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12
00-run.sh
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12
00-run.sh
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#!/bin/bash
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docker run --name r-pkg-binaries-rhel9 -e RED_HAT_DEV_PW -d redhat/ubi9 tail -f /dev/null
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docker exec -it r-pkg-binaries-rhel9 bash
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export R_VERSION=4.3.3
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export PACKAGES="sf"
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bash -c ./01-prepare.sh
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bash -c ./02-build-binaries.sh
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bash -c ./03-upload.sh
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38
01-prepare.sh
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38
01-prepare.sh
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#!/bin/bash
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### install R
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PLATFORM_ID=$(cat /etc/os-release | grep 'PLATFORM_ID=' | cut -d'=' -f2 | tr -d '"')
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if [ $PLATFORM_ID = "platform:el9" ]; then
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subscription-manager register --username pat-s --password $RED_HAT_DEV_PW
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subscription-manager repos --enable codeready-builder-for-rhel-9-$(arch)-rpms
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dnf -y install git rsync
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# dnf update -y
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# FIXME: protect PW
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echo "R Version: ${R_VERSION}"
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echo "Downloading R-${R_VERSION}.rpm from S3..."
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curl -o /tmp/R-${R_VERSION}.rpm https://cynkra-r-builds-arm64.s3.eu-central-1.amazonaws.com/el9/R-"${R_VERSION}"-1-1."$(arch)".rpm
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dnf install -y /tmp/R-${R_VERSION}.rpm
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fi
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export PATH=/opt/R/${R_VERSION}/bin:$PATH
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### install R packages needed for building
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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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R -q -e 'options(repos = c(CRAN="https://stat.ethz.ch/CRAN/")); pak::pak(c("pkgbuild", "cranlike", "drat"))'
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### install awscli
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curl -s "https://awscli.amazonaws.com/awscli-exe-linux-aarch64.zip" -o "awscliv2.zip"
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unzip -qq awscliv2.zip
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./aws/install
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rm -rf awscliv2.zip
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mkdir /root/.aws
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echo -e "[default]\n
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aws_access_key_id=AKIATHTKSC6FRVE5LNE7\n
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aws_secret_access_key=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\n" >/root/.aws/credentials
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154
02-build-binaries.sh
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154
02-build-binaries.sh
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#! /bin/bash
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R_VERSION=4.0.5
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PACKAGES="mlr3filters stringi"
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# install sysdeps for all packages
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for w in $PACKAGES; do
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### dynamic start
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export PACKAGE=$w
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export R_LIBS_USER=/root/user_lib
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mkdir -p /root/user_lib
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export R_VERSION=$(R --version | grep -Eo '[0-9.]+' | head -n 1)
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export R_VERSION_MINOR=$(echo "$R_VERSION" | cut -d. -f1,2)
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export ARCH=$(arch)
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DIST_FAM=$(grep 'ID_LIKE=' /etc/os-release | cut -d'=' -f2 | tr -d '"')
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if [[ $DIST_FAM == "debian" ]]; then
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export CODENAME=$(grep 'VERSION_CODENAME=' /etc/os-release | cut -d'=' -f2 | tr -d '"')
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elif [[ $DIST_FAM =~ ^(rhel) ]]; then
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if [[ $(grep 'PLATFORM_ID=' /etc/os-release | cut -d'=' -f2 | tr -d '"') == "platform:el9" ]]; then
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export CODENAME=rhel9
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elif [[ $(grep 'PLATFORM_ID=' /etc/os-release | cut -d'=' -f2 | tr -d '"') == "platform:el8" ]]; then
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export CODENAME=rhel8
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fi
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fi
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git clone https://github.com/cran/"${PACKAGE}".git
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cd "${PACKAGE}"
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# also installs system dependencies
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# FIXME: auto-detection does not work on arm-based systems
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export PKG_SYSREQS_PLATFORM=redhat-9
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export PKG_SYSREQS=TRUE
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export PKG_SYSREQS_VERBOSE=TRUE
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R -q -e 'options(repos = c(CRAN="https://stat.ethz.ch/CRAN/")); pak::local_install_dev_deps()'
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cd ..
