Merge branch 'master' into devel

mokymai · May 27, 2024 · 20bd5bc · 20bd5bc
2 parents 9b25bd6 + a6229cd
commit 20bd5bc
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Showing 12 changed files with 51 additions and 39 deletions.
diff --git a/R/get_os.R b/R/get_os.R
@@ -20,8 +20,8 @@ get_os_type <- function() {
     if (os == "Darwin") {os <- "mac"}
   } else {
     os <- .Platform$OS.type
-    if (grepl("^darwin",   R.version$os)) {os <- "mac"}
-    if (grepl("linux-gnu", R.version$os)) {os <- "linux"}
+    if (grepl("^darwin",   R.version$os, useBytes = TRUE)) {os <- "mac"}
+    if (grepl("linux-gnu", R.version$os, useBytes = TRUE)) {os <- "linux"}
   }
   unname(tolower(os))
 }

diff --git a/R/helpers--make_unique_obj_names.R b/R/helpers--make_unique_obj_names.R
@@ -1,6 +1,8 @@
 make_unique_obj_names <- function(names, prefix = "", suffix = "",
-                                  list_of_choices = objects(all.names = TRUE,
-                                                            envir = .GlobalEnv),
+                                  list_of_choices = objects(
+                                    all.names = TRUE,
+                                    envir = .GlobalEnv
+                                  ),
                                   all_numbered = TRUE) {
   if (length(names) == 0) {
     return(NULL)

diff --git a/R/helpers.R b/R/helpers.R
@@ -34,9 +34,9 @@ ui_msg_restart_rstudio <- function() {
 }
 # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 # str_glue_eval ==============================================================
-str_glue_eval <- function(..., envir = parent.frame(), .sep = "",
-  .open = "{", .close = "}", envir_eval = envir,  envir_glue = envir) {
-
+str_glue_eval <- function(
+    ..., envir = parent.frame(), .sep = "",
+    .open = "{", .close = "}", envir_eval = envir, envir_glue = envir) {
   commands_as_text <- glue::glue(...,
     .envir = envir_glue,
     .open  = .open,

diff --git a/R/packages--check.R b/R/packages--check.R
@@ -1027,7 +1027,7 @@ get_pkgs_installation_code <- function(x = NULL, ..., to_clipboard = FALSE,
     # help("options") # Opens help on options
     options(
       repos = "https://cran.rstudio.com/",
-      pkgType = "{ifelse(get_os_type() == "linux", "source", "both")}",
+      pkgType = "{ifelse(get_os_type() == "windows", "both", "source")}",
       install.packages.check.source = "yes",
       install.packages.compile.from.source = "always"
     )

diff --git a/R/packages--find.R b/R/packages--find.R
@@ -57,7 +57,7 @@ list_pkgs_used_in_dir_code <- function(path = ".", regexp = "(?i)[.](rmd|r)$", .
 # TODO: ignore code in comments
 list_pkgs_used_in_files <- function(files) {
   files %>%
-    purrr::map(~readr::read_file(.)) %>%
+    purrr::map(~ readr::read_file(.)) %>%
     stringr::str_extract_all(
       paste0(
         "(?<=(library|require|require2)\\()(.*?)(?=\\))|", # library(dplyr)
@@ -74,10 +74,10 @@ list_pkgs_used_in_files <- function(files) {
 
 list_pkgs_used_in_files_code <- function(files) {
   files %>%
-    purrr::map(~readr::read_file(.)) %>%
+    purrr::map(~ readr::read_file(.)) %>%
     stringr::str_extract_all(
       paste0(
-        "(library|require|require2)\\((.*?)\\)|",   # library(dplyr)
+        "(library|require|require2)\\((.*?)\\)|", # library(dplyr)
         "(\\s|\\n|\\(|\\{|\\[)[a-zA-Z0-9.]*?( )*:{2,3}[a-zA-Z0-9._]*|", # dplyr::select
         "package\\s*=\\s*(\"|')[a-zA-Z0-9.]*?(\"|')" # data(package = "dplyr")
       )
@@ -90,7 +90,6 @@ list_pkgs_used_in_files_code <- function(files) {
 get_pkg_dependencies <- function(pkg) {
   pkg <- stringr::str_replace(pkg, "[.]", "[.]")
   desc::desc_get_deps(fs::dir_ls(.libPaths(), regexp = glue::glue("/{pkg}$"))) %>%
-      dplyr::filter(.data$type %in% c("Depends", "Imports")) %>%
-      dplyr::pull(.data$package)
+    dplyr::filter(.data$type %in% c("Depends", "Imports")) %>%
+    dplyr::pull(.data$package)
 }
-
diff --git a/R/programs.R b/R/programs.R
@@ -288,7 +288,7 @@ check_r_version <- function(v_recommended = "4.3.0",
   )
 }
 # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-check_quarto_version <- function(v_recommended = "1.2.313",
+check_quarto_version <- function(v_recommended = "1.4.549",
                                  skip_online_check = FALSE) {
 
   check_program_version(
@@ -301,7 +301,7 @@ check_quarto_version <- function(v_recommended = "1.2.313",
 }
 
 # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-check_rs_version <- function(v_recommended = "2022.7.1", skip_online_check = FALSE) {
+check_rs_version <- function(v_recommended = "2023.12.1", skip_online_check = FALSE) {
 
   if (!rstudioapi::isAvailable()) {
     ui_oops("Program {red('RStudio')} is not installed or is not running. ")

diff --git a/R/restart_reload.R b/R/restart_reload.R
@@ -10,7 +10,7 @@
 #' @concept utilities
 #'
 rstudio_restart_r <- function() {
-  if (rstudioapi::isAvailable(version_needed = "1.2.1261") ) {
+  if (rstudioapi::isAvailable(version_needed = "1.2.1261")) {
     invisible(rstudioapi::executeCommand("restartR", quiet = TRUE))
   }
 }
@@ -19,7 +19,7 @@ rstudio_restart_r <- function() {
 #' @export
 #' @concept utilities
 rstudio_reload_ui <- function() {
-  if (rstudioapi::isAvailable(version_needed = "1.2.1261") ) {
+  if (rstudioapi::isAvailable(version_needed = "1.2.1261")) {
     invisible(rstudioapi::executeCommand("reloadUi", quiet = TRUE))
   }
 }
@@ -35,4 +35,3 @@ restart_r <- function() {
 restart_rstudio <- function() {
   rstudio_restart_r()
 }
-
diff --git a/R/settings--preferences.R b/R/settings--preferences.R
@@ -163,7 +163,7 @@ rstudio_set_preferences <- function(file) {
     pref <- jsonlite::fromJSON(file)
     purrr::walk2(
       names(pref), unname(pref),
-      ~{
+      ~ {
         tryCatch(
           rstudioapi::writeRStudioPreference(.x, .y),
           error = function(e) {
@@ -206,14 +206,16 @@ rstudio_set_preferences <- function(file) {
 #' }}
 rstudio_compare_user_settings <- function(to = "bio-default") {
   to <- match.arg(to, c("bio-default", "rstudio-default"))
+
   file <- get_path_rstudio_config_file(which = to)
   default_prefs <-
     jsonlite::fromJSON(file) %>%
-    purrr::map_if(is.integer, as.numeric)
+    purrr::map_if(is.integer, as.numeric) |>
+    purrr::map_at("busy_exclusion_list", as.list)
 
   pref_names <- names(default_prefs) %>% purrr::set_names(., .)
   current_prefs <-
-    purrr::map(pref_names, ~rstudioapi::readRStudioPreference(.,  NULL)) %>%
+    purrr::map(pref_names, ~rstudioapi::readRStudioPreference(., NULL)) %>%
     purrr::map_if(is.integer, as.numeric)
 
   usethis::ui_info(

diff --git a/README.Rmd b/README.Rmd
@@ -110,7 +110,7 @@ Options:
 ```{r README-7a, eval=FALSE}
 bio::check_installed_programs()
 ## ✔ Program R (4.3.1) is installed (recommended >= 4.3.1).
-## ✖ Program RStudio is not installed or is not running. 
+## ✖ Program RStudio is not installed or is not running.
 ## ✔ Tool Quarto (1.4.268) is installed (recommended >= 1.3.336).
 ## ✔ Tool Rtools is installed.
 ```
@@ -157,13 +157,13 @@ cat(res)
 
 ```{r README-8a, eval=FALSE, paged.print=FALSE}
 bio::check_packages_by_topic("mini")
-## ℹ Reading list 'mini' 
+## ℹ Reading list 'mini'
 ## ✔ Minimal required versions of all 19 packages (from list 'mini') are already installed.
 ```
 
 ```{r README-8b, eval=FALSE, paged.print=FALSE}
 bio::check_packages_by_topic("mini", include = "newer_on_cran")
-## ℹ Reading list 'mini' 
+## ℹ Reading list 'mini'
 ## ✔ Minimal required versions of all 19 packages (from list 'mini') are already installed.
 ## ℹ Note: 1 package has newer version on CRAN.
 ```
@@ -186,9 +186,9 @@ Check if there are updates for **bio** or its dependency packages.
 ```{r README-3b, eval=FALSE, paged.print=FALSE}
 bio::check_updates_pkg_bio()
 ## ℹ Analyzing dependencies of package bio
-## 
+##
 ## [... truncated ...]
-## 
+##
 ## ✔ Minimal required versions of all 26 packages (from list 'bio') are already installed.
 ```
 
@@ -221,7 +221,7 @@ bio::rstudio_install_spellcheck_dictionaries()
 Install improved Lithuanian dictionary.
 ```{r eval=FALSE}
 bio::rstudio_install_spellcheck_dictionary_lt()
-## ✔ lt_LT dictionary installed. 
+## ✔ lt_LT dictionary installed.
 ##   'C:/Users/ViG/AppData/Roaming/RStudio/dictionaries/languages-system/lt_LT.dic'
 ```
 
