v0.2.6

Merge pull request #37 from mokymai/devel
mokymai · Jul 31, 2024 · 79de00b · 79de00b
2 parents 730650f + 0f53f37
commit 79de00b
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: bio
 Type: Package
 Title: Resources Manager for R, RStudio and Related Software
-Version: 0.2.5
-Date: 2024-05-27
+Version: 0.2.6
+Date: 2024-07-31
 Authors@R: 
     person("Vilmantas", "Gegzna", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-9500-5167"),
@@ -18,12 +18,13 @@ Language: en-US
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Additional_repositories:
   https://mokymai.github.io/download/
 Imports:
   backup.tools (>= 0.0.3),
   checkmate,
+  cli,
   clipr,
   crayon,
   desc,

diff --git a/R/packages--check.R b/R/packages--check.R
@@ -208,7 +208,8 @@ read_pkgs_list <- function(list_name,
           "It seems that there is no online version of list ",
           "{list_name_blue} or it cannot be accessed. ",
           "\nCheck if the list name is correct. ",
-          "Did you mean one of: \n{usethis::ui_value(bio::get_pkg_lists_local())}, ..."
+          "Did you mean one of: \n",
+          "{usethis::ui_value(bio::get_pkg_lists_local())}, ..."
         ))
       } else {
         usethis::ui_stop(w$message)
@@ -239,7 +240,8 @@ get_path_pkgs_list <- function(list_name, local_list) {
       usethis::ui_stop(paste0(
         "List {list_name_blue} was not found on your computer. \n",
         "Check if the list name is correct. ",
-        "Did you mean one of: \n{usethis::ui_value(bio::get_pkg_lists_local())}, ..."
+        "Did you mean one of: \n",
+        "{usethis::ui_value(bio::get_pkg_lists_local())}, ..."
       ))
     }
 
@@ -475,7 +477,8 @@ merge_pkgs_status_lists <- function(pkgs_list, pkgs_installed,
 #' head(get_pkgs_installation_status_raw("mini"))
 get_pkgs_installation_status_raw <- function(list_name = NULL, pkgs = NULL,
                                              local_list = getOption(
-                                               "bio.local_list", TRUE)) {
+                                               "bio.local_list", TRUE
+                                             )) {
   checkmate::assert_character(list_name, null.ok = TRUE)
   checkmate::assert_character(pkgs, null.ok = TRUE)
   if (is.null(list_name) && is.null(pkgs)) {
@@ -508,7 +511,6 @@ get_pkgs_installation_status_raw <- function(list_name = NULL, pkgs = NULL,
 
 
 
-
 # Installation status --------------------------------------------------------
 # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 #

diff --git a/R/paths-and-files.R b/R/paths-and-files.R
@@ -195,7 +195,7 @@ get_path_rstudio_internal_state_dir <- function(..., .check = FALSE) {
   # Linux/Mac:     ~/.rstudio-desktop
 
 
-  if (rstudioapi::isAvailable() && rstudioapi::versionInfo()$version >= 1.4) {
+  if (rstudioapi::isAvailable() && rstudioapi::versionInfo()$version >= "1.4") {
     # RStudio 1.4
     base <-
       switch(get_os_type(),

diff --git a/R/programs.R b/R/programs.R
@@ -41,7 +41,7 @@ check_user_info <- function() {
 #' @param skip_online_check (logical) If `TRUE`, the numbers of newest available
 #'       stable programs are downloaded, when internet connection is connected.
 #' @param type (character) Which programs should be checked? Options:
-#'        `main`, `all`, `gmc-bs`, `gmc-r`.
+#'        `main`, `all`, `dev`, `gmc-bs`, `gmc-r`.
 #'
 #' @return
 #' Invisible `NULL`.
@@ -64,7 +64,7 @@ check_installed_programs <- function(type = "main", skip_online_check = FALSE) {
 
   type_lwr <- tolower(type)
 
-  if (!type_lwr %in% c("main", "all", "gmc-bs", "gmc-r")) {
+  if (!type_lwr %in% c("main", "dev", "all", "gmc-bs", "gmc-r")) {
     ui_warn("Unknown value of type = '{type}'")
   }
 