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done
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# build binaries from tags
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for w in $PACKAGES; do
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# this runs in parallel
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# run() {
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export PACKAGE=$w
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export R_LIBS_USER=/root/user_lib
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export R_VERSION=$(R --version | grep -Eo '[0-9.]+' | head -n 1)
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export R_VERSION_MINOR=$(echo "$R_VERSION" | cut -d. -f1,2)
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export ARCH=$(arch)
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DIST_FAM=$(grep 'ID_LIKE=' /etc/os-release | cut -d'=' -f2 | tr -d '"')
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if [[ $DIST_FAM == "debian" ]]; then
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export CODENAME=$(grep 'VERSION_CODENAME=' /etc/os-release | cut -d'=' -f2 | tr -d '"')
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elif [[ $DIST_FAM =~ ^(fedora) ]]; then
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if [[ $(grep 'PLATFORM_ID=' /etc/os-release | cut -d'=' -f2 | tr -d '"') == "platform:el9" ]]; then
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export CODENAME=rhel9
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elif [[ $(grep 'PLATFORM_ID=' /etc/os-release | cut -d'=' -f2 | tr -d '"') == "platform:el8" ]]; then
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export CODENAME=rhel8
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fi
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fi
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# example CRAN dir structure: https://cran.r-project.org/src/contrib
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mkdir -p /root/__linux__/"${CODENAME}"/"${R_VERSION_MINOR}"/latest/src/contrib/Archive
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mkdir -p /root/src/contrib/Archive
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cd "${PACKAGE}"
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# NB: we start with the latest tag as we make the greedy assumption that the latest release has all deps of the previous ones
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export TAGS=$(git tag -l --sort=-v:refname)
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for i in $TAGS; do
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git checkout -q -f $i
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# the tag might differ from the actual version
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TAG=$(grep "Version" DESCRIPTION | grep -Po "([0-9]+(\.[0-9]+)+)")
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# don't install syslibs again
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export PKG_SYSREQS=FALSE
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export PKG_SYSREQS_VERBOSE=FALSE
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# build source
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EXISTS=$(find /root/src/contrib/ | grep -P "${PACKAGE}_${TAG}")
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if [[ -n $EXISTS ]]; then
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printf "[Skip] ${PACKAGE} '${TAG}' (source), already exists.\n"
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# continue
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else
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printf "[Build] ${PACKAGE} '${TAG}' (source)\n"
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fi
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OUTPUT=$(R -q -e 'options(repos = c(CRAN="https://stat.ethz.ch/CRAN/")); pkgbuild::build(binary = FALSE, vignettes = FALSE, dest_path = "/root/src/contrib")')
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if [[ $(printf "$OUTPUT" | grep "Error") != "" ]]; then
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printf "[Error] ${PACKAGE} '${TAG}' (binary)\n"
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printf $OUTPUT >/root/__linux__/"${CODENAME}"/"${R_VERSION_MINOR}"/latest/src/contrib/"${PACKAGE}"_"${TAG}"_error
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continue
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else
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# build binary
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EXISTS=$(find /root/__linux__/"${CODENAME}"/"${R_VERSION_MINOR}"/latest/src/contrib/ | grep -P "${PACKAGE}_${TAG}")
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if [[ -n $EXISTS ]]; then
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printf "[Skip] ${PACKAGE} '${TAG}' (binary), already exists.\n"
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continue
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else
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printf "[Build] ${PACKAGE} '${TAG}' (binary)\n"
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fi
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R -q -e 'options(repos = c(CRAN="https://stat.ethz.ch/CRAN/")); pak::local_install_dev_deps()'
