Force installing ggplot2 version 3.5.2 to avoid CI errors

Author: elgabbas

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

@@ -41,14 +41,6 @@ jobs:
       - name: Set up Pandoc
         uses: r-lib/actions/setup-pandoc@v2
 
-      - name: Install system dependencies for GEOS, GDAL, PROJ
-        run: |
-          sudo apt-get update
-          sudo apt-get install -y \
-          libgeos-dev \
-          libgdal-dev \
-          libproj-dev      
-
       - name: Install GEOS, GDAL, PROJ on macOS
         if: matrix.config.os == 'macos-latest'
         run: |
@@ -59,7 +51,19 @@ jobs:
         if: matrix.config.os == 'ubuntu-latest'
         run: |
           sudo apt-get update
-          sudo apt-get install -y libgeos-dev libgdal-dev libproj-dev
+          sudo apt-get install -y \
+            libgeos-dev \
+            libgdal-dev \
+            libproj-dev \
+            libudunits2-dev \
+            libxml2-dev \
+            libssl-dev \
+            libcurl4-openssl-dev \
+            libfontconfig1-dev \
+            libfreetype6-dev \
+            libpng-dev \
+            libtiff5-dev \
+            libjpeg-dev
         shell: bash
 
       - name: Install GEOS, GDAL, PROJ on Windows
@@ -79,7 +83,7 @@ jobs:
       - name: Install necessary packages
         run: |
           Rscript -e 'cat("\nlibrary path:\n");.libPaths(); sessionInfo(); cat("\n")'
-          Rscript -e 'install.packages(c("rcmdcheck", "remotes", "Rcpp", "lubridate", "RcppArmadillo", "tidyverse", "terra", "sf", "coda", "foreach", "fs", "tibble", "dplyr", "future", "future.apply", "rlang", "DT", "kableExtra", "knitr", "httr", "foreign", "tidyselect", "purrr", "rvest", "stringr", "rmarkdown",  "archive", "magrittr", "arrow", "caret", "colorRamps", "devtools", "doParallel", "ecospat", "fastmatch", "float", "furrr", "gdata", "ggbreak", "ggnewscale", "ggtext", "gridtext", "gt", "gtools", "janitor", "jsonify", "lobstr", "ncdf4", "pak", "pbapply", "png", "quarto", "R.utils", "RCurl", "Rfast", "rgbif", "RNetCDF", "scales", "rworldmap", "smoothr", "snow", "spelling", "testthat", "writexl", "pkgdown", "lintr", "sessioninfo", "cowplot", "ggpubr", "ggExtra", "zip", "tidyterra", "exactextractr", "blockCV", "renv"), Ncpus = parallel::detectCores())'
+          Rscript -e 'install.packages(c("rcmdcheck", "remotes", "Rcpp", "lubridate", "RcppArmadillo", "tidyverse", "terra", "sf", "coda", "foreach", "fs", "tibble", "dplyr", "future", "future.apply", "rlang", "DT", "kableExtra", "knitr", "httr", "foreign", "tidyselect", "purrr", "rvest", "stringr", "rmarkdown",  "archive", "magrittr", "arrow", "caret", "colorRamps", "devtools", "doParallel", "ecospat", "fastmatch", "float", "furrr", "gdata", "ggbreak", "ggnewscale", "ggtext", "gridtext", "gt", "gtools", "janitor", "jsonify", "lobstr", "ncdf4", "pak", "pbapply", "png", "quarto", "R.utils", "RCurl", "Rfast", "rgbif", "RNetCDF", "scales", "rworldmap", "smoothr", "snow", "spelling", "testthat", "writexl", "pkgdown", "lintr", "sessioninfo", "cowplot", "ggpubr", "ggExtra", "zip", "tidyterra", "exactextractr", "blockCV", "renv", "abind", "ape", "automap", "bit64", "car", "crayon", "data.table", "gridExtra", "htmltools", "jsonlite", "lme4", "parallelly", "patchwork", "pROC", "qs2", "ragg", "raster", "RColorBrewer", "rstudioapi", "sp", "stringi", "units", "withr", "xml2", "ragg", "gdtools"), Ncpus = parallel::detectCores())'
       
       - name: Install packages from github
         run: |

.github/workflows/lint.yaml

@@ -32,7 +32,16 @@ jobs:
           sudo apt-get install -y \
           libgeos-dev \
           libgdal-dev \
-          libproj-dev
+          libproj-dev \
+          libudunits2-dev \
+          libxml2-dev \
+          libssl-dev \
+          libcurl4-openssl-dev \
+          libfontconfig1-dev \
+          libfreetype6-dev \
+          libpng-dev \
+          libtiff5-dev \
+          libjpeg-dev
 
