fix: bincraftr url for install
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This commit is contained in:
parent
919c960479
commit
b769276679
6 changed files with 32 additions and 32 deletions
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@ -64,6 +64,6 @@ RUN mkdir -p /mnt/cache/packages /mnt/cache/pkgcache /mnt/cache/R-pkgs
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# encoding -> https://github.com/r-hub/r-minimal/blob/fa9c117313e05860a0d20b113e5f794c51be8b8c/Dockerfile#L84
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RUN sed -i 's/,//g' /opt/R/${R_VERSION}/lib/R/library/utils/iconvlist
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RUN R -q -e 'pak::pak("git::https://gitlab.com/devxy/r-package-binaries/bincraftr.git", dependencies = TRUE)'
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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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@ -5,7 +5,7 @@ RUN apk add -q --no-cache curl tar make lapack lapack-dev blas blas-dev gcc gfor
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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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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 alpine:3.21 AS final
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@ -27,7 +27,7 @@ COPY --link --from=jags /JAGS-4.3.2 /JAGS-4.3.2
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# # xvfb: for graphical pkgs requiring tcl, like gWidgets2tcltk
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RUN apk add -q --no-cache curl tar make blas blas-dev gcc gfortran g++ htop git cmake tk-dev xvfb xvfb-run xorg-server xauth xinit xz libdeflate libdeflate-dev
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### CUSTOM DEPENDENCIES
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### CUSTOM DEPENDENCIES
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# linux-headers: ps
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# libxml2-dev: xml2
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@ -43,7 +43,7 @@ RUN apk add --no-cache --update --repository=https://dl-cdn.alpinelinux.org/alpi
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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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# dbarts: CFLAGS += -flax-vector-conversions (https://github.com/vdorie/dbarts/issues/66)
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# CXXFLAGS: -> Rcpp
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# CXXFLAGS: -> Rcpp
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# -DDMLC_USE_FOPEN64=0 -> xgboost (https://github.com/dmlc/xgboost/issues/8595)
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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\nCXXFLAGS=-D__MUSL__ -DDMLC_USE_FOPEN64=0\nCPPFLAGS=-D__MUSL__ -DDMLC_USE_FOPEN64=0\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'
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@ -64,6 +64,6 @@ RUN mkdir -p /mnt/cache/packages /mnt/cache/pkgcache /mnt/cache/R-pkgs
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# encoding -> https://github.com/r-hub/r-minimal/blob/fa9c117313e05860a0d20b113e5f794c51be8b8c/Dockerfile#L84
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RUN sed -i 's/,//g' /opt/R/${R_VERSION}/lib/R/library/utils/iconvlist
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RUN R -q -e 'pak::pak("git::https://gitlab.com/devxy/r-package-binaries/bincraftr.git", dependencies = TRUE)'
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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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CMD ["/bin/bash"]
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@ -3,16 +3,16 @@ ARG RED_HAT_DEV_PW
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RUN subscription-manager register --username mail@devxy.io --password "$RED_HAT_DEV_PW" && subscription-manager repos --enable codeready-builder-for-rhel-8-$(arch)-rpms
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RUN dnf install -y https://dl.fedoraproject.org/pub/epel/epel-release-latest-8.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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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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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/ubi8 AS final
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# renovate datasource=docker depName=rocker/r-ver
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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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@ -35,7 +35,7 @@ RUN dnf install -y https://dl.fedoraproject.org/pub/epel/epel-release-latest-8.n
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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_1.7-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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### 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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@ -57,6 +57,6 @@ RUN bash -c 'echo -e "PKG_SYSREQS = TRUE\nPKG_SYSREQS_VERBOSE = TRUE\nPKG_SYSREQ
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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 'install.packages("gert", repos = "cloud.r-project.org")'
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RUN R -q -e 'pak::pak("git::https://gitlab.com/devxy/r-package-binaries/bincraftr.git", dependencies = TRUE)'
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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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CMD ["/bin/bash"]
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@ -3,16 +3,16 @@ 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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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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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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# 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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@ -35,7 +35,7 @@ RUN dnf install -y https://dl.fedoraproject.org/pub/epel/epel-release-latest-9.n
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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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### 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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@ -56,6 +56,6 @@ RUN bash -c 'echo -e "PKG_SYSREQS = TRUE\nPKG_SYSREQS_VERBOSE = TRUE\nPKG_SYSREQ
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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://gitlab.com/devxy/r-package-binaries/bincraftr.git", dependencies = TRUE)'
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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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CMD ["/bin/bash"]
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@ -54,6 +54,6 @@ RUN apt install -y locales && echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen \
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&& locale-gen en_US.utf8 \
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&& /usr/sbin/update-locale LANG=en_US.UTF-8
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RUN R -q -e 'pak::pak("git::https://gitlab.com/devxy/r-package-binaries/bincraftr.git", dependencies = TRUE)'
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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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@ -3,14 +3,14 @@ FROM ubuntu:noble AS jags
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RUN apt update && apt install -y --no-install-recommends curl make ca-certificates gcc g++ gfortran liblapack-dev
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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
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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
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FROM ubuntu:noble AS final
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ARG R_VERSION=4.4.3
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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 DEBIAN_FRONTEND=noninteractive
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ENV DEBIAN_FRONTEND=noninteractive
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ARG ARCH=arm64
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ENV NCPUS=2
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@ -27,7 +27,7 @@ COPY --link --from=jags /JAGS-4.3.2 /JAGS-4.3.2
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# libfftw3-dev: ravetools -> actually auto-detect but somehow doesn't work in container?
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RUN apt update && apt install -y --no-install-recommends gdebi-core g++ gfortran libbz2-dev libblas-dev libicu-dev liblapack-dev liblzma-dev libpaper-utils libpcre2-dev libtcl8.6 libtk8.6 libxt6 unzip zip zlib1g-dev libpcre3-dev libopenblas-dev curl ca-certificates make ccache htop libgit2-dev git libpq-dev libxml2-dev libgit2-dev cmake xvfb libcurl4-openssl-dev xz-utils tcl tk tk-dev tk-table pkg-config libmecab-dev libfftw3-dev automake
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### CUSTOM DEPENDENCIES
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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 apt-get install -y software-properties-common && \
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add-apt-repository -y ppa:xtradeb/apps && \
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@ -54,6 +54,6 @@ RUN apt install -y locales && echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen \
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&& locale-gen en_US.utf8 \
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&& /usr/sbin/update-locale LANG=en_US.UTF-8
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RUN R -q -e 'pak::pak("git::https://gitlab.com/devxy/r-package-binaries/bincraftr.git", dependencies = TRUE)'
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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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CMD ["/bin/bash"]
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