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R -q -e 'options(repos = c(CRAN="https://stat.ethz.ch/CRAN/")); pkgbuild::build(binary = TRUE, vignettes = FALSE, dest_path = sprintf("/root/__linux__/%s/%s/latest/src/contrib", Sys.getenv("CODENAME"), Sys.getenv("R_VERSION_MINOR")))'
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# remove _aarch64-unknown-linux-gnu part in filename
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rsync -a /root/__linux__/"${CODENAME}"/"${R_VERSION_MINOR}"/latest/src/contrib/"${PACKAGE}"_"${TAG}"*.tar.gz /root/__linux__/"${CODENAME}"/"${R_VERSION_MINOR}"/latest/src/contrib/"${PACKAGE}"_"${TAG}".tar.gz
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fi
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# create archive dir for package
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mkdir -p /root/__linux__/"${CODENAME}"/"${R_VERSION_MINOR}"/latest/src/contrib/Archive/"${PACKAGE}"
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# list all files in dir
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all_versions=$(ls /root/__linux__/"${CODENAME}"/"${R_VERSION_MINOR}"/latest/src/contrib/"${PACKAGE}"*.tar.gz)
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# Find the latest version
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latest_version=$(ls /root/__linux__/"${CODENAME}"/"${R_VERSION_MINOR}"/latest/src/contrib/"${PACKAGE}"*.tar.gz | sort -V | tail -n 1)
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# Move all other versions to the Archived directory
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for file in $all_versions; do
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if [ "$file" != "$latest_version" ]; then
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rsync -a "$file" /root/__linux__/"${CODENAME}"/"${R_VERSION_MINOR}"/latest/src/contrib/Archive/"${PACKAGE}"/
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fi
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done
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# list all files in dir
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all_versions=$(ls /root/src/contrib/"${PACKAGE}"*.tar.gz)
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# Find the latest version
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latest_version=$(ls /root/src/contrib/"${PACKAGE}"*.tar.gz | sort -V | tail -n 1)
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# create archive dir for package
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mkdir -p /root/src/contrib/Archive/"${PACKAGE}"
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# Move all other versions to the Archived directory
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for file in $all_versions; do
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if [ "$file" != "$latest_version" ]; then
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rsync -a "$file" /root/src/contrib/Archive/"${PACKAGE}"/
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fi
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done
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done
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cd ..
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rm -rf /root/"${PACKAGE}"
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# }
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# run &
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done
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# src
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R -q -e "cranlike::add_PACKAGES(list.files('/root/src/contrib/', pattern='tar.gz'), '/root/src/contrib/')"
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R -q -e "cranlike::package_versions('/root/src/contrib/')"
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# bin
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R -q -e "cranlike::add_PACKAGES(list.files('/root/__linux__/${CODENAME}/${R_VERSION_MINOR}/latest/src/contrib/', pattern='tar.gz'), '/root/__linux__/${CODENAME}/${R_VERSION_MINOR}/latest/src/contrib/')"
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R -q -e "cranlike::package_versions('/root/__linux__/${CODENAME}/${R_VERSION_MINOR}/latest/src/contrib/')"
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44
03-upload.sh
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44
03-upload.sh
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#!/bin/bash
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PACKAGES="mlr3filters stringi"
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export R_VERSION=$(R --version | grep -Eo '[0-9.]+' | head -n 1)
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export R_VERSION_MINOR=$(echo "$R_VERSION" | cut -d. -f1,2)
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export ARCH=$(arch)
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DIST_FAM=$(grep 'ID_LIKE=' /etc/os-release | cut -d'=' -f2 | tr -d '"')
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if [[ $DIST_FAM == "debian" ]]; then
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export CODENAME=$(grep 'VERSION_CODENAME=' /etc/os-release | cut -d'=' -f2 | tr -d '"')
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elif [[ $DIST_FAM =~ ^(fedora) ]]; then
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if [[ $(grep 'PLATFORM_ID=' /etc/os-release | cut -d'=' -f2 | tr -d '"') == "platform:el9" ]]; then
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export CODENAME=rhel9
