55 lines
No EOL
3.3 KiB
Text
55 lines
No EOL
3.3 KiB
Text
FROM alpine:3.20
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ENV PATH=/opt/R/4.4.1/bin:$PATH
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ENV TZ="Europe/Berlin"
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ENV ARCH=arm64
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ENV NCPUS=2
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ENV AWS_ACCESS_KEY_ID=""
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ENV AWS_SECRET_ACCESS_KEY=""
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ENV PGPASS=""
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ARG GITHUB_PAT
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# Background: JAGS needs lapack & lapack-dev but these conflict with openblas-dev which is required by R-dev
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# Solution: first compile JAGS, then remove lapack & lapack-dev again
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RUN apk add -q --no-cache curl tar make lapack lapack-dev blas blas-dev gcc gfortran g++ htop git
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### CUSTOM DEPENDENCIES
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# These usually are not packaged in OS repositories and need to be installed from source
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# - JAGS (needed for runjags which itself is again a dependency of many packages)
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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 ..
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RUN apk del lapack lapack-dev
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# linux-headers: ps
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# libxml2-dev: xml2
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# libgit2-dev: gert
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# libpq-dev: RPostgres
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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
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# https://github.com/RcppCore/Rcpp/issues/448#issuecomment-220148774
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# LDFLAGS+=-fPIC -> arrow (https://github.com/r-hub/r-minimal/blob/main/examples/arrow/Dockerfile)
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# Makevars
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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'
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RUN mkdir -p ~/.R && bash -c 'echo -e "CXXFLAGS+=-D__MUSL__\nCPPFLAGS+= -D__MUSL__\nLDFLAGS+=-fPIC" >> root/.R/Makevars'
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# R repos
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RUN bash -c 'echo -e "options(crayon.enabled = TRUE, Ncpus = ${NCPUS}, future.globals.onReference = NULL, repos = structure(c(devxy = \"https://cran.devxy.io/${ARCH}/alpine320/latest\", INLA = \"https://inla.r-inla-download.org/R/stable\", CRAN = \"https://cloud.r-project.org\")))" > /root/.Rprofile'
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RUN bash -c 'echo -e "PKG_SYSREQS = TRUE\nPKG_SYSREQS_VERBOSE = TRUE" > /root/.Renviron'
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### INSTALL R
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RUN curl -O https://devxy-r-builds.s3.eu-central-2.amazonaws.com/alpine320/r-4.4.1_1_$(arch).apk
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RUN apk add --allow-untrusted r-4.4.1_1_$(arch).apk && rm r-4.4.1_1_$(arch).apk
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RUN R -q -e 'install.packages("remotes", repo = "cloud.r-project.org"); remotes::install_github("pat-s/pak@alpine")'
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# FIXME: switch to pak after https://github.com/r-lib/pak/issues/628
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# deps from pak::pkg_deps(".")$package
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RUN R -q -e 'pak::pak(c("DBI", "R6", "RPostgres", "Rcpp", "askpass", "base64enc", "bit64", "bit", "blob", "callr", "cli", "credentials", "curl", "data.table", "pat-s/desc@description-from-remote", "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", "pat-s/cranlike@s3", "RSQLite", "cachem", "crayon", "debugme", "fastmap", "memoise"))'
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COPY . .
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RUN R CMD INSTALL . && rm -rf r-pkg-binaries
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CMD ["/bin/bash"] |