Merge pull request #29 from NorwegianVeterinaryInstitute/dev

NVIverse v0.5.2

Author: PetterHopp

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: NVIbatch
 Title: Tools to facilitate the running of R-scripts in batch mode at NVI
-Version: 0.5.1
-Date: 2024-11-12
+Version: 0.5.2
+Date: 2024-12-13
 Authors@R: 
   c(person(given = "Petter",
            family = "Hopp",
@@ -16,6 +16,8 @@ URL: https://github.com/NorwegianVeterinaryInstitute/NVIbatch
 BugReports: https://github.com/NorwegianVeterinaryInstitute/NVIbatch/issues
 License: BSD_3_clause + file LICENSE
 Encoding: UTF-8
+Depends: 
+    R (>= 4.1.0)
 Imports:
     checkmate (>= 2.1.0),
     remotes,
@@ -41,5 +43,3 @@ Roxygen: list(markdown = FALSE)
 VignetteBuilder: knitr
 Language: en-GB
 RoxygenNote: 7.3.1
-Depends: 
-    R (>= 3.0.0)

NEWS.md

@@ -1,3 +1,10 @@
+# NVIbatch 0.5.2 - (2024-12-13)
+
+## Bug fixes:
+
+- `use_NVIverse` sets `build_vignettes` = `FALSE` if necessary packages for building vignettes are not installed.
+
+
 # NVIbatch 0.5.1 - (2024-11-12)
 
 ## New features:

R/use_NVIverse.R

@@ -7,8 +7,8 @@
 #' @param pkg [\code{character}]\cr
 #'     Name of one or more \code{NVIverse} packages.
 #' @param auth_token [\code{character}]\cr
-#'     To install \code{NVIconfig} a personal access token is needed. Generate a personal
-#'     access token (PAT) in "https://github.com/settings/tokens" and
+#'     To install \code{NVIconfig} a personal access token is needed. Generate a
+#'     personal access token (PAT) in "https://github.com/settings/tokens" and
 #'     supply to this argument. Defaults to \code{NULL}.
 #' @param dependencies [\code{logical(1) | character}]\cr
 #' The dependencies to check and eventually install. Can be
@@ -20,16 +20,17 @@
 #'     and is the default.
 #' @param upgrade [\code{logical(1) | character(1)}]\cr
 #' Should package dependencies be upgraded? One of c("ask", "always", "never").
-#'     \code{TRUE} and \code{FALSE} are also accepted and correspond to "always" and "never"
-#'     respectively. Defaults to \code{FALSE}.
+#'     \code{TRUE} and \code{FALSE} are also accepted and correspond to
+#'     "always" and "never" respectively. Defaults to \code{FALSE}.
 #' @param build [\code{logical(1)}]\cr
 #' If \code{TRUE} build the package before installing. Defaults to \code{TRUE}.
 #' @param build_manual [\code{logical(1)}]\cr
 #' If \code{FALSE}, don't build PDF manual ('--no-manual').
 #'     Defaults to \code{FALSE}.
 #' @param build_vignettes [\code{logical(1)}]\cr
 #' If \code{FALSE}, don't build package vignettes ("--no-build-vignettes").
-#'     Defaults to \code{TRUE}.
+#'     Defaults to \code{TRUE}, but is set to \code{FALSE} if necessary packages
+#'     for building vignettes are not installed.
 #' @param \dots Other arguments to be passed to
 #'     \ifelse{html}{\code{\link[remotes:install_github]{remotes::install_github}}}{\code{remotes::install_github}}.
 
@@ -45,6 +46,20 @@ use_NVIverse <- function(pkg,
                          build_manual = FALSE,
                          build_vignettes = TRUE,
                          ...) {
+
+  # PREPARE ARGUMENTS BEFORE CHECKING ----
+  ## Change build_vignettes to FALSE if packages to build vignettes is lacking
+  ## Building the vignettes requires knitr, rmarkdown, R.rsp and NVIrpackages
+  if (isTRUE(build_vignettes)) {
+    if (!isTRUE(NVIcheckmate::check_package(x = "knitr")) |
+        !isTRUE(NVIcheckmate::check_package(x = "rmarkdown")) |
+        !isTRUE(NVIcheckmate::check_package(x = "R.rsp")) |
+        !isTRUE(NVIcheckmate::check_package(x = "NVIrpackages"))) {
+      warning("Vignettes are not built as necessary packages for building vignettes are not installed.")
+      build_vignettes <- FALSE
+    }
+  }
+
   # ARGUMENT CHECKING ----
   # Check that NVIcheckmate is installed to avoid using NVIcheckmate functions if not installed
   NVIcheckmate_installed <- FALSE

man/use_NVIverse.Rd

@@ -65,10 +65,10 @@ nodename
 library(tidyverse)
 getCurrentFileLocation <-  function()
 {
-  this_file <- commandArgs() %>% 
-    tibble::enframe(name = NULL) %>%
-    tidyr::separate(col=value, into=c("key", "value"), sep="=", fill='right') %>%
-    dplyr::filter(key == "--file") %>%
+  this_file <- commandArgs()  |>  
+    tibble::enframe(name = NULL) |>
+    tidyr::separate(col=value, into=c("key", "value"), sep="=", fill='right') |>
+    dplyr::filter(key == "--file") |>
     dplyr::pull(value)
   if (length(this_file)==0)
   {