improved docker images
This commit is contained in:
parent
36d95cf5d9
commit
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GPG key ID:
3C6318841EF78925
7 changed files with 146 additions and 22 deletions
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@ -2,6 +2,9 @@ when:
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- event: cron
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cron: images
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depends_on:
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- warm_up_images
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matrix:
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include:
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- PLATFORM: redhat-9
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44
.woodpecker/warm_up_images.yaml
Normal file
44
.woodpecker/warm_up_images.yaml
Normal file
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@ -0,0 +1,44 @@
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when:
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event: [manual]
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skip_clone: true
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matrix:
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include:
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- PLATFORM: redhat-9
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ARCH: arm64
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- PLATFORM: redhat-8
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ARCH: arm64
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- PLATFORM: ubuntu-2404
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ARCH: arm64
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- PLATFORM: ubuntu-2204
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ARCH: arm64
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- PLATFORM: alpine-320
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ARCH: arm64
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- PLATFORM: alpine-320
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ARCH: amd64
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steps:
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- name: 'Warming up'
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image: busybox:latest
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failure: ignore
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commands:
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- sleep 300
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- echo "Warmed Up"
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backend_options:
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kubernetes:
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### PROD-sequential
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resources:
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requests:
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memory: 500Mi
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cpu: 1000m
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limits:
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memory: 800Mi
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cpu: 1000m
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nodeSelector:
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kubernetes.io/arch: "${ARCH}"
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tolerations:
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- key: "CI"
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operator: "Equal"
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value: "true"
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effect: "NoSchedule"
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@ -3,6 +3,14 @@ FROM alpine:3.20
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ENV PATH=/opt/R/4.4.1/bin:$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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@ -23,7 +31,13 @@ RUN apk add -q --no-cache R-dev curl ca-certificates bash g++ tzdata openjdk17 t
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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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# 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_$(arch).apk
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@ -31,11 +45,11 @@ RUN apk add --allow-untrusted r-4.4.1_1_$(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 $(uname -m | sed -e 's/x86_64/amd64/' -e 's/aarch64/arm64/')) && \
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R -q -e 'Sys.setenv(PKG_SYSREQS = TRUE, PKG_SYSREQS_VERBOSE = TRUE); options(Ncpus = 4, repos = structure(c(devxy = sprintf("https://cran.devxy.io/%s/alpine320/latest", Sys.getenv("ARCH")), CRAN = "https://cloud.r-project.org"))); install.packages("remotes"); remotes::install_deps()'
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RUN rm -rf r-pkg-binaries
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# deps from pak::pkg_deps(".")$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"]
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@ -4,12 +4,18 @@ ARG RED_HAT_DEV_PW
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ENV PATH=/opt/R/4.4.1/bin:$PATH
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ENV TZ="Europe/Berlin"
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ENV ARCH=arm64
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ENV NCPUS=2
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ENV AWS_ACCESS_KEY_ID=""
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ENV AWS_SECRET_ACCESS_KEY=""
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ENV PGPASS=""
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ARG GITHUB_PAT
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RUN subscription-manager register --username mail@devxy.io --password "$RED_HAT_DEV_PW" && subscription-manager repos --enable codeready-builder-for-rhel-8-aarch64-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 make lapack-devel git gcc gcc-c++ fontconfig-devel fribidi-devel libjpeg-turbo-devel libtiff-devel postgresql-devel htop libgit2-devel libxml2-devel
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RUN dnf install -y -q https://dl.fedoraproject.org/pub/epel/8/Everything/aarch64/Packages/h/hiredis-0.13.3-13.el8.aarch64.rpm && dnf install -y -q https://dl.fedoraproject.org/pub/epel/8/Everything/aarch64/Packages/c/ccache-3.7.7-1.el8.aarch64.rpm
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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
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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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@ -21,9 +27,18 @@ RUN curl -O https://devxy-r-builds.s3.eu-central-2.amazonaws.com/el8/R-4.4.1-1-1
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RUN dnf install -q -y R-4.4.1-1-1.aarch64.rpm
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RUN R -q -e 'install.packages("pak", repos = sprintf("https://r-lib.github.io/p/pak/stable/%s/%s/%s", .Platform$pkgType, R.Version()$os, R.Version()$arch))'
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COPY . .
