39 lines
No EOL
2.1 KiB
Text
39 lines
No EOL
2.1 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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# 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 libxml2-dev
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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 -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 && make && make install && 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
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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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RUN mkdir ~/.R && echo -e "CXXFLAGS+=-D__MUSL__\nCPPFLAGS+= -D__MUSL__\nLDFLAGS+=-fPIC" >> ~/.R/Makevars
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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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COPY . .
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RUN apk add libxml2-dev
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# FIXME: switch to pak after https://github.com/r-lib/pak/issues/628
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RUN export ARCH=$(echo $(uname -m | sed -e 's/x86_64/amd64/' -e 's/aarch64/arm64/')) && \
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R -q -e 'Sys.setenv(PKG_SYSREQS = TRUE, PKG_SYSREQS_VERBOSE = TRUE); options(Ncpus = 4, repos = structure(c(devxy = sprintf("https://cran.devxy.io/%s/alpine320/latest", Sys.getenv("ARCH")), CRAN = "https://cloud.r-project.org"))); install.packages("remotes"); remotes::install_deps()'
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RUN rm -rf r-pkg-binaries
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CMD ["/bin/bash"] |