diff --git a/.devcontainer/postCreateCommand.sh b/.devcontainer/postCreateCommand.sh index cee955a..0efb81b 100644 --- a/.devcontainer/postCreateCommand.sh +++ b/.devcontainer/postCreateCommand.sh @@ -9,18 +9,18 @@ if [ -f "python/requirements.txt" ]; then fi # Install R dependencies -if [ -f "R/install_packages.R" ]; then - Rscript R/install_packages.R +if [ -f "r/install_packages.R" ]; then + Rscript r/install_packages.R fi # This may be done by the user # Set up renv for R -#if [ -f "R/renv.lock" ]; then -# cd R && R -e 'renv::restore()' +#if [ -f "r/renv.lock" ]; then +# cd r && R -e 'renv::restore()' #fi # change the default working directory for RStudio -echo "session-default-working-dir=$CODESPACE_VSCODE_FOLDER" >> /etc/rstudio/rsession.conf +echo "session-default-working-dir=${CODESPACE_VSCODE_FOLDER}" >> /etc/rstudio/rsession.conf rstudio-server start && jupyter lab --ip=0.0.0.0 --no-browser --allow-root --NotebookApp.token='' diff --git a/Dockerfile b/Dockerfile index 857181a..a25c3e7 100644 --- a/Dockerfile +++ b/Dockerfile @@ -16,8 +16,15 @@ RUN apt-get update && apt-get install -y \ libxml2-dev \ libjpeg-dev \ libpng-dev \ + libtiff5-dev \ + libproj-dev \ + libgdal-dev \ libxt-dev \ libarchive-dev \ + libfontconfig1-dev \ + libharfbuzz-dev \ + libfribidi-dev \ + libfreetype6-dev \ gdebi-core \ software-properties-common \ ffmpeg \ @@ -44,6 +51,10 @@ ENV PATH="/opt/venv/bin:$PATH" # Create an IPython kernel for the virtual environment RUN /opt/venv/bin/python -m ipykernel install --user --name=venv --display-name "Python 3.12 (venv)" +# Install latest Quarto +RUN wget https://github.com/quarto-dev/quarto-cli/releases/download/v1.5.57/quarto-1.5.57-linux-amd64.deb +RUN dpkg -i quarto-1.5.57-linux-amd64.deb + # Expose ports for RStudio (8787) and Jupyter (8888) #WORKDIR /workspaces @@ -54,5 +65,12 @@ EXPOSE 8888 # Install renv globally for all users RUN R -e "install.packages('renv', repos='https://cran.rstudio.com/')" +# Add /usr/local/bin to the PATH for all users +ENV PATH="/usr/local/bin:$PATH" + +# Ensure the rstudio user's profile contains the updated PATH +RUN echo 'export PATH="/usr/local/bin:$PATH"' >> /home/rstudio/.bashrc +RUN usermod -aG sudo rstudio + # CMD to start both Jupyter and RStudio #CMD ["bash", "-c", "rstudio-server start; jupyter lab --ip=0.0.0.0 --no-browser --allow-root --NotebookApp.token=''"] diff --git a/r/install_packages.R b/r/install_packages.R index 1741e78..29f9149 100644 --- a/r/install_packages.R +++ b/r/install_packages.R @@ -8,7 +8,7 @@ if (.Platform$OS.type == "unix") { pkgnames <- c( -'devtools', 'DT', +'devtools', 'DT', 'languageserver', 'styler', 'httpgd', 'shiny', 'shinyjs', 'shinyalert', 'shinyWidgets', 'shinythemes', 'shinycssloaders', 'shinyBS', 'shinylive', 'dplyr','ggplot2', 'plotly', 'tidyr', 'stringr', 'logr', 'tidyverse', 'knitr', 'rmarkdown' diff --git a/r/shinylive_demo/renv.lock b/r/shinylive_demo/renv.lock index cf98a03..9fb8fd8 100644 --- a/r/shinylive_demo/renv.lock +++ b/r/shinylive_demo/renv.lock @@ -9,6 +9,49 @@ ] }, "Packages": { + "KernSmooth": { + "Package": "KernSmooth", + "Version": "2.23-24", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "stats" + ], + "Hash": "9f33a1ee37bbe8919eb2ec4b9f2473a5" + }, + "MASS": { + "Package": "MASS", + "Version": "7.3-60.2", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "grDevices", + "graphics", + "methods", + "stats", + "utils" + ], + "Hash": "2f342c46163b0b54d7b64d1f798e2c78" + }, + "Matrix": { + "Package": "Matrix", + "Version": "1.7-0", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "grDevices", + "graphics", + "grid", + "lattice", + "methods", + "stats", + "utils" + ], + "Hash": "1920b2f11133b12350024297d8a4ff4a" + }, "R6": { "Package": "R6", "Version": "2.5.1", @@ -19,6 +62,51 @@ ], "Hash": "470851b6d5d0ac559e9d01bb352b4021" }, + "RColorBrewer": { + "Package": "RColorBrewer", + "Version": "1.1-3", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R" + ], + "Hash": "45f0398006e83a5b10b72a90663d8d8c" + }, + "Rcpp": { + "Package": "Rcpp", + "Version": "1.0.13", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "methods", + "utils" + ], + "Hash": "f27411eb6d9c3dada5edd444b8416675" + }, + "archive": { + "Package": "archive", + "Version": "1.1.9", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "cli", + "glue", + "rlang", + "tibble" + ], + "Hash": "d26b62e131d4a8b65aba4e9554a4bf74" + }, + "askpass": { + "Package": "askpass", + "Version": "1.2.0", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "sys" + ], + "Hash": "cad6cf7f1d5f6e906700b9d3e718c796" + }, "base64enc": { "Package": "base64enc", "Version": "0.1-3", @@ -29,6 +117,28 @@ ], "Hash": "543776ae6848fde2f48ff3816d0628bc" }, + "boot": { + "Package": "boot", + "Version": "1.3-30", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "graphics", + "stats" + ], + "Hash": "96abeed416a286d4a0f52e550b612343" + }, + "brio": { + "Package": "brio", + "Version": "1.1.5", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R" + ], + "Hash": "c1ee497a6d999947c2c224ae46799b1a" + }, "bslib": { "Package": "bslib", "Version": "0.8.0", @@ -62,6 +172,32 @@ ], "Hash": "cd9a672193789068eb5a2aad65a0dedf" }, + "callr": { + "Package": "callr", + "Version": "3.7.6", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "R6", + "processx", + "utils" + ], + "Hash": "d7e13f49c19103ece9e58ad2d83a7354" + }, + "class": { + "Package": "class", + "Version": "7.3-22", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "MASS", + "R", + "stats", + "utils" + ], + "Hash": "f91f6b29f38b8c280f2b9477787d4bb2" + }, "cli": { "Package": "cli", "Version": "3.6.3", @@ -73,6 +209,99 @@ ], "Hash": "b21916dd77a27642b447374a5d30ecf3" }, + "cluster": { + "Package": "cluster", + "Version": "2.1.6", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "grDevices", + "graphics", + "stats", + "utils" + ], + "Hash": "0aaa05204035dc43ea0004b9c76611dd" + }, + "codetools": { + "Package": "codetools", + "Version": "0.2-20", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R" + ], + "Hash": "61e097f35917d342622f21cdc79c256e" + }, + "colorspace": { + "Package": "colorspace", + "Version": "2.1-1", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "grDevices", + "graphics", + "methods", + "stats" + ], + "Hash": "d954cb1c57e8d8b756165d7ba18aa55a" + }, + "commonmark": { + "Package": "commonmark", + "Version": "1.9.1", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "5d8225445acb167abf7797de48b2ee3c" + }, + "crayon": { + "Package": "crayon", + "Version": "1.5.3", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "grDevices", + "methods", + "utils" + ], + "Hash": "859d96e65ef198fd43e82b9628d593ef" + }, + "crosstalk": { + "Package": "crosstalk", + "Version": "1.2.1", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R6", + "htmltools", + "jsonlite", + "lazyeval" + ], + "Hash": "ab12c7b080a57475248a30f4db6298c0" + }, + "curl": { + "Package": "curl", + "Version": "5.2.3", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R" + ], + "Hash": "d91263322a58af798f6cf3b13fd56dde" + }, + "desc": { + "Package": "desc", + "Version": "1.4.3", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "R6", + "cli", + "utils" + ], + "Hash": "99b79fcbd6c4d1ce087f5c5c758b384f" + }, "digest": { "Package": "digest", "Version": "0.6.37", @@ -84,6 +313,29 @@ ], "Hash": "33698c4b3127fc9f506654607fb73676" }, + "dplyr": { + "Package": "dplyr", + "Version": "1.1.4", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "R6", + "cli", + "generics", + "glue", + "lifecycle", + "magrittr", + "methods", + "pillar", + "rlang", + "tibble", + "tidyselect", + "utils", + "vctrs" + ], + "Hash": "fedd9d00c2944ff00a0e2696ccf048ec" + }, "evaluate": { "Package": "evaluate", "Version": "1.0.0", @@ -94,6 +346,25 @@ ], "Hash": "6b567375113ceb7d9f800de4dd42218e" }, + "fansi": { + "Package": "fansi", + "Version": "1.0.6", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "grDevices", + "utils" + ], + "Hash": "962174cf2aeb5b9eea581522286a911f" + }, + "farver": { + "Package": "farver", + "Version": "2.1.2", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "680887028577f3fa2a81e410ed0d6e42" + }, "fastmap": { "Package": "fastmap", "Version": "1.2.0", @@ -101,6 +372,16 @@ "Repository": "CRAN", "Hash": "aa5e1cd11c2d15497494c5292d7ffcc8" }, + "filelock": { + "Package": "filelock", + "Version": "1.0.3", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R" + ], + "Hash": "192053c276525c8495ccfd523aa8f2d1" + }, "fontawesome": { "Package": "fontawesome", "Version": "0.5.2", @@ -113,6 +394,19 @@ ], "Hash": "c2efdd5f0bcd1ea861c2d4e2a883a67d" }, + "foreign": { + "Package": "foreign", + "Version": "0.8-86", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "methods", + "stats", + "utils" + ], + "Hash": "550170303dbb19d07b2bcc288068e7dc" + }, "fs": { "Package": "fs", "Version": "1.6.4", @@ -124,6 +418,70 @@ ], "Hash": "15aeb8c27f5ea5161f9f6a641fafd93a" }, + "generics": { + "Package": "generics", + "Version": "0.1.3", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "methods" + ], + "Hash": "15e9634c0fcd294799e9b2e929ed1b86" + }, + "ggplot2": { + "Package": "ggplot2", + "Version": "3.5.1", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "MASS", + "R", + "cli", + "glue", + "grDevices", + "grid", + "gtable", + "isoband", + "lifecycle", + "mgcv", + "rlang", + "scales", + "stats", + "tibble", + "vctrs", + "withr" + ], + "Hash": "44c6a2f8202d5b7e878ea274b1092426" + }, + "gh": { + "Package": "gh", + "Version": "1.4.1", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "cli", + "gitcreds", + "glue", + "httr2", + "ini", + "jsonlite", + "lifecycle", + "rlang" + ], + "Hash": "fbbbc48eba7a6626a08bb365e44b563b" + }, + "gitcreds": { + "Package": "gitcreds", + "Version": "0.1.2", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R" + ], + "Hash": "ab08ac61f3e1be454ae21911eb8bc2fe" + }, "glue": { "Package": "glue", "Version": "1.7.0", @@ -135,6 +493,21 @@ ], "Hash": "e0b3a53876554bd45879e596cdb10a52" }, + "gtable": { + "Package": "gtable", + "Version": "0.3.5", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "cli", + "glue", + "grid", + "lifecycle", + "rlang" + ], + "Hash": "e18861963cbc65a27736e02b3cd3c4a0" + }, "highr": { "Package": "highr", "Version": "0.11", @@ -146,6 +519,20 @@ ], "Hash": "d65ba49117ca223614f71b60d85b8ab7" }, + "hms": { + "Package": "hms", + "Version": "1.1.3", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "lifecycle", + "methods", + "pkgconfig", + "rlang", + "vctrs" + ], + "Hash": "b59377caa7ed00fa41808342002138f9" + }, "htmltools": { "Package": "htmltools", "Version": "0.5.8.1", @@ -162,29 +549,98 @@ ], "Hash": "81d371a9cc60640e74e4ab6ac46dcedc" }, - "jquerylib": { - "Package": "jquerylib", - "Version": "0.1.4", + "htmlwidgets": { + "Package": "htmlwidgets", + "Version": "1.6.4", "Source": "Repository", "Repository": "CRAN", "Requirements": [ - "htmltools" + "grDevices", + "htmltools", + "jsonlite", + "knitr", + "rmarkdown", + "yaml" ], - "Hash": "5aab57a3bd297eee1c1d862735972182" + "Hash": "04291cc45198225444a397606810ac37" }, - "jsonlite": { - "Package": "jsonlite", - "Version": "1.8.9", + "httpuv": { + "Package": "httpuv", + "Version": "1.6.15", "Source": "Repository", "Repository": "CRAN", "Requirements": [ - "methods" + "R", + "R6", + "Rcpp", + "later", + "promises", + "utils" ], - "Hash": "4e993b65c2c3ffbffce7bb3e2c6f832b" + "Hash": "d55aa087c47a63ead0f6fc10f8fa1ee0" }, - "knitr": { - "Package": "knitr", - "Version": "1.48", + "httr2": { + "Package": "httr2", + "Version": "1.0.4", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "R6", + "cli", + "curl", + "glue", + "lifecycle", + "magrittr", + "openssl", + "rappdirs", + "rlang", + "vctrs", + "withr" + ], + "Hash": "836e9564fbeca3bb390bb429a53cd401" + }, + "ini": { + "Package": "ini", + "Version": "0.3.1", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "6154ec2223172bce8162d4153cda21f7" + }, + "isoband": { + "Package": "isoband", + "Version": "0.2.7", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "grid", + "utils" + ], + "Hash": "0080607b4a1a7b28979aecef976d8bc2" + }, + "jquerylib": { + "Package": "jquerylib", + "Version": "0.1.4", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "htmltools" + ], + "Hash": "5aab57a3bd297eee1c1d862735972182" + }, + "jsonlite": { + "Package": "jsonlite", + "Version": "1.8.9", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "methods" + ], + "Hash": "4e993b65c2c3ffbffce7bb3e2c6f832b" + }, + "knitr": { + "Package": "knitr", + "Version": "1.48", "Source": "Repository", "Repository": "CRAN", "Requirements": [ @@ -198,6 +654,104 @@ ], "Hash": "acf380f300c721da9fde7df115a5f86f" }, + "labeling": { + "Package": "labeling", + "Version": "0.4.3", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "graphics", + "stats" + ], + "Hash": "b64ec208ac5bc1852b285f665d6368b3" + }, + "later": { + "Package": "later", + "Version": "1.3.2", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "Rcpp", + "rlang" + ], + "Hash": "a3e051d405326b8b0012377434c62b37" + }, + "lattice": { + "Package": "lattice", + "Version": "0.22-6", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "grDevices", + "graphics", + "grid", + "stats", + "utils" + ], + "Hash": "cc5ac1ba4c238c7ca9fa6a87ca11a7e2" + }, + "lazyeval": { + "Package": "lazyeval", + "Version": "0.2.2", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R" + ], + "Hash": "d908914ae53b04d4c0c0fd72ecc35370" + }, + "leaflet": { + "Package": "leaflet", + "Version": "2.2.2", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "RColorBrewer", + "crosstalk", + "htmltools", + "htmlwidgets", + "jquerylib", + "leaflet.providers", + "magrittr", + "methods", + "png", + "raster", + "scales", + "sp", + "stats", + "viridisLite", + "xfun" + ], + "Hash": "ca012d4a706e21ce217ba15f22d402b2" + }, + "leaflet.extras": { + "Package": "leaflet.extras", + "Version": "2.0.1", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "htmltools", + "htmlwidgets", + "leaflet", + "magrittr", + "stringr" + ], + "Hash": "1626fb22ec9e788f66c1d08fd863da4c" + }, + "leaflet.providers": { + "Package": "leaflet.providers", + "Version": "2.0.0", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "htmltools" + ], + "Hash": "c0b81ad9d5d932772f7a457ac398cf36" + }, "lifecycle": { "Package": "lifecycle", "Version": "1.0.4", @@ -211,6 +765,23 @@ ], "Hash": "b8552d117e1b808b09a832f589b79035" }, + "lpSolve": { + "Package": "lpSolve", + "Version": "5.6.21", + "Source": "Repository", + "Repository": "CRAN", + "Hash": "730a90bdc519fb0caff03df11218ddd8" + }, + "magrittr": { + "Package": "magrittr", + "Version": "2.0.3", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R" + ], + "Hash": "7ce2733a9826b3aeb1775d56fd305472" + }, "memoise": { "Package": "memoise", "Version": "2.0.1", @@ -222,6 +793,23 @@ ], "Hash": "e2817ccf4a065c5d9d7f2cfbe7c1d78c" }, + "mgcv": { + "Package": "mgcv", + "Version": "1.9-1", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "Matrix", + "R", + "graphics", + "methods", + "nlme", + "splines", + "stats", + "utils" + ], + "Hash": "110ee9d83b496279960e162ac97764ce" + }, "mime": { "Package": "mime", "Version": "0.12", @@ -232,6 +820,213 @@ ], "Hash": "18e9c28c1d3ca1560ce30658b22ce104" }, + "munsell": { + "Package": "munsell", + "Version": "0.5.1", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "colorspace", + "methods" + ], + "Hash": "4fd8900853b746af55b81fda99da7695" + }, + "nlme": { + "Package": "nlme", + "Version": "3.1-164", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "graphics", + "lattice", + "stats", + "utils" + ], + "Hash": "a623a2239e642806158bc4dc3f51565d" + }, + "nnet": { + "Package": "nnet", + "Version": "7.3-19", + "Source": "Repository", + "Repository": "CRAN", + "Requirements": [ + "R", + "stats", + "utils" + ], + "Hash": "2c797b46eea7fb58ede195bc0b1f1138" + }, + "openssl": { + "Package": "openssl", + "Version": "2.2.2", + "Source": "Repository", + "Repository": "CRAN", 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