55 lines
No EOL
3.3 KiB
Text
55 lines
No EOL
3.3 KiB
Text
FROM alpine:3.20
|
|
|
|
ENV PATH=/opt/R/4.4.1/bin:$PATH
|
|
ENV TZ="Europe/Berlin"
|
|
|
|
ARG ARCH=arm64
|
|
ENV NCPUS=2
|
|
|
|
ENV AWS_ACCESS_KEY_ID=""
|
|
ENV AWS_SECRET_ACCESS_KEY=""
|
|
ENV PGPASS=""
|
|
|
|
|
|
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
|
|
RUN apk add -q --no-cache curl tar make lapack lapack-dev blas blas-dev gcc gfortran g++ htop git cmake
|
|
|
|
### CUSTOM DEPENDENCIES
|
|
# These usually are not packaged in OS repositories and need to be installed from source
|
|
# - JAGS (needed for runjags which itself is again a dependency of many packages)
|
|
RUN curl -q -L -O https://sourceforge.net/projects/mcmc-jags/files/JAGS/4.x/Source/JAGS-4.3.2.tar.gz && tar -xzf JAGS-4.3.2.tar.gz && cd JAGS-4.3.2 && ./configure --enable-silent-rules && make 2>&1 >/dev/null && rm -rf JAGS-4.3.2.tar.gz JAGS-4.3.2 && cd ..
|
|
RUN apk del lapack lapack-dev
|
|
|
|
# linux-headers: ps
|
|
# libxml2-dev: xml2
|
|
# libgit2-dev: gert
|
|
# libpq-dev: RPostgres
|
|
RUN apk add -q --no-cache R-dev curl ca-certificates bash g++ tzdata openjdk17 tar sed patch openblas-dev pkgconfig linux-headers ccache libxml2-dev libgit2-dev libpq-dev
|
|
|
|
# https://github.com/RcppCore/Rcpp/issues/448#issuecomment-220148774
|
|
# LDFLAGS+=-fPIC -> arrow (https://github.com/r-hub/r-minimal/blob/main/examples/arrow/Dockerfile)
|
|
# Makevars
|
|
RUN mkdir -p /root/.R && bash -c 'echo -e "CXX_STD = CXX14\nCC=ccache gcc\nCPP=ccache gcc\nCXX=ccache g++\nCXX11=ccache g++\nCXX14=ccache g++\nCXX17=ccache g++\nF77=ccache /usr/bin/gfortran\nFC=ccache /usr/bin/gfortran" >> /root/.R/Makevars'
|
|
RUN mkdir -p ~/.R && bash -c 'echo -e "CXXFLAGS+=-D__MUSL__\nCPPFLAGS+= -D__MUSL__\nLDFLAGS+=-fPIC" >> root/.R/Makevars'
|
|
|
|
# R repos
|
|
RUN bash -c 'echo -e "options(crayon.enabled = TRUE, Ncpus = ${NCPUS}, future.globals.onReference = NULL, repos = structure(c(CRAN = \"https://cloud.r-project.org\", INLA = \"https://inla.r-inla-download.org/R/stable\")))" > /root/.Rprofile'
|
|
RUN bash -c 'echo -e "PKG_SYSREQS = TRUE\nPKG_SYSREQS_VERBOSE = TRUE" > /root/.Renviron'
|
|
|
|
### INSTALL R
|
|
RUN curl -O https://devxy-r-builds.s3.eu-central-2.amazonaws.com/alpine320/r-4.4.1_1_$(arch).apk
|
|
RUN apk add --allow-untrusted r-4.4.1_1_$(arch).apk && rm r-4.4.1_1_$(arch).apk
|
|
|
|
RUN R -q -e 'install.packages("remotes", repo = "cloud.r-project.org"); remotes::install_github("pat-s/pak@alpine")'
|
|
|
|
# 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", "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", "RSQLite", "cachem", "crayon", "debugme", "fastmap", "memoise", "pat-s/cranlike@s3", "pat-s/desc@description-from-remote"))'
|
|
|
|
COPY . .
|
|
RUN R CMD INSTALL . && rm -rf r-pkg-binaries
|
|
|
|
CMD ["/bin/bash"] |