Merge branch 'master' into fix_tinytex

.github/workflows/coverage.yaml

@@ -12,7 +12,7 @@ name: test-coverage
 
 jobs:
   test-coverage:
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
     env:
       GITHUB_PAT: ${{ secrets.GH_TOKEN }}
       GITHUB_ACTIONS_RUN_DB_UNIT_TESTS: true

.github/workflows/lint.yaml

@@ -12,7 +12,7 @@ name: lint
 
 jobs:
   lint:
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
     env:
       GITHUB_PAT: ${{ secrets.GH_TOKEN }}
     steps:
@@ -24,14 +24,11 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-           cache-version: 2
-           extra-packages: |
-             any::lintr
-           needs: lint
+          extra-packages: any::lintr, local::.
+          needs: lint
 
       - name: Lint
-        run: |
-          lintr::lint_package()
+        run: lintr::lint_package()
         shell: Rscript {0}
         env:
-          LINTR_ERROR_ON_LINT: false
+          LINTR_ERROR_ON_LINT: true

.github/workflows/pkgdown.yaml

@@ -14,7 +14,7 @@ permissions: read-all
 
 jobs:
   pkgdown:
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
     # Only restrict concurrency for non-PR jobs
     concurrency:
       group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
@@ -42,7 +42,7 @@ jobs:
 
       - name: Deploy to GitHub pages 🚀
         if: github.event_name != 'pull_request'
-        uses: JamesIves/github-pages-deploy-action@v4.6.1
+        uses: JamesIves/github-pages-deploy-action@v4.6.8
         with:
           clean: false
           branch: gh-pages

.lintr

@@ -2,3 +2,4 @@ linters: linters_with_defaults(
   object_name_linter(c("camelCase", "snake_case")),
   cyclocomp_linter(complexity_limit = 30),
   line_length_linter(80))
+exclusions: list("data-raw", "tests")

R/autoReport.R

@@ -289,9 +289,12 @@ writeAutoReportData <- function(fileName = "autoReport.yml", config,
       )
       # to maintain some order, remove files older than 30 days
       files <- file.info(list.files(bckFilePath, full.names = TRUE))
-      rmFiles <- rownames(files[difftime(Sys.time(), files[, "mtime"],
-        units = "days"
-      ) > 30, ])
+      rmFiles <- rownames(files[difftime(Sys.time(),
+            files[, "mtime"],
+            units = "days"
+          ) > 30,
+        ]
+      )
       file.remove(rmFiles)
       con <- file(oriFile, "w")
     }
@@ -453,10 +456,13 @@ getRegs <- function(config) {
 #' runAutoReport()
 #' }
 #'
+
 runAutoReport <- function(dayNumber = as.POSIXlt(Sys.Date())$yday + 1,
                           type = c("subscription", "dispatchment"),
                           dryRun = FALSE) {
+  # nolint start: object_name_linter
   . <- ""
+  # nolint end
 
   # get report candidates
   reps <- readAutoReportData() %>%
@@ -474,8 +480,8 @@ runAutoReport <- function(dayNumber = as.POSIXlt(Sys.Date())$yday + 1,
       {
         rep <- reps[[i]]
         if (dayNumber %in% rep$runDayOfYear &
-          as.Date(rep$terminateDate) > Sys.Date() &
-          as.Date(rep$startDate) <= Sys.Date()) {
+              as.Date(rep$terminateDate) > Sys.Date() &
+              as.Date(rep$startDate) <= Sys.Date()) {
           # get explicit referenced function and call it
           f <- .getFun(paste0(rep$package, "::", rep$fun))
           content <- do.call(what = f, args = rep$params)
@@ -709,7 +715,9 @@ makeAutoReportTab <- function(session,
                               includeReportId = FALSE) {
   stopifnot(type %in% c("subscription", "dispatchment", "bulletin"))
 
+  # nolint start: object_name_linter
   . <- ""
+  # nolint end
 
   l <- list()
   autoRep <- readAutoReportData() %>%

R/fireInTheHole.R

@@ -25,7 +25,7 @@ fireInTheHole <- function(flipPeriod = FALSE) {
   conf <- getConfig(fileName = "rapbaseConfig.yml")
 
   if (hour >= conf$r$schedule$nocturnal$startHour &&
-    hour < conf$r$schedule$nocturnal$endHour) {
+        hour < conf$r$schedule$nocturnal$endHour) {
     night <- TRUE
   } else {
     night <- FALSE

R/log.R

@@ -231,7 +231,7 @@ appendLog <- function(event, name) {
     doAppend <- TRUE
     doColNames <- FALSE
     if (!file.exists(file.path(path, name)) ||
-      file.size(file.path(path, name)) == 0) {
+          file.size(file.path(path, name)) == 0) {
       doAppend <- FALSE
       doColNames <- TRUE
     }
@@ -440,13 +440,13 @@ sanitizeLog <- function() {
         lf <- lf %>%
           dplyr::filter(as.Date(.data$time) > eolDate)
         write.table(
-          lf,
-          logFile[i],
-          append = FALSE,
-          sep = ",",
-          row.names = FALSE,
-          col.names = TRUE,
-          qmethod = "double")
+                    lf,
+                    logFile[i],
+                    append = FALSE,
+                    sep = ",",
+                    row.names = FALSE,
+                    col.names = TRUE,
+                    qmethod = "double")
       }
     }
   }

R/misc.R

@@ -62,7 +62,7 @@ getRapPackages <- function() {
 #'
 isRapContext <- function() {
   if (Sys.getenv("R_RAP_INSTANCE") %in%
-      c("DEV", "TEST", "QA", "PRODUCTION", "PRODUCTIONC")) {
+        c("DEV", "TEST", "QA", "PRODUCTION", "PRODUCTIONC")) {
     return(TRUE)
   } else {
     return(FALSE)

