diff --git a/.lintr b/.lintr new file mode 100644 index 0000000..a75a010 --- /dev/null +++ b/.lintr @@ -0,0 +1,4 @@ +linters: linters_with_defaults( + line_length_linter = line_length_linter(120), + object_usage_linter = NULL + ) diff --git a/Dockerfile b/Dockerfile index d0ea097..b627e43 100644 --- a/Dockerfile +++ b/Dockerfile @@ -7,8 +7,13 @@ FROM ${OS_NAME}:${OS_VERSION} ARG R_VERSION=latest ARG CRAN=https://packagemanager.posit.co/cran/__linux__/jammy/latest + +# https://github.com/jgm/pandoc/tags ARG PANDOC_VERSION=2.9.2.1 +# https://github.com/quarto-dev/quarto-cli/tags ARG QUARTO_VERSION=1.3.450 +# https://github.com/lycheeverse/lychee-action/tags +ARG LYCHEE_VERSION=0.14.3 # Set up environment ENV R_HOME=/usr/local/lib/R @@ -21,8 +26,7 @@ RUN /rocker_scripts/install_R_source.sh && \ /rocker_scripts/setup_R.sh && \ /rocker_scripts/install_pandoc.sh && \ /rocker_scripts/install_quarto.sh && \ - /rocker_scripts/install_texlive.sh && \ - /rocker_scripts/install_tidyverse.sh + /rocker_scripts/install_texlive.sh COPY scripts /scripts RUN /scripts/install_sys_deps.sh && \ diff --git a/scripts/install_r_pkgs.R b/scripts/install_r_pkgs.R index 91fb78e..5aa139b 100755 --- a/scripts/install_r_pkgs.R +++ b/scripts/install_r_pkgs.R @@ -5,8 +5,15 @@ install.packages("pak") # Packages to install install_pkgs <- c( - "shinytest2", + "boehringer-ingelheim/davinci", + "rcmdcheck", + "roxygen2", "lintr", + "pkgdown", + "rmarkdown", + "devtools", + "pharmaverseadam", + "shinytest2", "golem", "shinymeta", "shinyjs", @@ -24,3 +31,6 @@ pak::pak( ask = FALSE, upgrade = FALSE ) + +# Remove DaVinci packages from image +grep("^dv.", rownames(installed.packages()), value = TRUE) |> sapply(remove.packages) diff --git a/scripts/install_sys_deps.sh b/scripts/install_sys_deps.sh index f3e2463..fde8dd9 100755 --- a/scripts/install_sys_deps.sh +++ b/scripts/install_sys_deps.sh @@ -7,6 +7,7 @@ curl \ lbzip2 \ rsync \ qpdf \ +wget \ " apt-get update -y # shellcheck disable=SC2086 @@ -18,4 +19,4 @@ apt-get autoclean -y rm -rf /var/lib/apt/lists/* # Install lychee URL checker -curl -sL "https://github.com/lycheeverse/lychee/releases/download/v0.14.3/lychee-v0.14.3-x86_64-unknown-linux-gnu.tar.gz" | tar -xvzf - -C "/usr/local/bin" \ No newline at end of file +curl -Ls https://github.com/lycheeverse/lychee/releases/download/v"${LYCHEE_VERSION}"/lychee-v"${LYCHEE_VERSION}"-"$(arch)"-unknown-linux-gnu.tar.gz | tar xz -C /usr/local/bin