -## Libraries and constants +### Libraries and constants ```{r libraries-2, warning=FALSE} # devtools::install_github("NCEAS/metajam") @@ -120,7 +115,7 @@ library(metajam) ```{r constants-2} # Directory to save the data set -path_folder <- "Data_alaska" +path_folder <- file.path(tempdir(), "Data_alaska") # URL to download the dataset from DataONE data_url <- "https://cn.dataone.org/cn/v2/resolve/4139539e-94e7-49cc-9c7a-5f879e438b16" @@ -128,7 +123,7 @@ data_url <- "https://cn.dataone.org/cn/v2/resolve/4139539e-94e7-49cc-9c7a-5f879e ``` -## Download the dataset +### Download the dataset ```{r download-2, eval=FALSE} @@ -138,8 +133,6 @@ dir.create(path_folder, showWarnings = FALSE) # Download the dataset and associated metdata data_folder <- metajam::download_d1_data(data_url, path_folder) - - ``` At this point, you should have the data and the metadata downloaded inside your main directory; `Data_alaska` in this example. `metajam` organize the files as follow: @@ -151,24 +144,3 @@ At this point, you should have the data and the metadata downloaded inside your - the package level metadata summary with the naming convention _file name_ + `__summary_metadata.csv`: `my_data__summary_metadata.csv` -```{r, out.width="90%", echo=FALSE, fig.align="center", fig.cap="Local file structure of a dataset downloaded by metajam"} -knitr::include_graphics("../man/figures/metajam_v1_folder.png") -``` - - -## Read the data and metadata in your R environment - -```{r read_data-2, eval=FALSE} -# Read all the datasets and their associated metadata in as a named list -coweeta_diatom <- metajam::read_d1_files(data_folder) - -``` - -## Structure of the named list object - -You have now loaded in your R environment one named list object that contains the data `coweeta_diatom$data`, the general (summary) metadata `coweeta_diatom$summary_metadata` - such as title, creators, dates, locations - and the attribute level metadata information `coweeta_diatom$attribute_metadata`, allowing user to get more information, such as units and definitions of your attributes. - - -```{r, out.width="90%", echo=FALSE, fig.align="center", fig.cap="Structure of the named list object containing tabular metadata and data as loaded by metajam"} -knitr::include_graphics("../man/figures/metajam_v1_named_list.png") -``` From c6c6e475093cae2c55a520acb326eb75fe40fc01 Mon Sep 17 00:00:00 2001 From: Julien Brun Date: Mon, 31 Aug 2026 14:04:57 -0700 Subject: [PATCH 02/15] switch to tempdir per CRAN request --- vignettes/use03_dataset-batch-processing.Rmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/vignettes/use03_dataset-batch-processing.Rmd b/vignettes/use03_dataset-batch-processing.Rmd index 2f4ecf2..46d1c98 100644 --- a/vignettes/use03_dataset-batch-processing.Rmd +++ b/vignettes/use03_dataset-batch-processing.Rmd @@ -40,7 +40,7 @@ library(stringr) ```{r constants} # Download the data from DataONE on your local machine -data_folder <- "Data_SEC" +data_folder <- file.path(tempdir(), "Data_SEC") # Ammonium to Ammoniacal-nitrogen conversion. We will use this conversion later. coeff_conv_NH4_to_NH4N <- 0.7764676534 From 6cdfeb7f17e56ad0e1ddc84e464b9efa3c5b6b6f Mon Sep 17 00:00:00 2001 From: Julien Brun Date: Mon, 31 Aug 2026 14:33:53 -0700 Subject: [PATCH 03/15] small changes to the vignette --- vignettes/use02_dataset-single-dataone.Rmd | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/vignettes/use02_dataset-single-dataone.Rmd b/vignettes/use02_dataset-single-dataone.Rmd index 7a6fcb8..c6ec0a3 100644 --- a/vignettes/use02_dataset-single-dataone.Rmd +++ b/vignettes/use02_dataset-single-dataone.Rmd @@ -50,7 +50,6 @@ For the first example, we are using