       - name: Set up Pandoc
         uses: r-lib/actions/setup-pandoc@v2
@@ -45,8 +54,8 @@ jobs:
       - name: Install necessary packages
         run: |
           Rscript -e 'cat("\nlibrary path:\n");.libPaths(); sessionInfo(); cat("\n")'
-          Rscript -e 'install.packages(c("rcmdcheck", "remotes", "Rcpp", "lubridate", "RcppArmadillo", "tidyverse", "terra", "sf", "coda", "foreach", "fs", "tibble", "dplyr", "future", "future.apply", "rlang", "DT", "kableExtra", "knitr", "httr", "foreign", "tidyselect", "purrr", "rvest", "stringr", "rmarkdown",  "archive", "magrittr", "arrow", "caret", "colorRamps", "devtools", "doParallel", "ecospat", "fastmatch", "float", "furrr", "gdata", "ggbreak", "ggnewscale", "ggtext", "gridtext", "gt", "gtools", "janitor", "jsonify", "lobstr", "ncdf4", "pak", "pbapply", "png", "quarto", "R.utils", "RCurl", "Rfast", "rgbif", "RNetCDF", "scales", "rworldmap", "smoothr", "snow", "spelling", "testthat", "writexl", "pkgdown", "lintr", "sessioninfo", "cowplot", "ggpubr", "ggExtra", "zip", "tidyterra", "exactextractr", "blockCV", "renv"), Ncpus = parallel::detectCores())'
-      
+          Rscript -e 'install.packages(c("rcmdcheck", "remotes", "Rcpp", "lubridate", "RcppArmadillo", "tidyverse", "terra", "sf", "coda", "foreach", "fs", "tibble", "dplyr", "future", "future.apply", "rlang", "DT", "kableExtra", "knitr", "httr", "foreign", "tidyselect", "purrr", "rvest", "stringr", "rmarkdown",  "archive", "magrittr", "arrow", "caret", "colorRamps", "devtools", "doParallel", "ecospat", "fastmatch", "float", "furrr", "gdata", "ggbreak", "ggnewscale", "ggtext", "gridtext", "gt", "gtools", "janitor", "jsonify", "lobstr", "ncdf4", "pak", "pbapply", "png", "quarto", "R.utils", "RCurl", "Rfast", "rgbif", "RNetCDF", "scales", "rworldmap", "smoothr", "snow", "spelling", "testthat", "writexl", "pkgdown", "lintr", "sessioninfo", "cowplot", "ggpubr", "ggExtra", "zip", "tidyterra", "exactextractr", "blockCV", "renv", "abind", "ape", "automap", "bit64", "car", "crayon", "data.table", "gridExtra", "htmltools", "jsonlite", "lme4", "parallelly", "patchwork", "pROC", "qs2", "ragg", "raster", "RColorBrewer", "rstudioapi", "sp", "stringi", "units", "withr", "xml2", "ragg", "gdtools"), Ncpus = parallel::detectCores())'
+
       - name: Install packages from github
         run: |
           Rscript -e 'remotes::install_github(c("elgabbas/ecokit", "hmsc-r/HMSC", "EmilHvitfeldt/paletteer", "YuLab-SMU/ggtree", "babaknaimi/sdm"))'

.github/workflows/pkgdown.yaml

@@ -52,7 +52,7 @@ jobs:
       - name: Install necessary packages
         run: |
           Rscript -e 'cat("\nlibrary path:\n");.libPaths(); sessionInfo(); cat("\n")'
-          Rscript -e 'install.packages(c("rcmdcheck", "remotes", "Rcpp", "lubridate", "RcppArmadillo", "tidyverse", "terra", "sf", "coda", "foreach", "fs", "tibble", "dplyr", "future", "future.apply", "rlang", "DT", "kableExtra", "knitr", "httr", "foreign", "tidyselect", "purrr", "rvest", "stringr", "rmarkdown",  "archive", "magrittr", "arrow", "caret", "colorRamps", "devtools", "doParallel", "ecospat", "fastmatch", "float", "furrr", "gdata", "ggbreak", "ggnewscale", "ggtext", "gridtext", "gt", "gtools", "janitor", "jsonify", "lobstr", "ncdf4", "pak", "pbapply", "png", "quarto", "R.utils", "RCurl", "Rfast", "rgbif", "RNetCDF", "scales", "rworldmap", "smoothr", "snow", "spelling", "testthat", "writexl", "pkgdown", "lintr", "sessioninfo", "cowplot", "ggpubr", "ggExtra", "zip", "tidyterra", "exactextractr", "blockCV", "renv"), Ncpus = parallel::detectCores())'
+          Rscript -e 'install.packages(c("rcmdcheck", "remotes", "Rcpp", "lubridate", "RcppArmadillo", "tidyverse", "terra", "sf", "coda", "foreach", "fs", "tibble", "dplyr", "future", "future.apply", "rlang", "DT", "kableExtra", "knitr", "httr", "foreign", "tidyselect", "purrr", "rvest", "stringr", "rmarkdown",  "archive", "magrittr", "arrow", "caret", "colorRamps", "devtools", "doParallel", "ecospat", "fastmatch", "float", "furrr", "gdata", "ggbreak", "ggnewscale", "ggtext", "gridtext", "gt", "gtools", "janitor", "jsonify", "lobstr", "ncdf4", "pak", "pbapply", "png", "quarto", "R.utils", "RCurl", "Rfast", "rgbif", "RNetCDF", "scales", "rworldmap", "smoothr", "snow", "spelling", "testthat", "writexl", "pkgdown", "lintr", "sessioninfo", "cowplot", "ggpubr", "ggExtra", "zip", "tidyterra", "exactextractr", "blockCV", "renv", "abind", "ape", "automap", "bit64", "car", "crayon", "data.table", "gridExtra", "htmltools", "jsonlite", "lme4", "parallelly", "patchwork", "pROC", "qs2", "ragg", "raster", "RColorBrewer", "rstudioapi", "sp", "stringi", "units", "withr", "xml2", "ragg", "gdtools"), Ncpus = parallel::detectCores())'
       
       - name: Install packages from github
         run: |