@@ -348,7 +348,7 @@ snippets::install_snippets_from_package("snippets", backup = TRUE)
 ##   'C:/Users/User/AppData/Roaming/RStudio/snippets/markdown.snippets'
 ## ✔ File with r snippets was updated:
 ##   'C:/Users/User/AppData/Roaming/RStudio/snippets/r.snippets'
-## 
+##
 ## ℹ You will be able to use the snippets after RStudio is closed and reopened.
 ```
 

diff --git a/README.md b/README.md
@@ -6,9 +6,9 @@ Package ***bio***
 <!-- badges: start -->
 
 [![GitHub
-version](https://img.shields.io/badge/GitHub-0.2.2.3-brightgreen.svg)](https://github.com/mokymai/bio)
+version](https://img.shields.io/badge/GitHub-0.2.4-brightgreen.svg)](https://github.com/mokymai/bio)
 [![R-CMD-check](https://github.com/mokymai/bio/workflows/R-CMD-check/badge.svg)](https://github.com/mokymai/bio/actions)
-[![Updated-on](https://img.shields.io/badge/Updated%20on-2023--08--24-yellowgreen.svg)](/commits/master)
+[![Updated-on](https://img.shields.io/badge/Updated%20on-2024--02--08-yellowgreen.svg)](/commits/master)
 [![Lifecycle:
 experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://www.tidyverse.org/lifecycle/#experimental)
 [![R-CMD-check](https://github.com/mokymai/bio/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/mokymai/bio/actions/workflows/R-CMD-check.yaml)
@@ -91,7 +91,7 @@ Options:
 ``` r
 bio::check_installed_programs()
 ## ✔ Program R (4.3.1) is installed (recommended >= 4.3.1).
-## ✖ Program RStudio is not installed or is not running. 
+## ✖ Program RStudio is not installed or is not running.
 ## ✔ Tool Quarto (1.4.268) is installed (recommended >= 1.3.336).
 ## ✔ Tool Rtools is installed.
 ```
@@ -149,13 +149,13 @@ Details
 
 ``` r
 bio::check_packages_by_topic("mini")
-## ℹ Reading list 'mini' 
+## ℹ Reading list 'mini'
 ## ✔ Minimal required versions of all 19 packages (from list 'mini') are already installed.
 ```
 
 ``` r
 bio::check_packages_by_topic("mini", include = "newer_on_cran")
-## ℹ Reading list 'mini' 
+## ℹ Reading list 'mini'
 ## ✔ Minimal required versions of all 19 packages (from list 'mini') are already installed.
 ## ℹ Note: 1 package has newer version on CRAN.
 ```
@@ -176,9 +176,9 @@ Check if there are updates for **bio** or its dependency packages.
 ``` r
 bio::check_updates_pkg_bio()
 ## ℹ Analyzing dependencies of package bio
-## 
+##
 ## [... truncated ...]
-## 
+##
 ## ✔ Minimal required versions of all 26 packages (from list 'bio') are already installed.
 ```
 
@@ -213,7 +213,7 @@ Install improved Lithuanian dictionary.
 
 ``` r
 bio::rstudio_install_spellcheck_dictionary_lt()
-## ✔ lt_LT dictionary installed. 
+## ✔ lt_LT dictionary installed.
 ##   'C:/Users/ViG/AppData/Roaming/RStudio/dictionaries/languages-system/lt_LT.dic'
 ```
 
@@ -336,7 +336,7 @@ snippets::install_snippets_from_package("snippets", backup = TRUE)
 ##   'C:/Users/User/AppData/Roaming/RStudio/snippets/markdown.snippets'
 ## ✔ File with r snippets was updated:
 ##   'C:/Users/User/AppData/Roaming/RStudio/snippets/r.snippets'
-## 
+##
 ## ℹ You will be able to use the snippets after RStudio is closed and reopened.
 ```
 

diff --git a/inst/install-r/programs-required-version.txt b/inst/install-r/programs-required-version.txt
@@ -1,6 +1,10 @@
 ---
 title: "Minimal required versions of programs"
+<<<<<<< HEAD
 date:  2024-05-27
+=======
+date:  2024-02-08
+>>>>>>> master
 notes: ""
 
 
@@ -9,7 +13,13 @@ notes: ""
 ---
 # This text must be in line 10 -----------------------------------------------
 program                     | required_version | ignore | notes_version
+<<<<<<< HEAD
 R                           | 4.3.3            | FALSE  |
 RStudio                     | 2023.12.1        | FALSE  | For 32-bit systems v 1.1.463
 Quarto                      | 1.4.554          | FALSE  |
+=======
+R                           | 4.3.2            | FALSE  |
+RStudio                     | 2023.12.1        | FALSE  | For 32-bit systems v 1.1.463
+Quarto                      | 1.4.549          | FALSE  |
+>>>>>>> master
 
diff --git a/man/bio-package.Rd b/man/bio-package.Rd