Diatom Community Data from Coweeta LTER, 200 ```{r libraries, warning=FALSE} # devtools::install_github("NCEAS/metajam") library(metajam) - ``` ```{r constants} @@ -92,7 +91,6 @@ At this point, you should have the data and the metadata downloaded inside your ```{r read_data, eval=FALSE} # Read all the datasets and their associated metadata in as a named list coweeta_diatom <- metajam::read_d1_files(data_folder) - ``` ### Structure of the named list object @@ -100,7 +98,8 @@ coweeta_diatom <- metajam::read_d1_files(data_folder) You have now loaded in your R environment one named list object that contains the data `coweeta_diatom$data`, the general (summary) metadata `coweeta_diatom$summary_metadata` - such as title, creators, dates, locations - and the attribute level metadata information `coweeta_diatom$attribute_metadata`, allowing user to get more information, such as units and definitions of your attributes. -## Example 2: ISO metatdata + +## Example 2: ISO metadata For the second example, we are using Marine bird survey observation and density data from Northern Gulf of Alaska LTER cruises, 2018. Kathy Kuletz, Daniel Cushing, and Elizabeth Labunski. Research Workspace. @@ -110,7 +109,6 @@ For the second example, we are using Marine bird survey observation and density ```{r libraries-2, warning=FALSE} # devtools::install_github("NCEAS/metajam") library(metajam) - ``` ```{r constants-2} @@ -119,7 +117,6 @@ path_folder <- file.path(tempdir(), "Data_alaska") # URL to download the dataset from DataONE data_url <- "https://cn.dataone.org/cn/v2/resolve/4139539e-94e7-49cc-9c7a-5f879e438b16" - ``` From b42366352a5c89fc2dddc11d315eb34ff530530c Mon Sep 17 00:00:00 2001 From: Julien Brun Date: Mon, 31 Aug 2026 15:45:12 -0700 Subject: [PATCH 04/15] handle the case where metadata might not be synced --- R/download_d1_data.R | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/R/download_d1_data.R b/R/download_d1_data.R index 83a4793..c761ddf 100644 --- a/R/download_d1_data.R +++ b/R/download_d1_data.R @@ -91,7 +91,8 @@ download_d1_data <- function(data_url, path) { } metadata_nodes <- dataone::resolve(cn, meta_id) - meta_obj <- dataone::getObject(d1c@mn, meta_id) + meta_d1c <- dataone::D1Client("PROD", metadata_nodes$data$nodeIdentifier[[1]]) + meta_obj <- dataone::getObject(meta_d1c@mn, meta_id) # Preparing some objects for input into language specific functions below From c428799a806c2db022388cb00090f9b215128ce1 Mon Sep 17 00:00:00 2001 From: Julien Brun Date: Mon, 31 Aug 2026 15:45:26 -0700 Subject: [PATCH 05/15] fix bug if filename is null --- R/download_ISO_data.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/download_ISO_data.R b/R/download_ISO_data.R index e97e691..4caab65 100644 --- a/R/download_ISO_data.R +++ b/R/download_ISO_data.R @@ -110,7 +110,7 @@ ISO_type <- metadata2 %>% filter(name == "doc.children.MD_Metadata.children.meta pid <- data_id data_sys <- suppressMessages(dataone::getSystemMetadata(d1c@mn, pid)) - data_name <- data_sys@fileName %|||% ifelse(exists("entity_data"), entity_data$physical$objectName %|||% entity_data$entityName, NA) %|||% data_id + data_name <- data_sys@fileName %|||% data_id data_name <- gsub("[^a-zA-Z0-9. -]+", "_", data_name) #remove special characters & replace with _ data_extension <- gsub("(.*\\.)([^.]*$)", "\\2", data_name) data_name <- gsub("\\.[^.]*$", "", data_name) #remove extension From 34ed579917930e0f5609f79a6032178dc8d78724 Mon Sep 17 00:00:00 2001 From: Julien Brun Date: Mon, 31 Aug 2026 15:45:42 -0700 Subject: [PATCH 06/15] handle the case when filename is null --- R/utils.