diff --git a/docker/Dockerfile-alpine-320 b/docker/Dockerfile-alpine-320 index 0882bb8..baabc06 100644 --- a/docker/Dockerfile-alpine-320 +++ b/docker/Dockerfile-alpine-320 @@ -16,7 +16,7 @@ ARG GITHUB_PAT # Background: JAGS needs lapack & lapack-dev but these conflict with openblas-dev which is required by R-dev # Solution: first compile JAGS, then remove lapack & lapack-dev again # # xvfb: for graphical pkgs requiring tcl, like gWidgets2tcltk -RUN apk add -q --no-cache curl tar make lapack lapack-dev blas blas-dev gcc gfortran g++ htop git cmake tk-dev xvfb xvfb-run +RUN apk add -q --no-cache curl tar make lapack lapack-dev blas blas-dev gcc gfortran g++ htop git cmake tk-dev xvfb xvfb-run xz ### CUSTOM DEPENDENCIES # These usually are not packaged in OS repositories and need to be installed from source @@ -50,7 +50,7 @@ RUN R -q -e 'install.packages("remotes", repo = "cloud.r-project.org"); remotes: # deps from pak::pkg_deps(".")$package RUN R -q -e 'pak::pak(c("DBI", "R6", "RPostgres", "Rcpp", "askpass", "base64enc", "bit64", "bit", "blob", "callr", "cli", "credentials", "curl", "data.table", "desc", "digest", "dplyr", "fansi", "fs", "future.apply", "future", "generics", "gert", "globals", "glue", "hms", "httr", "jsonlite", "lgr", "lifecycle", "listenv", "lubridate", "magrittr", "mime", "openssl", "parallelly", "paws.common", "paws.storage", "pillar", "pkgbuild", "pkgconfig", "processx", "progressr", "ps", "purrr", "rlang", "rstudioapi", "s3fs", "stringi", "stringr", "sys", "tibble", "tidyselect", "timechange", "utf8", "vctrs", "withr", "xml2", "zip", "codetools", "cranlike", "RSQLite", "cachem", "crayon", "debugme", "fastmap", "memoise", "progress"))' -COPY . . +COPY --link . . # remove secrets from COPY RUN touch /.Renviron /.envrc && rm /.Renviron /.envrc RUN R CMD INSTALL . && rm -rf r-pkg-binaries diff --git a/docker/Dockerfile-redhat-8 b/docker/Dockerfile-redhat-8 index 8808568..15e83bd 100644 --- a/docker/Dockerfile-redhat-8 +++ b/docker/Dockerfile-redhat-8 @@ -18,7 +18,7 @@ RUN subscription-manager register --username mail@devxy.io --password "$RED_HAT_ RUN dnf install -y https://dl.fedoraproject.org/pub/epel/epel-release-latest-8.noarch.rpm && dnf install -y epel-release # xvfb: for graphical pkgs requiring tcl, like gWidgets2tcltk # ImageMagick-c++-devel ImageMagick-devel: boths are not auto-installed via pak sysreqs -RUN dnf install -y -q make lapack-devel git gcc gcc-c++ fontconfig-devel fribidi-devel libjpeg-turbo-devel libtiff-devel postgresql-devel htop libgit2-devel libxml2-devel hiredis ccache cmake xorg-x11-server-Xvfb ImageMagick-c++-devel ImageMagick-devel +RUN dnf install -y -q make lapack-devel git gcc gcc-c++ fontconfig-devel fribidi-devel libjpeg-turbo-devel libtiff-devel postgresql-devel htop libgit2-devel libxml2-devel hiredis ccache cmake xorg-x11-server-Xvfb ImageMagick-c++-devel ImageMagick-devel xz ### CUSTOM DEPENDENCIES # These usually are not packaged in OS repositories and need to be installed from source @@ -41,7 +41,7 @@ RUN bash -c 'echo -e "PKG_SYSREQS = TRUE\nPKG_SYSREQS_VERBOSE = TRUE" > /root/.R # deps from pak::pkg_deps(".")