R/moduleAutoReport.R

@@ -236,12 +236,13 @@ autoReportServer <- function(id, registryName, type, org = NULL,
 
   stopifnot(freq %in% c("day", "week", "month", "quarter", "year"))
 
-  defaultFreq <- switch(freq,
-                        day = "Daglig-day",
-                        week = "Ukentlig-week",
-                        month = "M\u00E5nedlig-month",
-                        quarter = "Kvartalsvis-quarter",
-                        year = "\u00C5rlig-year"
+  defaultFreq <- switch(
+    freq,
+    day = "Daglig-day",
+    week = "Ukentlig-week",
+    month = "M\u00E5nedlig-month",
+    quarter = "Kvartalsvis-quarter",
+    year = "\u00C5rlig-year"
   )
 
   shiny::moduleServer(id, function(input, output, session) {
@@ -416,8 +417,8 @@ autoReportServer <- function(id, registryName, type, org = NULL,
           Sys.Date() + 1
         } else {
           seq.Date(Sys.Date(),
-                   by = strsplit(input$freq, "-")[[1]][2],
-                   length.out = 2
+            by = strsplit(input$freq, "-")[[1]][2],
+            length.out = 2
           )[2]
         },
         min = Sys.Date() + 1,
@@ -555,17 +556,17 @@ autoReportServer <- function(id, registryName, type, org = NULL,
 #' @rdname autoReport
 #' @export
 autoReportServer2 <- function(
-    id,
-    registryName,
-    type,
-    org = NULL,
-    paramNames = shiny::reactiveVal(c("")),
-    paramValues = shiny::reactiveVal(c("")),
-    reports = NULL,
-    orgs = NULL,
-    eligible = TRUE,
-    freq = "month",
-    user
+  id,
+  registryName,
+  type,
+  org = NULL,
+  paramNames = shiny::reactiveVal(c("")),
+  paramValues = shiny::reactiveVal(c("")),
+  reports = NULL,
+  orgs = NULL,
+  eligible = TRUE,
+  freq = "month",
+  user
 ) {
   stopifnot(
     all(unlist(lapply(user, shiny::is.reactive), use.names = FALSE))
@@ -608,16 +609,16 @@ autoReportServer2 <- function(
     )
     shiny::observeEvent(
       userEvent(),
-        autoReport$tab <- makeAutoReportTab(
-          session = session,
-          namespace = id,
-          user = user$name(),
-          group = registryName,
-          orgId = user$org(),
-          type = type,
-          mapOrgId = orgList2df(orgs)
-        ),
-        ignoreNULL = FALSE
+      autoReport$tab <- makeAutoReportTab(
+        session = session,
+        namespace = id,
+        user = user$name(),
+        group = registryName,
+        orgId = user$org(),
+        type = type,
+        mapOrgId = orgList2df(orgs)
+      ),
+      ignoreNULL = FALSE
     )
 
     shiny::observeEvent(input$addEmail, {

R/moduleNavbarWidget.R

@@ -27,7 +27,7 @@
 #'   called from outside the registry environment \code{caller} must be set to
 #'   the actual name of the R package.
 #'
-#' @return Shiny objects, mostly.  \code{navbarWidgetServer2()} invisibly returns
+#' @return Shiny objects, mostly. \code{navbarWidgetServer2()} invisibly returns
 #'   a list of reactive values representing user metadata and privileges. See
 #'   \code{\link{userAttribute}} for further details on these values.
 #' @name navbarWidget
@@ -110,9 +110,9 @@ navbarWidgetServer <- function(id, orgName,
 #' @rdname navbarWidget
 #' @export
 navbarWidgetServer2 <- function(
-    id,
-    orgName,
-    caller = environmentName(topenv(parent.frame()))
+  id,
+  orgName,
+  caller = environmentName(topenv(parent.frame()))
 ) {
 
   shiny::moduleServer(id, function(input, output, session) {

R/userAttribute.R

@@ -46,12 +46,12 @@
 #' @export
 
 userInfo <- function(
-    entity,
-    shinySession = NULL,
-    devContexts = c("DEV"),
-    testContexts = c("TEST"),
-    prodContexts = c("QA", "QAC", "PRODUCTION", "PRODUCTIONC"),
-    group = NULL
+  entity,
+  shinySession = NULL,
+  devContexts = c("DEV"),
+  testContexts = c("TEST"),
+  prodContexts = c("QA", "QAC", "PRODUCTION", "PRODUCTIONC"),
+  group = NULL
 ) {
 
   # stop helper function
@@ -200,7 +200,7 @@ userAttribute <- function(group, unit = NULL) {
   stopifnot(group %in% utils::installed.packages()[, 1])
 
   if (Sys.getenv("SHINYPROXY_USERGROUPS") == "" ||
-      Sys.getenv("USERORGID") == "") {
+        Sys.getenv("USERORGID") == "") {
     stop(paste(
       "Environmental variables SHINYPROXY_USERGROUPS and USERORGID must both",
       "be set!"
@@ -249,7 +249,7 @@ userAttribute <- function(group, unit = NULL) {
   orgs <- vector()
   roles <- vector()
   orgNames <- vector()
-    for (i in seq_len(length(units))) {
+  for (i in seq_len(length(units))) {
     orgs[i] <- unitAttribute(units[i], "resh")
     roles[i] <- unitAttribute(units[i], "role")
     orgNames[i] <- unitAttribute(units[i], "titlewithpath")