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elif [[ $(grep 'PLATFORM_ID=' /etc/os-release | cut -d'=' -f2 | tr -d '"') == "platform:el8" ]]; then
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export CODENAME=rhel8
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fi
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fi
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for w in $PACKAGES; do
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# source
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aws s3 sync /root/src/contrib/ s3://cynkra-r-binaries-arm64/src/contrib/ --exclude '*error' --acl public-read
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# binaries
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aws s3 sync /root/__linux__/${CODENAME}/${R_VERSION_MINOR}/latest/src/contrib/ s3://cynkra-r-binaries-arm64/__linux__/${CODENAME}/${R_VERSION_MINOR}/latest/src/contrib/ --exclude '*error' --acl public-read
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done
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### WORKING
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# R -q -e 'install.packages("mlr3filters", repos="https://cynkra-r-binaries-arm64.s3.eu-central-1.amazonaws.com/__linux__/rhel9/4.3/latest/")'
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# R -q -e 'remotes::install_version("mlr3filters", "0.7.0", repos="https://cynkra-r-binaries-arm64.s3.eu-central-1.amazonaws.com/__linux__/rhel9/4.3/latest")'
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# install.packages("Rcpp", repos="https://cynkra-r-binaries-arm64.s3.eu-central-1.amazonaws.com/__linux__/rhel9/43/latest/")
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# R -q -e 'options(repos = structure(c(CRAN = "https://cynkra-r-binaries-arm64.s3.eu-central-1.amazonaws.com/__linux__/rhel9/4.3/latest"))); remove.packages("mlr3filters"); pak::cache_delete(); pak::meta_clean(force=T); pak::pak("mlr3filters"); packageVersion("mlr3filters")'
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# R -q -e 'options(repos = structure(c(CRAN = "https://cloud.r-project.org"))); remove.packages("mlr3filters"); pak::cache_delete(); pak::meta_clean(force=T); pak::pak("mlr3filters"); packageVersion("mlr3filters")'
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# con <- gzcon(url(sprintf("%s/src/contrib/Meta/archive.rds",
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# c("CRAN" = "https://cynkra-r-binaries-arm64.s3.eu-central-1.amazonaws.com/__linux__/rhel9/4.3/latest")), "rb"))
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# readRDS(con)
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# remotes:::package_find_archives("mlr3filters", "https://cynkra-r-binaries-arm64.s3.eu-central-1.amazonaws.com/__linux__/rhel9/4.3/latest", verbose = T)
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31
04-create-archive-rds.sh
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31
04-create-archive-rds.sh
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#!/bin/bash
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# source: https://stackoverflow.com/a/55337537/4185785
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echo '
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library(plyr)
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generateArchive <- function(archiveDir) {
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archive <- file.info(list.files(archiveDir, recursive = TRUE, full.names = TRUE, pattern = "*.tar.gz"))
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archive$packageName <- basename(dirname(rownames(archive)))
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archive$packageFile <- basename(rownames(archive))
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archive <- dlply(archive, "packageName", function(x) {
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rownames(x) <- paste0(x$packageName, "/", x$packageFile)
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x$packageName <- NULL
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x$packageFile <- NULL
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x
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})
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}
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archiveDir <- "/root/__linux__/rhel9/4.3/latest/src/contrib/Archive"
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metaPath <- "/root/__linux__/rhel9/4.3/latest/src/contrib//Meta"
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dir.create(metaPath, showWarnings = FALSE)
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archive <- generateArchive(archiveDir)
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attr(archive, "split_type") <- NULL
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attr(archive, "split_labels") <- NULL
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saveRDS(archive, file.path(metaPath, "archive.rds"))
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' >/root/create-archive.R
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Rscript /root/create-archive.R
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# sync Meta/archive.rds
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aws s3 cp /root/__linux__/rhel9/4.3/latest/src/contrib/Meta/archive.rds s3://cynkra-r-binaries-arm64/__linux__/rhel9/4.3/latest/src/contrib/Meta/archive.rds --acl public-read
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