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/utils.R b/R/utils.R index 3fbed7b..9852296 100644 --- a/R/utils.R +++ b/R/utils.R @@ -1,6 +1,6 @@ `%|||%` <- function (x, y) { #based on the purrr/rlang op-null-default - if (is.null(x) || is.na(x)) { + if (is.null(x) || length(x) == 0 || is.na(x)) { y } else { From ecff12c2077dafe5d9638da7b7bcfce8a997e1aa Mon Sep 17 00:00:00 2001 From: Julien Brun Date: Wed, 2 Sep 2026 11:40:23 -0700 Subject: [PATCH 07/15] fix quote in example --- R/download_d1_data_pkg.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/download_d1_data_pkg.R b/R/download_d1_data_pkg.R index b471a30..91b9c43 100644 --- a/R/download_d1_data_pkg.R +++ b/R/download_d1_data_pkg.R @@ -17,7 +17,7 @@ #' @examples #' \donttest{ #' download_d1_data_pkg("doi:10.18739/A2CJ87M3J", tempdir()) -#' download_d1_data_pkg("https://doi.org/10.18739/A2CJ87M3J, tempdir()) +#' download_d1_data_pkg("https://doi.org/10.18739/A2CJ87M3J", tempdir()) #' } download_d1_data_pkg <- function(meta_obj, path) { From 20ec92035bda84eb4bde7461b22b277c63e2b1fd Mon Sep 17 00:00:00 2001 From: Julien Brun Date: Wed, 2 Sep 2026 13:07:49 -0700 Subject: [PATCH 08/15] rolling this back as it broke the download of some EDI packages --- R/download_d1_data.R | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/R/download_d1_data.R b/R/download_d1_data.R index c761ddf..2a3fe69 100644 --- a/R/download_d1_data.R +++ b/R/download_d1_data.R @@ -31,7 +31,6 @@ #' } download_d1_data <- function(data_url, path) { - # TODO: add meta_doi to explicitly specify doi # Silence visible bindings note entity_data <- eml <- dir_name <- NULL @@ -91,8 +90,8 @@ download_d1_data <- function(data_url, path) { } metadata_nodes <- dataone::resolve(cn, meta_id) - meta_d1c <- dataone::D1Client("PROD", metadata_nodes$data$nodeIdentifier[[1]]) - meta_obj <- dataone::getObject(meta_d1c@mn, meta_id) + # meta_d1c <- dataone::D1Client("PROD", metadata_nodes$data$nodeIdentifier[[1]]) + meta_obj <- dataone::getObject(d1c@mn, meta_id) # Preparing some objects for input into language specific functions below From 5332349e44220faca97f9043c00e4375496186f9 Mon Sep 17 00:00:00 2001 From: Julien Brun Date: Wed, 2 Sep 2026 13:24:07 -0700 Subject: [PATCH 09/15] update doc --- DESCRIPTION | 2 +- man/check_version.Rd | 6 +++--- man/download_d1_data.Rd | 6 +++--- man/download_d1_data_pkg.Rd | 6 +++--- man/tabularize_eml.Rd | 5 ++--- 5 files changed, 12 insertions(+), 13 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 10e202d..b2911f7 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -45,7 +45,7 @@ Description: A set of tools to foster the development of reproducible analytical License: Apache License (== 2.0) Encoding: UTF-8 Language: en-US -RoxygenNote: 7.3.3 +RoxygenNote: 8.1.0 SystemRequirements: Mac OSX: redland (>= 1.0.14) ; Linux: librdf0 (>= 1.0.14), librdf0-dev (>= 1.0.14) URL: https://nceas.github.io/metajam/, https://github.com/NCEAS/metajam diff --git a/man/check_version.Rd b/man/check_version.Rd index c658cd1..e00797b 100644 --- a/man/check_version.Rd +++ b/man/check_version.Rd @@ -18,13 +18,13 @@ check_version(pid, formatType = NULL) This function takes an identifier and checks to see if it has been obsoleted. } \examples{ -\dontrun{ +\donttest{ # Most data URLs and identifiers work check_version("https://cn.dataone.org/cn/v2/resolve/urn:uuid:a2834e3e-f453-4c2b-8343-99477662b570") -check_version("doi:10.18739/A2ZF6M") +check_version("doi:10.18739/A2J09W56F") # Specify a formatType (data, metadata, or resource) -check_version("doi:10.18739/A2ZF6M", formatType = "metadata") +check_version("doi:10.18739/A2J09W56F", formatType = "metadata") # Returns a warning if the identifier has been obsoleted check_version("doi:10.18739/A2HF7Z", formatType = "metadata") diff --git a/man/download_d1_data.Rd b/man/download_d1_data.Rd index 0a63093..f45a633 100644 --- a/man/download_d1_data.Rd +++ b/man/download_d1_data.Rd @@ -18,11 +18,11 @@ download_d1_data(data_url, path) Downloads a data object from DataONE along with metadata. } \examples{ -\dontrun{ -download_d1_data("urn:uuid:a2834e3e-f453-4c2b-8343-99477662b570", path = file.path(".")) +\dontest{ +download_d1_data("urn:uuid:a2834e3e-f453-4c2b-8343-99477662b570", path = tempdir()) download_d1_data( "https://cn.dataone.org/cn/v2/resolve/urn:uuid:a2834e3e-f453-4c2b-8343-99477662b570", - path = file.path(".") + path = tempdir() ) } } diff --git a/man/download_d1_data_pkg.Rd b/man/download_d1_data_pkg.Rd index 34d7355..fedfbe3 100644 --- a/man/download_d1_data_pkg.Rd +++ b/man/download_d1_data_pkg.Rd @@ -18,9 +18,9 @@ download_d1_data_pkg(meta_obj, path) Downloads all the data objects of a data package from DataONE along with metadata. } \examples{ -\dontrun{ -download_d1_data_pkg("doi:10.18739/A2028W", ".") -download_d1_data_pkg("https://doi.org/10.18739/A2028W", ".") +\donttest{ +download_d1_data_pkg("doi:10.18739/A2CJ87M3J", tempdir()) +download_d1_data_pkg("https://doi.org/10.18739/A2CJ87M3J", tempdir()) } } \seealso{ diff --git a/man/tabularize_eml.Rd b/man/tabularize_eml.Rd index 14b198c..56399ec 100644 --- a/man/tabularize_eml.Rd +++ b/man/tabularize_eml.Rd @@ -19,7 +19,6 @@ If \code{full = TRUE} is specified, the full set of metadata fields are returned This function takes a path to an EML (.xml) metadata file and returns a data frame. } \examples{ - eml <- system.file("extdata", "test_data", "SoilMois2012_2017__full_metadata.xml", - package = "metajam") - tabularize_eml(eml) +eml <- system.file("extdata", "test_data", "SoilMois2012_2017__full_metadata.xml", package = "metajam") +tabularize_eml(eml) } From dd8503d27221a7404496d25ce6636495ac2b5e1f Mon Sep 17 00:00:00 2001 From: Julien Brun Date: Wed, 2 Sep 2026 13:26:09 -0700 Subject: [PATCH 10/15] fix donttest typo --- R/download_d1_data.R | 2 +- man/download_d1_data.Rd | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/R/download_d1_data.R b/R/download_d1_data.R index 2a3fe69..31db43d 100644 --- a/R/download_d1_data.R +++ b/R/download_d1_data.R @@ -22,7 +22,7 @@ #' @seealso [read_d1_files()] [download_d1_data_pkg()] #' #' @examples -#' \dontest{ +#' \donttest{ #' download_d1_data("urn:uuid:a2834e3e-f453-4c2b-8343-99477662b570", path = tempdir()) #' download_d1_data( #' "https://cn.dataone.org/cn/v2/resolve/urn:uuid:a2834e3e-f453-4c2b-8343-99477662b570", diff --git a/man/download_d1_data.Rd b/man/download_d1_data.Rd index f45a633..b02e065 100644 --- a/man/download_d1_data.Rd +++ b/man/download_d1_data.Rd @@ -18,7 +18,7 @@ download_d1_data(data_url, path) Downloads a data object from DataONE along with metadata. } \examples{ -\dontest{ +\donttest{ download_d1_data("urn:uuid:a2834e3e-f453-4c2b-8343-99477662b570", path = tempdir()) download_d1_data( "https://cn.dataone.org/cn/v2/resolve/urn:uuid:a2834e3e-f453-4c2b-8343-99477662b570", From 93b5cda038a16466a83e41ab1be2b58cc7f29832 Mon Sep 17 00:00:00 2001 From: Julien Brun Date: Wed, 2 Sep 2026 13:45:47 -0700 Subject: [PATCH 11/15] fix note on line beeing too long --- R/tabularize_eml.R | 5 ++++- man/tabularize_eml.Rd | 5 ++++- 2 files changed, 8 insertions(+), 2 deletions(-) diff --git a/R/tabularize_eml.R b/R/tabularize_eml.R index 29b0dbe..37769b7 100644 --- a/R/tabularize_eml.R +++ b/R/tabularize_eml.R @@ -16,7 +16,10 @@ #' @export #' #' @examples -#' eml <- system.file("extdata", "test_data", "SoilMois2012_2017__full_metadata.xml", package = "metajam") +#' eml <- system.file("extdata", +#' "test_data", +#' "SoilMois2012_2017__full_metadata.xml", +#' package = "metajam") #' tabularize_eml(eml) tabularize_eml <- function(eml, full = FALSE) { diff --git a/man/tabularize_eml.Rd b/man/tabularize_eml.Rd index 56399ec..a4361ae 100644 --- a/man/tabularize_eml.Rd +++ b/man/tabularize_eml.Rd @@ -19,6 +19,9 @@ If \code{full = TRUE} is specified, the full set of metadata fields are returned This function takes a path to an EML (.xml) metadata file and returns a data frame. } \examples{ -eml <- system.file("extdata", "test_data", "SoilMois2012_2017__full_metadata.xml", package = "metajam") +eml <- system.file("extdata", + "test_data", + "SoilMois2012_2017__full_metadata.xml", + package = "metajam") tabularize_eml(eml) } From a85a9fd8098460838d1aacee8d012847af82f94b Mon Sep 17 00:00:00 2001 From: Julien Brun Date: Wed, 2 Sep 2026 13:45:56 -0700 Subject: [PATCH 12/15] update date --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index b2911f7..491d995 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,7 +2,7 @@ Package: metajam Type: Package Title: Easily Download Data and Metadata from 'DataONE' Version: 0.3.2 -Date: 2026-06-23 +Date: 2026-08-31 Authors@R: c( person("Julien", "Brun", email = "julien.brun@alumni.duke.edu", From 1e9b3737051f7959f76eac59c4e51b5905bc1d0b Mon Sep 17 00:00:00 2001 From: Julien Brun Date: Wed, 2 Sep 2026 13:46:20 -0700 Subject: [PATCH 13/15] revert back to dontrun since some examples are meant to fail --- R/check_version.R | 2 +- man/check_version.Rd | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/R/check_version.R b/R/check_version.R index 4e07bcf..2f4e24b 100644 --- a/R/check_version.R +++ b/R/check_version.R @@ -12,7 +12,7 @@ #' @export #' #' @examples -#' \donttest{ +#' \dontrun{ #' # Most data URLs and identifiers work #' check_version("https://cn.dataone.org/cn/v2/resolve/urn:uuid:a2834e3e-f453-4c2b-8343-99477662b570") #' check_version("doi:10.18739/A2J09W56F") diff --git a/man/check_version.Rd b/man/check_version.Rd index e00797b..ba3111a 100644 --- a/man/check_version.Rd +++ b/man/check_version.Rd @@ -18,7 +18,7 @@ check_version(pid, formatType = NULL) This function takes an identifier and checks to see if it has been obsoleted. } \examples{ -\donttest{ +\dontrun{ # Most data URLs and identifiers work check_version("https://cn.dataone.org/cn/v2/resolve/urn:uuid:a2834e3e-f453-4c2b-8343-99477662b570") check_version("doi:10.18739/A2J09W56F") From d3b5f448fdbff65f59107effd40a3ddcd5a1df08 Mon Sep 17 00:00:00 2001 From: Julien Brun Date: Wed, 2 Sep 2026 13:47:20 -0700 Subject: [PATCH 14/15] update comments --- cran-comments.md | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/cran-comments.md b/cran-comments.md index 858617d..08adc82 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -2,4 +2,8 @@ 0 errors | 0 warnings | 1 note -* This is a new release. +* Archived on 2025-12-04 as requires archived package 'dataone' + +This is a new release + +Addresses previous submission comments about /dontrun and using temporary folders From a69dd8b9e909cb44ca932a4043dc7477ec154a6b Mon Sep 17 00:00:00 2001 From: Julien Brun Date: Wed, 2 Sep 2026 14:02:02 -0700 Subject: [PATCH 15/15] remove unused line of code --- R/download_d1_data.R | 1 - 1 file changed, 1 deletion(-) diff --git a/R/download_d1_data.R b/R/download_d1_data.R index 31db43d..78b8e69 100644 --- a/R/download_d1_data.R +++ b/R/download_d1_data.R @@ -90,7 +90,6 @@ download_d1_data <- function(data_url, path) { } metadata_nodes <- dataone::resolve(cn, meta_id) - # meta_d1c <- dataone::D1Client("PROD", metadata_nodes$data$nodeIdentifier[[1]]) meta_obj <- dataone::getObject(d1c@mn, meta_id)