Merge pull request #203 from FAIRDataPipeline/fix-new-r

Fixes for latest R
FAIRDataPipeline · Oct 7, 2024 · 9077ec6 · 9077ec6
2 parents bab526f + 5108fd9
commit 9077ec6
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Showing 69 changed files with 167 additions and 78 deletions.
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -15,3 +15,5 @@ README.md
 ^config.yaml$
 ^cran-comments.md$
 ^software-checklist.md$
+^check$
+^venv$
diff --git a/.gitignore b/.gitignore
@@ -50,3 +50,5 @@ docs
 /test
 /tests/testthat/test
 sonia.yaml
+/venv
+/check
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,9 +1,9 @@
 Package: rDataPipeline
 Title: Functions to Interact with the 'FAIR Data Pipeline'
-Version: 0.54.3
+Version: 0.6.0
 Authors@R: c(person("Sonia", "Mitchell", email = "sonia.mitchell@glasgow.ac.uk",
                   role = c("cre", "aut"), comment = c(ORCID = "0000-0003-1536-2066")),
-             person("Ryan", "Field", role = "ctb", 
+             person("Ryan", "Field", email = "ryan.field@glasgow.ac.uk", role = "aut", 
                   comment = c(ORCID = "0000-0002-4424-9890")))
 Description: R implementation of the 'FAIR Data Pipeline API'. The 'FAIR Data 
     Pipeline' is intended to enable tracking of provenance of FAIR (findable, 
@@ -33,6 +33,6 @@ biocViews:
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.2
+RoxygenNote: 7.3.2
 URL: https://www.fairdatapipeline.org/rDataPipeline/, https://github.com/FAIRDataPipeline/rDataPipeline
 BugReports: https://github.com/FAIRDataPipeline/rDataPipeline/issues
diff --git a/NEWS.md b/NEWS.md
@@ -1,5 +1,7 @@
 # NEWS
-
+# rDataPipeline v0.6.0
+## Improvements:
+  Updates to work with latest versions of R
 - v0.54.1
   - Initial release
 - v0.54.2

diff --git a/R/check_fields.R b/R/check_fields.R
@@ -14,7 +14,7 @@ check_fields <- function(table, query, method, endpoint) {
   expected_types <- get_fields(table = table, endpoint = endpoint) %>%
     dplyr::filter(.data$field %in% fields) %>%
     dplyr::arrange(factor(.data$field, levels = fields)) %>%
-    dplyr::select(.data$data_type) %>%
+    dplyr::select("data_type") %>%
     unlist() %>%
     unname()
 

diff --git a/R/class-fdp.R b/R/class-fdp.R
@@ -5,7 +5,7 @@
 #' @name fdp-class
 #' @rdname fdp-class
 #'
-fdp <- R6::R6Class("fdp", list(
+fdp <- R6::R6Class("fdp", public = list(
   #' @field yaml a \code{list} containing the contents of the working
   #' config.yaml
   #' @field fdp_config_dir a \code{string} specifying the directory passed
@@ -80,7 +80,7 @@ fdp <- R6::R6Class("fdp", list(
   },
 
   #' @description Print method
-  #'
+  #' @param ... additional parameters, currently none are used
   #' @export
   #'
   print = function(...) {

diff --git a/R/get_components.R b/R/get_components.R
@@ -18,7 +18,7 @@ get_components <- function(filename) {
   tmp <- rhdf5::H5Fopen(filename) %>%
     h5ls() %>%
     dplyr::filter(.data$name == "array" | .data$name == "table") %>%
-    dplyr::select(.data$group) %>%
+    dplyr::select("group") %>%
     unlist() %>%
     unname()
 

diff --git a/R/rDataPipeline-package.R b/R/rDataPipeline-package.R
@@ -25,4 +25,4 @@
 #' @importFrom utils download.file read.csv unzip write.csv type.convert
 #' @import yaml
 #'
-NULL
+"_PACKAGE"
diff --git a/man/check_config.Rd b/man/check_config.Rd
diff --git a/man/check_dataproduct_exists.Rd b/man/check_dataproduct_exists.Rd
diff --git a/man/check_datetime.Rd b/man/check_datetime.Rd
diff --git a/man/check_exists.Rd b/man/check_exists.Rd
diff --git a/man/check_field.Rd b/man/check_field.Rd
diff --git a/man/check_fields.Rd b/man/check_fields.Rd
diff --git a/man/check_handle.Rd b/man/check_handle.Rd
diff --git a/man/check_integer.Rd b/man/check_integer.Rd
diff --git a/man/check_local_repo.Rd b/man/check_local_repo.Rd
diff --git a/man/check_string.Rd b/man/check_string.Rd
diff --git a/man/check_table_exists.Rd b/man/check_table_exists.Rd
diff --git a/man/check_yaml_write.Rd b/man/check_yaml_write.Rd
diff --git a/man/clean_query.Rd b/man/clean_query.Rd
diff --git a/man/create_index.Rd b/man/create_index.Rd
diff --git a/man/create_version_number.Rd b/man/create_version_number.Rd
diff --git a/man/download_from_database.Rd b/man/download_from_database.Rd
diff --git a/man/download_from_url.Rd b/man/download_from_url.Rd
diff --git a/man/extract_id.Rd b/man/extract_id.Rd
diff --git a/man/fdp-class.Rd b/man/fdp-class.Rd
diff --git a/man/fdp_resolve_read.Rd b/man/fdp_resolve_read.Rd
diff --git a/man/fdp_resolve_write.Rd b/man/fdp_resolve_write.Rd
diff --git a/man/get_author_url.Rd b/man/get_author_url.Rd
diff --git a/man/get_entity.Rd b/man/get_entity.Rd
diff --git a/man/get_existing.Rd b/man/get_existing.Rd
diff --git a/man/get_fields.Rd b/man/get_fields.Rd
diff --git a/man/get_file_hash.Rd b/man/get_file_hash.Rd
diff --git a/man/get_github_hash.Rd b/man/get_github_hash.Rd
diff --git a/man/get_id.Rd b/man/get_id.Rd
diff --git a/man/get_index.Rd b/man/get_index.Rd
diff --git a/man/get_max_version.Rd b/man/get_max_version.Rd
diff --git a/man/get_storage_location.Rd b/man/get_storage_location.Rd
diff --git a/man/get_token.Rd b/man/get_token.Rd
diff --git a/man/get_url.Rd b/man/get_url.Rd
diff --git a/man/increment_filename.Rd b/man/increment_filename.Rd
diff --git a/man/is_queryable.Rd b/man/is_queryable.Rd
diff --git a/man/new_author.Rd b/man/new_author.Rd
-Original file line number
+Diff line change
@@ Expand Up / @@ -50,3 +50,5 @@ docs @@
     /test
     /tests/testthat/test
     sonia.yaml
+    /venv
+    /check