Merge branch 'main' into 0063-unexported-fns

.github/workflows/build_docker_image.yml

@@ -32,7 +32,7 @@ jobs:
 
       - name: Get changed files in renv/profiles
         id: changed-files
-        uses: tj-actions/changed-files@v35
+        uses: tj-actions/changed-files@v41
         with:
           files: renv/profiles/**/renv.lock
 
@@ -86,7 +86,7 @@ jobs:
           else
               echo "platforms=linux/amd64" >> $GITHUB_OUTPUT
           fi
-          
+
 
       - name: Call deploy docker image action for every renv
         uses: insightsengineering/r-image-creator@v1

.github/workflows/r-renv-lock.yml

@@ -130,7 +130,7 @@ jobs:
           install_min_version("vctrs", "0.4.1")
           install_min_version("rlang", "1.0.6")
           renv::install("[email protected]", dependencies = "none")
-          renv::install("[email protected].1", dependencies = "none")
+          renv::install("[email protected].2", dependencies = "none")
 
           renv::settings$snapshot.type("custom")
           renv::snapshot(force = TRUE, prompt = FALSE)

.github/workflows/rhub.yaml

@@ -0,0 +1,95 @@
+# R-hub's generic GitHub Actions workflow file. It's canonical location is at
+# https://github.com/r-hub/actions/blob/v1/workflows/rhub.yaml
+# You can update this file to a newer version using the rhub2 package:
+#
+# rhub::rhub_setup()
+#
+# It is unlikely that you need to modify this file manually.
+
+name: R-hub
+run-name: "${{ github.event.inputs.id }}: ${{ github.event.inputs.name || format('Manually run by {0}', github.triggering_actor) }}"
+
+on:
+  workflow_dispatch:
+    inputs:
+      config:
+        description: 'A comma separated list of R-hub platforms to use.'
+        type: string
+        default: 'linux,windows,macos'
+      name:
+        description: 'Run name. You can leave this empty now.'
+        type: string
+      id:
+        description: 'Unique ID. You can leave this empty now.'
+        type: string
+
+jobs:
+
+  setup:
+    runs-on: ubuntu-latest
+    outputs:
+      containers: ${{ steps.rhub-setup.outputs.containers }}
+      platforms: ${{ steps.rhub-setup.outputs.platforms }}
+
+    steps:
+    # NO NEED TO CHECKOUT HERE
+    - uses: r-hub/actions/setup@v1
+      with:
+        config: ${{ github.event.inputs.config }}
+      id: rhub-setup
+
+  linux-containers:
+    needs: setup
+    if: ${{ needs.setup.outputs.containers != '[]' }}
+    runs-on: ubuntu-latest
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.containers) }}
+    container:
+      image: ${{ matrix.config.container }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+
+  other-platforms:
+    needs: setup
+    if: ${{ needs.setup.outputs.platforms != '[]' }}
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.platforms) }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/setup-r@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}

.lycheeignore

@@ -5,5 +5,6 @@ https://packagemanager.posit.co/cran/2022-03-10/
 https://packagemanager.posit.co/cran/latest
 [email protected]
 [email protected]
+[email protected]
 [email protected]
 .*@users.noreply.github.com

DESCRIPTION

@@ -14,9 +14,14 @@ Authors@R: c(
     person("Omar", "Garcia", email = "[email protected]", role = "aut"),
     person("Ramiro", "Magno", email = "[email protected]",
     role = "aut", comment = c(ORCID = "0000-0001-5226-3441")),
+    person("Kamil", "Sijko", email = "[email protected]",
+    role = "aut", comment = c(ORCID = "0000-0002-2203-1065")),
+    person("Shiyu", "Chen", email = "[email protected]", 
+    role = "aut"),
     person("Pattern Institute", role = c("cph", "fnd")),
     person("F. Hoffmann-La Roche AG", role = c("cph", "fnd")),
-    person("Pfizer Inc", role = c("cph", "fnd"))
+    person("Pfizer Inc", role = c("cph", "fnd")),
+    person("Transition Technologies Science", role = c("cph", "fnd"))
     )
 Maintainer: Rammprasad Ganapathy <[email protected]>
 Description: An EDC and Data Standard-agnostic SDTM data transformation engine
@@ -33,30 +38,30 @@ URL: https://pharmaverse.github.io/sdtm.oak/, https://github.com/pharmaverse/sdt
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Depends: R (>= 4.2)
 Imports: 
-    admiraldev,
+    admiraldev (>= 1.1.0),
     dplyr (>= 1.0.0),
-    memoise,
-    assertthat,
-    purrr (>= 0.3.3),
-    rlang (>= 0.4.4),
+    purrr (>= 1.0.1),
+    rlang (>= 1.0.2),
+    tibble (>= 3.2.0),
+    vctrs (>= 0.5.0),
     stringr (>= 1.4.0),
-    tibble,
-    vctrs,
-    readr,
-    glue,
-    DT,
-    pillar
+    memoise (>= 2.0.1),
+    assertthat,
+    pillar,
+    cli
 Suggests:
     knitr,
     htmltools,
     lifecycle,
     magrittr,
     rmarkdown,
     spelling,
-    testthat (>= 3.1.7)
+    testthat (>= 3.1.7),
+    DT,
+    readr
 VignetteBuilder: knitr
 Config/testthat/edition: 3
 Config/testthat/parallel: true