@@ -92,17 +92,17 @@ check_installed_programs <- function(type = "main", skip_online_check = FALSE) {
       "R Build Tools"
     }
 
-  check_tool_installed(
-    tool_name,
-    if (rstudioapi::isAvailable()) {
-      # Requires RStudio to be running
-      rstudioapi::buildToolsCheck()
-    } else {
-      pkgbuild::has_build_tools()
-    }
-  )
-
-
+  if (type_lwr %in% c("all", "dev")) {
+    check_tool_installed(
+      tool_name,
+      if (rstudioapi::isAvailable()) {
+        # Requires RStudio to be running
+        rstudioapi::buildToolsCheck()
+      } else {
+        pkgbuild::has_build_tools()
+      }
+    )
+  }
 
   # XQuartz (on Mac)
   if (type_lwr %in% c("all", "gmc-bs")) {
@@ -177,14 +177,11 @@ get_available_r_version <- function(force = FALSE, skip = FALSE) {
       purrr::reduce(c) %>%
       stringr::str_extract("(?<=R-).\\d*[.].\\d*[.]\\d*(?=.tar.gz)") %>%
       .[!is.na(.)] %>%
-      numeric_version() %>%
+      as.numeric_version() %>%
       max()
 
   } else {
-    ui_warn(paste(
-      "To get the newest availableR version, network connection is required.",
-      "You are offline. "
-    ))
+    msg_offline(get_what = "R version")
     NULL
   }
 }
@@ -202,28 +199,30 @@ get_available_rs_version <- function(force = FALSE, skip = FALSE) {
       readr::read_lines() %>%
       stringr::str_extract("(?<=RStudio-).*?(?=.exe)") %>%
       .[!is.na(.)] %>%
-      numeric_version() %>%
+      as.numeric_version() %>%
       max()
 
   } else {
-    ui_warn(paste(
-      "To get the newest available RStudio version,",
-      "network connection is required. You are offline. "
-    ))
+    msg_offline(get_what = "RStudio version")
   }
 }
 
 
 # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-check_internet_connection <- function() {
+msg_offline <- function(get_what = "versions") {
+  cli::cli_warn(c(
+    "To get the newest available {get_what}, network connection is required.",
+    "x" = "This computer is offline. "
+  ))
+}
+
+# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+check_internet_connection <- function(get_what = "versions") {
   if (pingr::is_online()) {
     FALSE # Online
 
   } else {
-    ui_warn(paste0(
-      "To get the newest available versions, network connection is required. ",
-      "You are offline. "
-    ))
+    msg_offline(get_what = get_what)
     TRUE # Offline
   }
 }
@@ -238,8 +237,8 @@ check_program_version  <- function(name = "", v_installed = NULL,
   r_color   <- red
   install_status <- ""
 
-  v_recommended <- numeric_version(v_recommended)
-  v_installed   <- numeric_version(v_installed)
+  v_recommended <- as.numeric_version(v_recommended)
+  v_installed   <- as.numeric_version(v_installed)
 
   if (!is.null(v_available)) {
 

diff --git a/README.Rmd b/README.Rmd
@@ -39,8 +39,8 @@ Convenience functions to facilitate installation and management of required reso
 <center>
 <br>
 <font color="darkred" size=4>
-This package is intended to be used with <b>RStudio 2022.06.0</b> or newer<br>
-and <b>R 4.3.1</b> or newer.<br>
+This package is intended to be used with <b>RStudio 2024.04</b> or newer<br>
+and <b>R 4.4.0</b> or newer.<br>
 </font>
 <font color="darkred" size=3>
 Functions may not work correctly with the previous versions of RStudio and R.

diff --git a/inst/install-r/pkgs-required-version.txt b/inst/install-r/pkgs-required-version.txt
@@ -1,6 +1,6 @@
 ---
 title: "Minimal required versions of packages"
-date:  2024-05-27
+date:  2024-07-31
 notes: ""
 
