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fix x-server on alpine, install callr

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This commit is contained in:
Patrick Schratz 2024-09-30 11:31:33 +02:00
commit 0dedbdf060
Signed by: pat-s
GPG key ID: 3C6318841EF78925
1 changed files with 6 additions and 4 deletions
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10
docker/Dockerfile-alpine-320
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@ -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