Hms update

.github/workflows/R-CMD-check.yaml

@@ -1,5 +1,5 @@
-# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
-# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
     branches:
@@ -12,7 +12,9 @@ on:
       - master
       - dev
 
-name: R-CMD-check
+name: R-CMD-check.yaml
+
+permissions: read-all
 
 jobs:
   R-CMD-check:
@@ -32,56 +34,26 @@ jobs:
           - {os: ubuntu-latest,  r: 'release'}
 
     env:
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      RSPM: ${{ matrix.config.rspm }}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
 
       - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
 
-      - uses: r-lib/actions/setup-pandoc@v2
-
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
-
-      - name: Cache R packages
-        if: runner.os != 'Windows'
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
-
-      - name: Install system dependencies
-        if: runner.os == 'Linux'
-        run: |
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
-
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
-        shell: Rscript {0}
-
-      - name: Check
-        env:
-          _R_CHECK_CRAN_INCOMING_REMOTE_: false
-        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
+          extra-packages: any::rcmdcheck
+          needs: check
 
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
+      - uses: r-lib/actions/check-r-package@v2
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

DESCRIPTION

@@ -26,7 +26,7 @@ Depends: R (>= 4.0)
 Imports:
     yyjsonr (>= 0.1.18),
     jsonvalidate (>= 1.3.1),
-    lubridate
+    hms
 Suggests:
     testthat (>= 2.1.0),
     jsonlite (>= 1.8.0),
@@ -37,7 +37,7 @@ Suggests:
     purrr,
     tibble,
     dplyr,
-    hms,
+    lubridate,
     data.table
 VignetteBuilder: knitr
 Config/testthat/edition: 3

NAMESPACE

@@ -16,8 +16,8 @@ export(set_study_oid)
 export(set_variable_attributes)
 export(validate_dataset_json)
 export(write_dataset_json)
+importFrom(hms,as_hms)
 importFrom(jsonvalidate,json_validate)
-importFrom(lubridate,hms)
 importFrom(tools,file_path_sans_ext)
 importFrom(utils,tail)
 importFrom(yyjsonr,opts_read_json)

R/utils.R

@@ -127,7 +127,7 @@ date_time_conversions <- function(d, dt, tdt){
                              as.POSIXct,
                              tz = "UTC",
                              tryFormats = "%Y-%m-%dT%H:%M:%S")
-  d[time_cols] <- lapply(d[time_cols], hms)
+  d[time_cols] <- lapply(d[time_cols], as_hms)
   d
 }
 

R/zzz.R

@@ -2,7 +2,7 @@
 #' @importFrom yyjsonr opts_write_json opts_read_json write_json_file write_json_str read_json_str read_json_file
 #' @importFrom tools file_path_sans_ext
 #' @importFrom utils tail
-#' @importFrom lubridate hms
+#' @importFrom hms as_hms
 NULL
 
 #' @keywords internal

data-raw/data.R

@@ -89,7 +89,7 @@ time_options <- c("12:34:56", "15:34:34", "11:12:52", "21:16:11")
 
 adsl$VIST1TMC <- sample(time_options, 254, replace=TRUE)
 adsl$VIST1DTC <-paste(format(adsl$VISIT1DT, "%Y-%m-%d"), sample(time_options, 254, replace=TRUE), sep="T")
-adsl$VISIT1TM <- lubridate::hms(adsl$VIST1TMC)
+adsl$VISIT1TM <- hms::as_hms(adsl$VIST1TMC)
 adsl$VIST1DTM <- as.POSIXct(strptime(adsl$VIST1DTC, "%Y-%m-%dT%H:%M:%S", tz="UTC"))
 
 new_meta <- tibble::tribble(

tests/testthat/test-read_dataset_json.R

@@ -84,11 +84,11 @@ test_that("datetime conversions work properly",{
   iris_timetest <- read_dataset_json(test_path("testdata", "iris_timetest.json"))
 
   expect_s3_class(iris_timetest$Datetime, "POSIXct")
-  expect_equal(class(iris_timetest$Time), "Period", ignore_attr=TRUE)
+  expect_equal(class(iris_timetest$Time), c("hms", "difftime"), ignore_attr=TRUE)
 
   expect_equal(sort(unique(iris_timetest$Datetime)),
                as.POSIXct(strptime(c("2024-01-01T12:34:56", "2024-01-17T18:45:56"),
                         "%Y-%m-%dT%H:%M:%S", tz="UTC")))
   expect_equal(sort(unique(as.numeric(iris_timetest$Time))),
-               as.numeric(hms(c("12:34:56", "18:45:56"))))
+               as.numeric(as_hms(c("12:34:56", "18:45:56"))))
 })

tests/testthat/test-utils.R

@@ -42,5 +42,5 @@ test_that("Date, datetime and time conversions work as expected", {
   expect_equal(df_converted$datetime, as.POSIXct(c("2020-01-01 12:00:00",
                                                    "2020-01-01 12:00:01",
                                                    NA), tz = "UTC"))
-  expect_equal(df_converted$time, hms(c("12:00:00", "12:00:01", NA)))
+  expect_equal(df_converted$time, as_hms(c("12:00:00", "12:00:01", NA)))
 })

vignettes/converting_files.Rmd

@@ -49,6 +49,9 @@ extract_xpt_meta <- function(n, .data) {
   } else if (inherits(.data[[n]],"numeric")) {
     if (any(is.double(.data[[n]]))) out$dataType <- "float"
     else out$dataType <- "integer"
+  }  else if (inherits(.data[[n]],"hms")) {
+    out$dataType <- "time"
+    out$targetDataType <- "integer"
   } else {
     out$dataType <- "string"
     out$length <- max(purrr::map_int(.data[[n]], nchar))

vignettes/date_time_datetime.Rmd

@@ -43,8 +43,8 @@ tibble::tribble(
 In the table above, we have the metadata for both character and numeric dates, times, and date times. Both sets of variables have the same values within `dataType`. The difference is the optional field of `targetDataType`, where the value for the numeric variables is set to `integer`. Both `read_dataset_json()` and `write_dataset_json()` rely on these fields and as such they must be set properly. This comes with a few assumption and requirements.
 
 -   Numeric dates will be converted into the type of `Date` (see `help("Date", package="base")`)
--   Numeric times will be converted to the **{lubridate}** type of `Period`
-  - R doesn't have a specific built in type of time. We decided to take on **{lubridate}** as a dependency given package stability and **{lubridate}**'s inclusion in the tidyverse. The `Period` objects on read are produced using the `lubridate::hms()`. 
+-   Numeric times will be converted to the **{hms}** type of `hms`
+  - R doesn't have a specific built in type of time. We decided to take on **{hms}** as a dependency given that this is the type using by the **{haven}** package when reading SAS Version 5 Transport files. As such, similar behavior can be expected when importing an XPT or a Dataset JSON file. 
 -   Numeric date times will be converted to the base R type of `POSIXct` and anchored to the UTC timezone.
   - CDISC dates are generally not timezone qualified, though for character dates, this is optional. Unless a timezone is explicitly specified systems may default to the user's current timezone. To decrease ambiguity, we've introduced a hard requirement that datetimes are anchored to UTC. If the datetime variable is found to be using a different timezone, an error will be thrown.