Covid19Mirai 3.1.1 (#269)

* Updated status badge
* Updated renv and workflow
* new version terra
* Update system dependencies in WF
* Sp importFrom
* remove suggested packages not required

.Rprofile

@@ -0,0 +1 @@
+source("renv/activate.R")

.github/workflows/ci-cd.yml

@@ -22,7 +22,7 @@ jobs:
       # single OS and R version, aligned with the target deployment environment
       matrix:
         config:
-          - {os: ubuntu-latest, r: '4.2.1'}
+          - {os: ubuntu-latest, r: 'renv'}
 
     env:
       # Access token for GitHub
@@ -33,31 +33,33 @@ jobs:
     steps:
 
       - name: Checkout repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Setup R
         uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
           # Enable RStudio Package Manager to speed up package installation
-          use-public-rspm: true
-
-      # - name: Install system dependencies
-      #   # This is not taken care of (yet) by r-lib/actions/setup-renv
-      #   # Package distro used to get the distro for the used ubuntu-latest
-      #   run: |
-      #     Rscript -e "install.packages(c('remotes', 'distro'))"
-      #     while read -r cmd
-      #     do
-      #       eval sudo $cmd
+          use-public-rspm: false
+
+      - name: Install system dependencies
+        # This is not taken care of (yet) by r-lib/actions/setup-renv
+        # See https://github.com/r-lib/actions/issues/785
+        run: |
+          # We rely on pkgdepends from the library embedded in pak
+          install.packages("pak", repos = "https://r-lib.github.io/p/pak/stable/")
+          install.packages("jsonlite")
+          .libPaths(c(system.file("library", package = "pak"), .libPaths()))
+          pkgdepends::new_pkg_installation_proposal(
+            names(jsonlite::read_json("renv.lock")$Packages), config = list(dependencies = FALSE)
+          )$solve()$install_sysreqs()
+        shell: Rscript {0}
       #     done < <(Rscript -e 'writeLines(with(distro::distro(), remotes::system_requirements(id, short_version)))')
 
       - name: Activate renv and restore packages with cache
         uses: r-lib/actions/setup-renv@v2
 
-      # - name: Install renv Development tools
-      #   run: renv::install()
-      #   shell: Rscript {0}
+
 
       - name: Fetch and rebuild latest data
         if: false && github.event_name == 'schedule' # switched off

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: Covid19Mirai
 Title: Covid-19 Data Analysis
-Version: 3.1.0
+Version: 3.1.1
 Authors@R: 
     c(person("Riccardo", "Porreca", role = ("aut"),
              email = "[email protected]"),
@@ -42,11 +42,9 @@ Imports:
     zoo
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Suggests: 
     rsconnect,
     spelling,
     pkgload,
-    testthat (>= 3.0.0),
-    sf,
-    packrat
+    testthat (>= 3.0.0)

NAMESPACE

@@ -73,7 +73,6 @@ import(lubridate)
 import(markdown)
 import(purrr)
 import(shiny)
-import(sp)
 import(stringr)
 import(tidyr)
 import(zoo)
@@ -119,4 +118,5 @@ importFrom(shiny,selectInput)
 importFrom(shiny,shinyApp)
 importFrom(shiny,tagList)
 importFrom(shinycssloaders,withSpinner)
+importFrom(sp,merge)
 importFrom(stringr,str_to_title)

NEWS.md

@@ -1,3 +1,6 @@
+### Covid19Mirai 3.1.1
+* Updated status badge
+
 ### Covid19Mirai 3.1.0
 - Added action Buttons (#262)
 - Added data to RDS

R/mod_map.R

@@ -72,6 +72,7 @@ mod_map_ui <- function(id){
 #' @import tidyr
 #' @import leaflet
 #' @import leaflet.extras
+#' @importFrom sp merge
 #' @noRd
 mod_map_server <- function(input, output, session, orig_data_aggregate, countries_data_map){
   ns <- session$ns

R/mod_map_calc_continent.R

@@ -37,6 +37,7 @@ mod_map_area_calc_ui <- function(id){
 #' @import tidyr
 #' @import leaflet
 #' @import leaflet.extras
+#' @importFrom sp merge
 #'
 #' @noRd
 mod_map_area_calc_server <- function(input, output, session, df, countries_data_map, area, variable = "confirmed", max.pop = 100000, countrymap = FALSE){

R/mod_map_continent.R

@@ -40,7 +40,7 @@ mod_map_cont_ui <- function(id){
 #' @import dplyr
 #' @import tidyr
 #' @import leaflet
-#' @import sp
+#' @importFrom sp merge
 #'
 #' @noRd
 mod_map_cont_server <- function(input, output, session, orig_data_aggregate, countries_data_map, area, g_palette){

README.md

@@ -5,9 +5,9 @@
 
 <!-- badges: start -->
 
-[![R build
-status](https://github.com/miraisolutions/Covid19/workflows/CI-CD/badge.svg)](https://github.com/miraisolutions/Covid19/actions)
+[![ci-cd](https://github.com/miraisolutions/Covid19/actions/workflows/ci-cd.yml/badge.svg)](https://github.com/miraisolutions/Covid19/actions/workflows/ci-cd.yml)
 [![eRum2020::CovidR](https://badgen.net/https/runkit.io/erum2020-covidr/badge/branches/master/vitalini-covid19?cache=300)](https://milano-r.github.io/erum2020-covidr-contest/vitalini-covid19.html)
+
 <!-- badges: end -->
 
 The goal of Covid19Mirai is to provide an insight on corona virus data
@@ -39,7 +39,7 @@ Ardia](https://ardiad.github.io/). We are very thankful to [David
 Bumbeishvili](https://github.com/bumbeishvili) for his great
 [work](https://github.com/bumbeishvili/covid19-daily-data)
 
-**Update October 2023**, the app stops updating data and is frozen to `2022-09-01`.
+**Update October 2023**, the app stops updating data and is frozen to `2022-06-01`.
 
 
 ## Data Storage