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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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# 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}/rhel8/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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# FIXME: switch to pak after https://github.com/r-lib/pak/issues/628
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RUN R -q -e 'Sys.setenv(PKG_SYSREQS = TRUE, PKG_SYSREQS_VERBOSE = TRUE); options(Ncpus = 4, repos = structure(c(devxy = "https://cran.devxy.io/arm64/rhel8/latest", 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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# deps from pak::pkg_deps(".")$package
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RUN R -q -e 'pak::pak(c("DBI", "R6", "RPostgres", "Rcpp", "askpass", "base64enc", "bit64", "bit", "blob", "callr", "cli", "credentials", "curl", "data.table", "pat-s/desc@description-from-remote", "digest", "dplyr", "fansi", "fs", "future.apply", "future", "generics", "gert", "globals", "glue", "hms", "httr", "jsonlite", "lgr", "lifecycle", "listenv", "lubridate", "magrittr", "mime", "openssl", "parallelly", "paws.common", "paws.storage", "pillar", "pkgbuild", "pkgconfig", "processx", "progressr", "ps", "purrr", "rlang", "rstudioapi","s3fs", "stringi", "stringr", "sys", "tibble", "tidyselect", "timechange", "utf8", "vctrs", "withr", "xml2", "zip", "codetools", "pat-s/cranlike@s3", "RSQLite", "cachem", "crayon", "debugme", "fastmap", "memoise"))'
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COPY . .
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RUN R CMD INSTALL . && rm -rf r-pkg-binaries
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CMD ["/bin/bash"]
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@ -4,11 +4,18 @@ ARG RED_HAT_DEV_PW
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ENV PATH=/opt/R/4.4.1/bin:$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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RUN subscription-manager register --username devxy --password "$RED_HAT_DEV_PW" && subscription-manager repos --enable codeready-builder-for-rhel-9-aarch64-rpms
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RUN subscription-manager register --username mail@devxy.io --password "$RED_HAT_DEV_PW" && subscription-manager repos --enable codeready-builder-for-rhel-9-aarch64-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 lapack-devel git gcc g++ fontconfig-devel fribidi-devel libjpeg-turbo-devel libtiff-devel htop libgit2-devel hiredis ccache libpq-devel libxml2-devel libgit2-devel
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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
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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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@ -20,9 +27,18 @@ RUN curl -O https://devxy-r-builds.s3.eu-central-2.amazonaws.com/el9/R-4.4.1-1-1
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RUN dnf install -q -y R-4.4.1-1-1.aarch64.rpm
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RUN R -q -e 'install.packages("pak", repos = sprintf("https://r-lib.github.io/p/pak/stable/%s/%s/%s", .Platform$pkgType, R.Version()$os, R.Version()$arch))'
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COPY . .
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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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# 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}/rhel9/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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# FIXME: switch to pak after https://github.com/r-lib/pak/issues/628
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RUN R -q -e 'Sys.setenv(PKG_SYSREQS = TRUE, PKG_SYSREQS_VERBOSE = TRUE); options(Ncpus = 4, repos = structure(c(devxy = "https://cran.devxy.io/arm64/rhel9/latest", 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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# deps from pak::pkg_deps(".")$package
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RUN R -q -e 'pak::pak(c("DBI", "R6", "RPostgres", "Rcpp", "askpass", "base64enc", "bit64", "bit", "blob", "callr", "cli", "credentials", "curl", "data.table", "pat-s/desc@description-from-remote", "digest", "dplyr", "fansi", "fs", "future.apply", "future", "generics", "gert", "globals", "glue", "hms", "httr", "jsonlite", "lgr", "lifecycle", "listenv", "lubridate", "magrittr", "mime", "openssl", "parallelly", "paws.common", "paws.storage", "pillar", "pkgbuild", "pkgconfig", "processx", "progressr", "ps", "purrr", "rlang", "rstudioapi","s3fs", "stringi", "stringr", "sys", "tibble", "tidyselect", "timechange", "utf8", "vctrs", "withr", "xml2", "zip", "codetools", "pat-s/cranlike@s3", "RSQLite", "cachem", "crayon", "debugme", "fastmap", "memoise"))'
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COPY . .