R/assertions.R

@@ -5,11 +5,7 @@ assert_logical_vector <- function(arg, optional = FALSE) {
   }
 
   if (!is.logical(arg)) {
-    err_msg <- sprintf(
-      "`arg` must be a logical vector but is %s.",
-      admiraldev::what_is_it(arg)
-    )
-    rlang::abort(err_msg)
+    cli::cli_abort("`arg` must be a logical vector but is {.obj_type_friendly {arg}}")
   }
 
   invisible(arg)

R/ct.R

@@ -69,11 +69,11 @@ assert_ct_spec <- function(ct_spec, optional = FALSE) {
   }
 
   if (!is.null(ct_spec) && anyNA(ct_spec[[ct_spec_vars("ct_clst")]])) {
-    rlang::abort(glue::glue("`{ct_spec_vars('ct_clst')}` can't have any NA values."))
+    rlang::abort(stringr::str_glue("`{ct_spec_vars('ct_clst')}` can't have any NA values."))
   }
 
   if (!is.null(ct_spec) && anyNA(ct_spec[[ct_spec_vars("to")]])) {
-    rlang::abort(glue::glue("`{ct_spec_vars('to')}` can't have any NA values."))
+    rlang::abort(stringr::str_glue("`{ct_spec_vars('to')}` can't have any NA values."))
   }
 
   invisible(ct_spec)
@@ -279,7 +279,8 @@ ct_map <-
 #'
 #' @export
 read_ct_spec <- function(file = stop("`file` must be specified")) {
-  ct_spec <- readr::read_csv(file = file, col_types = "c")
+  ct_spec <- utils::read.csv(file = file, na.strings = c("NA", ""), colClasses = "character") |>
+    tibble::as_tibble()
   assert_ct_spec(ct_spec)
 
   ct_spec
@@ -327,7 +328,7 @@ ct_spec_example <- function(example) {
 
   if (identical(local_path, "")) {
     stop(
-      glue::glue(
+      stringr::str_glue(
         "'{example}' does not match any ct spec files. Run `ct_spec_example()` for options."
       ),
       call. = FALSE

R/derive_blfl.R

@@ -40,7 +40,6 @@ dtc_datepart <- function(dtc, partial_as_na = TRUE) {
 #' @return Character vector containing ISO 8601 times.
 #'
 #' @keywords internal
-
 dtc_timepart <- function(dtc, partial_as_na = TRUE, ignore_seconds = TRUE) {
   # Assert that dtc is a character vector
   admiraldev::assert_character_vector(dtc)

R/domain_example.R

@@ -80,7 +80,7 @@ domain_example <- function(example) {
 
   if (identical(local_path, "")) {
     stop(
-      glue::glue(
+      stringr::str_glue(
         "'{example}' does not match any domain example files. Run `domain_example()` for options."
       ),
       call. = FALSE
@@ -125,5 +125,8 @@ read_domain_example <- function(example) {
   }
 
   path <- domain_example(example)
-  readr::read_rds(file = path)
+  con <- file(path)
+  on.exit(close(con))
+
+  readRDS(con)
 }

_pkgdown.yml

@@ -13,6 +13,7 @@ reference:
   contents:
   - assign
   - harcode
+  - derive_blfl
   - derive_seq
   - derive_study_day
   - assign_datetime

renv.lock

@@ -1165,7 +1165,7 @@
     },
     "roxygen2": {
       "Package": "roxygen2",
-      "Version": "7.3.1",
+      "Version": "7.3.2",
       "Source": "Repository",
       "Repository": "RSPM",
       "Requirements": [
@@ -1187,7 +1187,7 @@
         "withr",
         "xml2"
       ],
-      "Hash": "c25fe7b2d8cba73d1b63c947bf7afdb9"
+      "Hash": "6ee25f9054a70f44d615300ed531ba8d"
     },
     "rprojroot": {
       "Package": "rprojroot",

renv/profiles/4.2/renv.lock

@@ -1165,7 +1165,7 @@
     },
     "roxygen2": {
       "Package": "roxygen2",
-      "Version": "7.3.1",
+      "Version": "7.3.2",
       "Source": "Repository",
       "Repository": "RSPM",
       "Requirements": [
@@ -1187,7 +1187,7 @@
         "withr",
         "xml2"
       ],
-      "Hash": "c25fe7b2d8cba73d1b63c947bf7afdb9"
+      "Hash": "6ee25f9054a70f44d615300ed531ba8d"
     },
     "rprojroot": {
       "Package": "rprojroot",

renv/profiles/4.3/renv.lock

@@ -1165,7 +1165,7 @@
     },
     "roxygen2": {
       "Package": "roxygen2",
-      "Version": "7.3.1",
+      "Version": "7.3.2",
       "Source": "Repository",
       "Repository": "RSPM",
       "Requirements": [
@@ -1187,7 +1187,7 @@
         "withr",
         "xml2"
       ],
-      "Hash": "c25fe7b2d8cba73d1b63c947bf7afdb9"
+      "Hash": "6ee25f9054a70f44d615300ed531ba8d"
     },
     "rprojroot": {
       "Package": "rprojroot",