pat-s
b769276679
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61 lines
3.6 KiB
Text
61 lines
3.6 KiB
Text
FROM redhat/ubi9 AS jags
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ARG RED_HAT_DEV_PW
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RUN subscription-manager register --username mail@devxy.io --password "$RED_HAT_DEV_PW" && subscription-manager repos --enable codeready-builder-for-rhel-9-$(arch)-rpms
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RUN dnf install -y https://dl.fedoraproject.org/pub/epel/epel-release-latest-9.noarch.rpm && dnf install -y epel-release
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RUN dnf install -y -q gcc-c++ lapack-devel make git ca-certificates
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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 -s -L -O https://sourceforge.net/projects/mcmc-jags/files/JAGS/4.x/Source/JAGS-4.3.2.tar.gz && \
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tar -xzf JAGS-4.3.2.tar.gz && cd JAGS-4.3.2 && ./configure --enable-silent-rules && make 2>&1
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FROM redhat/ubi9 AS final
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# renovate datasource=docker depName=rocker/r-ver
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ARG R_VERSION=4.4.3
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ARG RED_HAT_DEV_PW
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ENV PATH=/opt/R/${R_VERSION}/bin:$PATH
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ENV TZ="Europe/Berlin"
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ENV R_LIBS_USER=/mnt/cache/R-pkgs
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ENV R_PKG_CACHE_DIR=/mnt/cache/pkgcache
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ARG ARCH=arm64
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ENV NCPUS=2
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ARG GITHUB_PAT
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COPY --link --from=jags /JAGS-4.3.2 /JAGS-4.3.2
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RUN subscription-manager register --username mail@devxy.io --password "$RED_HAT_DEV_PW" && subscription-manager repos --enable codeready-builder-for-rhel-9-$(arch)-rpms
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RUN dnf install -y https://dl.fedoraproject.org/pub/epel/epel-release-latest-9.noarch.rpm && dnf install -y epel-release
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# xvfb: for graphical pkgs requiring tcl, like gWidgets2tcltk
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# ImageMagick-c++-devel ImageMagick-devel: boths are not auto-installed via pak sysreqs
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# mecab-devel: RcppMeCab -> no autodetection yet
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# libfftw3-dev: ravetools -> actually auto-detect but somehow doesn't work in container?
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RUN dnf install -y -q make lapack-devel git gcc gcc-c++ fontconfig-devel fribidi-devel libjpeg-turbo-devel libtiff-devel postgresql-devel htop libgit2-devel libxml2-devel hiredis ccache cmake xorg-x11-server-Xvfb ImageMagick-c++-devel ImageMagick-devel xz pkg-config mecab-devel fftw-devel tk-devel automake readline-devel
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### CUSTOM DEPENDENCIES
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# - Chromium should be auto-installed once pkgdepends merges the latest system-requirements rule changes
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RUN dnf install -y chromium
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### INSTALL R
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RUN curl -O "https://devxy-r-builds.fsn1.your-objectstorage.com/el9/R-${R_VERSION}-1-1.$(arch).rpm"
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RUN dnf install -q -y "R-${R_VERSION}-1-1.$(arch).rpm" && rm "R-${R_VERSION}-1-1.$(arch).rpm"
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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))'
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### Makevars
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# dbarts: CFLAGS += -flax-vector-conversions (https://github.com/vdorie/dbarts/issues/66)
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# can't set ccache for gfortran because of https://gitlab.com/roigrp/solver/highs/-/issues/4
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RUN mkdir -p /root/.R && bash -c 'echo -e "CXX_STD = CXX14\nCFLAGS += -flax-vector-conversions\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'
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# R repos
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RUN bash -c 'echo -e "options(crayon.enabled = TRUE, Ncpus = ${NCPUS}, future.globals.onReference = NULL, repos = structure(c(CRAN = \"https://cran.devxy.io/$ARCH/rhel9/latest\", INLA = \"https://inla.r-inla-download.org/R/stable\")))" > /root/.Rprofile'
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RUN bash -c 'echo -e "PKG_SYSREQS = TRUE\nPKG_SYSREQS_VERBOSE = TRUE\nPKG_SYSREQS_PLATFORM=\"redhat-9\"" > /root/.Renviron'
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# these dirs will later be used by the CI with existing mounts
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RUN mkdir -p /mnt/cache/packages /mnt/cache/pkgcache /mnt/cache/R-pkgs
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RUN R -q -e 'pak::pak("git::https://codefloe.com/rpkgs/bincraftr.git", dependencies = TRUE)'
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CMD ["/bin/bash"]
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