$package RUN R -q -e 'Sys.setenv("PKG_SYSREQS_PLATFORM" = "redhat-8"); pak::pak(c("DBI", "R6", "RPostgres", "Rcpp", "askpass", "base64enc", "bit64", "bit", "blob", "callr", "cli", "credentials", "curl", "data.table", "desc", "digest", "dplyr", "fansi", "fs", "future.apply", "future", "generics", "gert", "globals", "glue", "hms", "httr", "jsonlite", "lgr", "lifecycle", "listenv", "lubridate", "magrittr", "mime", "openssl", "parallelly", "paws.common", "paws.storage", "pillar", "pkgbuild", "pkgconfig", "processx", "progressr", "ps", "purrr", "rlang", "rstudioapi", "s3fs", "stringi", "stringr", "sys", "tibble", "tidyselect", "timechange", "utf8", "vctrs", "withr", "xml2", "zip", "codetools", "cranlike", "RSQLite", "cachem", "crayon", "debugme", "fastmap", "memoise", "progress"))' -COPY . . +COPY --link . . # remove secrets from COPY RUN touch /.Renviron /.envrc && rm /.Renviron /.envrc RUN R CMD INSTALL . && rm -rf r-pkg-binaries diff --git a/docker/Dockerfile-redhat-9 b/docker/Dockerfile-redhat-9 index fc0f400..e4012c2 100644 --- a/docker/Dockerfile-redhat-9 +++ b/docker/Dockerfile-redhat-9 @@ -18,7 +18,7 @@ RUN subscription-manager register --username mail@devxy.io --password "$RED_HAT_ RUN dnf install -y https://dl.fedoraproject.org/pub/epel/epel-release-latest-9.noarch.rpm && dnf install -y epel-release # xvfb: for graphical pkgs requiring tcl, like gWidgets2tcltk # ImageMagick-c++-devel ImageMagick-devel: boths are not auto-installed via pak sysreqs -RUN dnf install -y -q make lapack-devel git gcc gcc-c++ fontconfig-devel fribidi-devel libjpeg-turbo-devel libtiff-devel postgresql-devel htop libgit2-devel libxml2-devel hiredis ccache cmake xorg-x11-server-Xvfb tk-devel ImageMagick-c++-devel ImageMagick-devel +RUN dnf install -y -q make lapack-devel git gcc gcc-c++ fontconfig-devel fribidi-devel libjpeg-turbo-devel libtiff-devel postgresql-devel htop libgit2-devel libxml2-devel hiredis ccache cmake xorg-x11-server-Xvfb tk-devel ImageMagick-c++-devel ImageMagick-devel xz ### CUSTOM DEPENDENCIES # These usually are not packaged in OS repositories and need to be installed from source @@ -38,7 +38,7 @@ RUN bash -c 'echo -e "options(crayon.enabled = TRUE, Ncpus = ${NCPUS}, future.gl RUN R -q -e 'Sys.setenv("PKG_SYSREQS_PLATFORM" = "redhat-9"); pak::pak(c("DBI", "R6", "RPostgres", "Rcpp", "askpass", "base64enc", "bit64", "bit", "blob", "callr", "cli", "credentials", "curl", "data.table", "desc", "digest", "dplyr", "fansi", "fs", "future.apply", "future", "generics", "gert", "globals", "glue", "hms", "httr", "jsonlite", "lgr", "lifecycle", "listenv", "lubridate", "magrittr", "mime", "openssl", "parallelly", "paws.common", "paws.storage", "pillar", "pkgbuild", "pkgconfig", "processx", "progressr", "ps", "purrr", "rlang", "rstudioapi", "s3fs", "stringi", "stringr", "sys", "tibble", "tidyselect", "timechange", "utf8", "vctrs", "withr", "xml2", "zip", "codetools", "cranlike", "RSQLite", "cachem", "crayon", "debugme", "fastmap", "memoise", "progress"))' -COPY . . +COPY --link . . # remove secrets from COPY RUN touch /.Renviron /.envrc && rm /.Renviron /.envrc RUN R CMD INSTALL . && rm -rf r-pkg-binaries diff --git a/docker/Dockerfile-ubuntu-2204 b/docker/Dockerfile-ubuntu-2204 index 2d6d17f..1500c32 100644 --- a/docker/Dockerfile-ubuntu-2204 +++ b/docker/Dockerfile-ubuntu-2204 @@ -15,7 +15,7 @@ ENV PGPASS="" ARG GITHUB_PAT # xvfb: for graphical pkgs requiring tcl, like gWidgets2tcltk -RUN apt update && apt install -y --no-install-recommends gdebi-core g++ gfortran libbz2-dev libblas-dev libicu-dev liblapack-dev liblzma-dev libpaper-utils libpcre2-dev libtcl8.6 libtk8.6 libxt6 unzip zip zlib1g-dev libpcre3-dev libopenblas-dev curl ca-certificates make ccache htop libgit2-dev git libpq-dev libxml2-dev libgit2-dev cmake xvfb libcurl4-openssl-dev +RUN apt update && apt install -y --no-install-recommends gdebi-core g++ gfortran