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RUN R CMD INSTALL . && rm -rf r-pkg-binaries
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CMD ["/bin/bash"]
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@ -4,6 +4,13 @@ ENV PATH=/opt/R/4.4.1/bin:$PATH
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ENV TZ="Europe/Berlin"
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ENV DEBIAN_FRONTEND=noninteractive
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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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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
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@ -18,9 +25,18 @@ RUN curl -O https://devxy-r-builds.s3.eu-central-2.amazonaws.com/2204/r-4.4.1_1_
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RUN gdebi -n -qq r-4.4.1_1_arm64.deb && rm r-4.4.1_1_arm64.deb
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RUN R -q -e 'install.packages("pak", repos = sprintf("https://r-lib.github.io/p/pak/stable/%s/%s/%s", .Platform$pkgType, R.Version()$os, R.Version()$arch))'
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COPY . .
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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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# 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}/jammy/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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# FIXME: switch to pak after https://github.com/r-lib/pak/issues/628
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RUN R -q -e 'Sys.setenv(PKG_SYSREQS = TRUE, PKG_SYSREQS_VERBOSE = TRUE); options(Ncpus = 4, repos = structure(c(devxy = "https://cran.devxy.io/arm64/jammy/latest", 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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# deps from pak::pkg_deps(".")$package
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RUN R -q -e 'pak::pak(c("DBI", "R6", "RPostgres", "Rcpp", "askpass", "base64enc", "bit64", "bit", "blob", "callr", "cli", "credentials", "curl", "data.table", "pat-s/desc@description-from-remote", "digest", "dplyr", "fansi", "fs", "future.apply", "future", "generics", "gert", "globals", "glue", "hms", "httr", "jsonlite", "lgr", "lifecycle", "listenv", "lubridate", "magrittr", "mime", "openssl", "parallelly", "paws.common", "paws.storage", "pillar", "pkgbuild", "pkgconfig", "processx", "progressr", "ps", "purrr", "rlang", "rstudioapi","s3fs", "stringi", "stringr", "sys", "tibble", "tidyselect", "timechange", "utf8", "vctrs", "withr", "xml2", "zip", "codetools", "pat-s/cranlike@s3", "RSQLite", "cachem", "crayon", "debugme", "fastmap", "memoise"))'
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COPY . .
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RUN R CMD INSTALL . && rm -rf r-pkg-binaries
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CMD ["/bin/bash"]
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@ -4,6 +4,13 @@ ENV PATH=/opt/R/4.4.1/bin:$PATH
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ENV TZ="Europe/Berlin"
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ENV DEBIAN_FRONTEND=noninteractive
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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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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
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@ -18,9 +25,18 @@ RUN curl -O https://devxy-r-builds.s3.eu-central-2.amazonaws.com/2404/r-4.4.1_1_
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RUN gdebi -n -qq r-4.4.1_1_arm64.deb && rm r-4.4.1_1_arm64.deb
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RUN R -q -e 'install.packages("pak", repos = sprintf("https://r-lib.github.io/p/pak/stable/%s/%s/%s", .Platform$pkgType, R.Version()$os, R.Version()$arch))'
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COPY . .
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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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# 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}/noble/latest\", INLA = \"https://inla.r-inla-download.org/R/stable\", CRAN = \"https://cloud.r-project.org\")))" > /root/.Rprofile'
|
||||
RUN bash -c 'echo -e "PKG_SYSREQS = TRUE\nPKG_SYSREQS_VERBOSE = TRUE" > /root/.Renviron'
|
||||
|
||||
# FIXME: switch to pak after https://github.com/r-lib/pak/issues/628
|
||||
RUN R -q -e 'Sys.setenv(PKG_SYSREQS = TRUE, PKG_SYSREQS_VERBOSE = TRUE); options(Ncpus = 4, repos = structure(c(devxy = "https://cran.devxy.io/arm64/noble/latest", CRAN = "https://cloud.r-project.org"))); install.packages("remotes"); remotes::install_deps()'
|
||||
RUN rm -rf r-pkg-binaries
|
||||
# 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", "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"))'
|
||||
|
||||
COPY . .
|
||||
RUN R CMD INSTALL . && rm -rf r-pkg-binaries
|
||||
|
||||
CMD ["/bin/bash"]
|
||||
Loading…
Reference in a new issue