From 0dedbdf0604f706f61ccdcab0a6427c31d8bdd1f Mon Sep 17 00:00:00 2001 From: pat-s Date: Mon, 30 Sep 2024 11:31:33 +0200 Subject: [PATCH] fix x-server on alpine, install callr --- docker/Dockerfile-alpine-320 | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/docker/Dockerfile-alpine-320 b/docker/Dockerfile-alpine-320 index e6b4456..5bab53f 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 xz +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 xorg-server xauth xinit xz ### CUSTOM DEPENDENCIES # These usually are not packaged in OS repositories and need to be installed from source @@ -41,18 +41,20 @@ RUN apk add -q --no-cache chromium RUN mkdir -p /root/.R && bash -c 'echo -e "CXX_STD = CXX14\nCXXFLAGS=-D__MUSL__\nCPPFLAGS=-D__MUSL__\nCFLAGS += -flax-vector-conversions\nLDFLAGS+=-fPIC\nCC=ccache gcc\nCPP=gcc -E\nCXXCPP=gcc -e\nCXX=ccache g++\nCXX11=ccache g++\nCXX14=ccache g++\nCXX17=ccache g++\nF77=gfortran\nFC=gfortran" > /root/.R/Makevars' # R repos -RUN bash -c 'echo -e "options(crayon.enabled = TRUE, Ncpus = ${NCPUS}, future.globals.onReference = NULL, repos = structure(c(CRAN = \"https://cloud.r-project.org\", INLA = \"https://inla.r-inla-download.org/R/stable\")))" > /root/.Rprofile' +RUN bash -c 'echo -e "options(encoding = \"UTF-8\", crayon.enabled = TRUE, Ncpus = ${NCPUS}, future.globals.onReference = NULL, repos = structure(c(CRAN = \"https://cloud.r-project.org\", INLA = \"https://inla.r-inla-download.org/R/stable\")))" > /root/.Rprofile' RUN bash -c 'echo -e "PKG_SYSREQS=TRUE\nPKG_SYSREQS_VERBOSE=TRUE" > ~/.Renviron' ### INSTALL R RUN curl -O "https://devxy-r-builds.s3.eu-central-2.amazonaws.com/alpine320/r-${R_VERSION}_1_$(arch).apk" RUN apk add --allow-untrusted "r-${R_VERSION}_1_$(arch).apk" && rm "r-${R_VERSION}_1_$(arch).apk" -RUN R -q -e 'install.packages("remotes", repo = "cloud.r-project.org"); remotes::install_github("pat-s/pak@alpine")' +RUN R -q -e 'install.packages("pak", repos = sprintf("https://r-lib.github.io/p/pak/devel/%s/%s/%s", .Platform$pkgType, R.Version()$os, R.Version()$arch))' # FIXME: switch to pak after https://github.com/r-lib/pak/issues/628 # deps from pak::pkg_deps(".")$package -RUN R -q -e 'pak::pak(c("DBI", "R6", "RPostgres", "Rcpp", "askpass", "base64enc", "bit64", "bit", "blob", "callr", "cli", "credentials", "curl", "data.table", "desc", "digest", "dplyr", "fansi", "fs", "future.apply", "future", "generics", "gert", "globals", "glue", "hms", "httr", "jsonlite", "lgr", "lifecycle", "listenv", "lubridate", "magrittr", "mime", "openssl", "parallelly", "paws.common", "paws.storage", "pillar", "pkgbuild", "pkgconfig", "processx", "progressr", "ps", "purrr", "rlang", "rstudioapi", "s3fs", "stringi", "stringr", "sys", "tibble", "tidyselect", "timechange", "utf8", "vctrs", "withr", "xml2", "zip", "codetools", "cranlike", "RSQLite", "cachem", "crayon", "debugme", "fastmap", "memoise", "progress"))' +RUN R -q -e 'pak::pak(c("DBI", "R6", "RPostgres", "Rcpp", "askpass", "base64enc", "bit64", "bit", "blob", "callr", "cli", "credentials", "curl", "data.table", "desc", "digest", "dplyr", "fansi", "fs", "future.apply", "future", "generics", "gert", "globals", "glue", "hms", "httr", "jsonlite", "lgr", "lifecycle", "listenv", "lubridate", "magrittr", "mime", "openssl", "parallelly", "paws.common", "paws.storage", "pillar", "pkgbuild", "pkgconfig", "processx", "progressr", "ps", "purrr", "rlang", "rstudioapi", "s3fs", "stringi", "stringr", "sys", "tibble", "tidyselect", "timechange", "utf8", "vctrs", "withr", "xml2", "zip", "codetools", "cranlike", "RSQLite", "cachem", "crayon", "debugme", "fastmap", "memoise", "progress", "future.callr"))' +# encoding -> https://github.com/r-hub/r-minimal/blob/fa9c117313e05860a0d20b113e5f794c51be8b8c/Dockerfile#L84 +RUN sed -i 's/,//g' /opt/R/${R_VERSION}/lib/R/library/utils/iconvlist COPY --link . . # remove secrets from COPY