libbz2-dev libblas-dev libicu-dev liblapack-dev liblzma-dev libpaper-utils libpcre2-dev libtcl8.6 libtk8.6 libxt6 unzip zip zlib1g-dev libpcre3-dev libopenblas-dev curl ca-certificates make ccache htop libgit2-dev git libpq-dev libxml2-dev libgit2-dev cmake xvfb libcurl4-openssl-dev xz-utils ### CUSTOM DEPENDENCIES # These usually are not packaged in OS repositories and need to be installed from source @@ -35,7 +35,7 @@ RUN bash -c 'echo -e "options(pkg.sysreqs_verbose = TRUE, crayon.enabled = TRUE, RUN R -q -e 'pak::pak(c("DBI", "R6", "RPostgres", "Rcpp", "askpass", "base64enc", "bit64", "bit", "blob", "callr", "cli", "credentials", "curl", "data.table", "desc", "digest", "dplyr", "fansi", "fs", "future.apply", "future", "generics", "gert", "globals", "glue", "hms", "httr", "jsonlite", "lgr", "lifecycle", "listenv", "lubridate", "magrittr", "mime", "openssl", "parallelly", "paws.common", "paws.storage", "pillar", "pkgbuild", "pkgconfig", "processx", "progressr", "ps", "purrr", "rlang", "rstudioapi", "s3fs", "stringi", "stringr", "sys", "tibble", "tidyselect", "timechange", "utf8", "vctrs", "withr", "xml2", "zip", "codetools", "cranlike", "RSQLite", "cachem", "crayon", "debugme", "fastmap", "memoise", "progress"))' -COPY . . +COPY --link . . # remove secrets from COPY RUN touch /.Renviron /.envrc && rm /.Renviron /.envrc RUN R CMD INSTALL . && rm -rf r-pkg-binaries diff --git a/docker/Dockerfile-ubuntu-2404 b/docker/Dockerfile-ubuntu-2404 index 983f35d..cb53857 100644 --- a/docker/Dockerfile-ubuntu-2404 +++ b/docker/Dockerfile-ubuntu-2404 @@ -15,7 +15,7 @@ ENV PGPASS="" ARG GITHUB_PAT # xvfb: for graphical pkgs requiring tcl, like gWidgets2tcltk -RUN apt update && apt install -y --no-install-recommends gdebi-core g++ gfortran libbz2-dev libblas-dev libicu-dev liblapack-dev liblzma-dev libpaper-utils libpcre2-dev libtcl8.6 libtk8.6 libxt6 unzip zip zlib1g-dev libpcre3-dev libopenblas-dev curl ca-certificates make ccache htop libgit2-dev git libpq-dev libxml2-dev libgit2-dev cmake xvfb libcurl4-openssl-dev +RUN apt update && apt install -y --no-install-recommends gdebi-core g++ gfortran libbz2-dev libblas-dev libicu-dev liblapack-dev liblzma-dev libpaper-utils libpcre2-dev libtcl8.6 libtk8.6 libxt6 unzip zip zlib1g-dev libpcre3-dev libopenblas-dev curl ca-certificates make ccache htop libgit2-dev git libpq-dev libxml2-dev libgit2-dev cmake xvfb libcurl4-openssl-dev xz-utils ### CUSTOM DEPENDENCIES # These usually are not packaged in OS repositories and need to be installed from source @@ -35,7 +35,7 @@ RUN bash -c 'echo -e "options(pkg.sysreqs_verbose = TRUE, crayon.enabled = TRUE, RUN R -q -e 'pak::pak(c("DBI", "R6", "RPostgres", "Rcpp", "askpass", "base64enc", "bit64", "bit", "blob", "callr", "cli", "credentials", "curl", "data.table", "desc", "digest", "dplyr", "fansi", "fs", "future.apply", "future", "generics", "gert", "globals", "glue", "hms", "httr", "jsonlite", "lgr", "lifecycle", "listenv", "lubridate", "magrittr", "mime", "openssl", "parallelly", "paws.common", "paws.storage", "pillar", "pkgbuild", "pkgconfig", "processx", "progressr", "ps", "purrr", "rlang", "rstudioapi", "s3fs", "stringi", "stringr", "sys", "tibble", "tidyselect", "timechange", "utf8", "vctrs", "withr", "xml2", "zip", "codetools", "cranlike", "RSQLite", "cachem", "crayon", "debugme", "fastmap", "memoise", "progress"))' -COPY . . +COPY --link . . # remove secrets from COPY RUN touch /.Renviron /.envrc && rm /.Renviron /.envrc RUN R CMD INSTALL . && rm -rf r-pkg-binaries