 
@@ -13,7 +13,7 @@ addin.tools                 | 0.0.10           | FALSE  | -
 addins.rmd                  | 0.0.14           | FALSE  | -
 addins.rs                   | 0.0.12           | FALSE  | -
 backup.tools                | 0.0.3            | FALSE  | -
-bio                         | 0.2.5            | FALSE  | -
+bio                         | 0.2.6            | FALSE  | -
 BiocManager                 | 1.30.20          | FALSE  | -
 blogdown                    | 1.9              | FALSE  | -
 bookdown                    | 0.32             | FALSE  | -

diff --git a/inst/install-r/programs-required-version.txt b/inst/install-r/programs-required-version.txt
@@ -1,6 +1,6 @@
 ---
 title: "Minimal required versions of programs"
-date:  2024-05-27
+date:  2024-07-31
 notes: ""
 
 
@@ -9,8 +9,8 @@ notes: ""
 ---
 # This text must be in line 10 -----------------------------------------------
 program                     | required_version | ignore | notes_version
-R                           | 4.3.3            | FALSE  |
-RStudio                     | 2023.12.1        | FALSE  | For 32-bit systems v 1.1.463
-Quarto                      | 1.4.554          | FALSE  |
+R                           | 4.4.0            | FALSE  |
+RStudio                     | 2024.04          | FALSE  | For 32-bit systems v 1.1.463
+Quarto                      | 1.5.55           | FALSE  |
 
 
diff --git a/inst/rs-settings/keybindings--addins.json b/inst/rs-settings/keybindings--addins.json
@@ -1,6 +1,5 @@
 {
-    "addins.rmd::rmd_code_block_python"            : "Ctrl+R",
-    "addins.rmd::rmd_code_block_r"                 : "Ctrl+E",
+    "addins.rmd::rmd_code_block_r"                 : "Ctrl+R",
     "addins.rmd::rmd_code_inline_highlighted_as_r" : "Ctrl+Shift+Alt+T",
     "addins.rmd::rmd_equation_a_inline"            : "Shift+Alt+S",
     "addins.rmd::rmd_format_bold"                  : "Ctrl+Alt+B",

diff --git a/inst/rs-settings/rstudio-prefs--bio-default.json b/inst/rs-settings/rstudio-prefs--bio-default.json
@@ -105,7 +105,7 @@
     "memory_query_interval_seconds"                : 10,
     "native_file_dialogs"                          : true,
     "navigate_to_build_error"                      : true,
-    "new_proj_git_init"                            : true,
+    "new_proj_git_init"                            : false,
     "new_proj_use_renv"                            : false,
     "num_spaces_for_tab"                           : 2,
     "packages_pane_enabled"                        : true,
@@ -116,7 +116,7 @@
     "publish_ca_bundle"                            : "",
     "publish_check_certificates"                   : true,
     "python_project_environment_automatic_activate": true,
-    "rainbow_fenced_divs"                          : true,
+    "rainbow_fenced_divs"                          : false,
     "rainbow_parentheses"                          : true,
     "real_time_spellchecking"                      : true,
     "reduced_motion"                               : false,
@@ -167,7 +167,7 @@
     "show_rmd_render_command"                      : false,
     "show_terminal_tab"                            : true,
     "show_user_home_page"                          : "sessions",
-    "soft_wrap_r_files"                            : true,
+    "soft_wrap_r_files"                            : false,
     "soft_wrap_rmd_files"                          : true,
     "sort_file_names_naturally"                    : true,
     "source_with_echo"                             : true,
@@ -198,7 +198,6 @@
     "ui_language"                                  : "en",
     "use_dataimport"                               : true,
     "use_devtools"                                 : true,
-    "use_internet2"                                : true,
     "use_newlines_in_makefiles"                    : true,
     "use_publish_ca_bundle"                        : false,
     "use_roxygen"                                  : false,
@@ -215,7 +214,7 @@
     "visual_markdown_editing_font_size_points"     : 0,
     "visual_markdown_editing_is_default"           : false,
     "visual_markdown_editing_list_spacing"         : "tight",
-    "visual_markdown_editing_max_content_width"    : 700,
+    "visual_markdown_editing_max_content_width"    : 1000,
     "visual_markdown_editing_references_location"  : "section",
     "visual_markdown_editing_show_doc_outline"     : true,
     "visual_markdown_editing_show_margin"          : true,

diff --git a/man/check_installed_programs.Rd b/man/check_installed_programs.Rd