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use pak stable

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This commit is contained in:
Patrick Schratz 2024-11-24 13:49:31 +01:00
commit 78a0b95e36
Signed by: pat-s
GPG key ID: 3C6318841EF78925
9 changed files with 11 additions and 11 deletions
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2
.woodpecker/build-alpine-320-amd64.yaml
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.woodpecker/build-alpine-320-arm64.yaml
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.woodpecker/build-redhat-8-amd64.yaml
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docker/Containerfile-alpine-320
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@ -44,7 +44,7 @@ RUN bash -c 'echo -e "PKG_SYSREQS=TRUE\nPKG_SYSREQS_VERBOSE=TRUE" > ~/.Renviron'
RUN curl -O "https://devxy-r-builds.s3.eu-central-2.amazonaws.com/alpine320/r-${R_VERSION}_1_$(arch).apk"
RUN apk add --allow-untrusted "r-${R_VERSION}_1_$(arch).apk" && rm "r-${R_VERSION}_1_$(arch).apk"
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()$arch))'
RUN R -q -e 'install.packages("pak", repos = sprintf("https://r-lib.github.io/p/pak/stable/%s/%s/%s", .Platform$pkgType, R.Version()$os, R.Version()$arch))'
# FIXME: switch to pak after https://github.com/r-lib/pak/issues/628
# deps from pak::pkg_deps(".")$package

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docker/Containerfile-redhat-8
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@ -29,7 +29,7 @@ RUN dnf install -y chromium
### INSTALL R
RUN curl -O "https://devxy-r-builds.s3.eu-central-2.amazonaws.com/el8/R-${R_VERSION}-1-1.$(arch).rpm"
RUN dnf install -q -y "R-${R_VERSION}-1-1.$(arch).rpm" && rm "R-${R_VERSION}-1-1.$(arch).rpm"
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()$arch))'
RUN R -q -e 'install.packages("pak", repos = sprintf("https://r-lib.github.io/p/pak/stable/%s/%s/%s", .Platform$pkgType, R.Version()$os, R.Version()$arch))'
### Makevars
# dbarts: CFLAGS += -flax-vector-conversions (https://github.com/vdorie/dbarts/issues/66)

2
docker/Containerfile-redhat-9
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@ -28,7 +28,7 @@ RUN dnf install -y chromium
### INSTALL R
RUN curl -O "https://devxy-r-builds.s3.eu-central-2.amazonaws.com/el9/R-${R_VERSION}-1-1.$(arch).rpm"
RUN dnf install -q -y "R-${R_VERSION}-1-1.$(arch).rpm" && rm "R-${R_VERSION}-1-1.$(arch).rpm"
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()$arch))'
RUN R -q -e 'install.packages("pak", repos = sprintf("https://r-lib.github.io/p/pak/stable/%s/%s/%s", .Platform$pkgType, R.Version()$os, R.Version()$arch))'
### Makevars
# dbarts: CFLAGS += -flax-vector-conversions (https://github.com/vdorie/dbarts/issues/66)

2
docker/Containerfile-shiny-app
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@ -1,7 +1,7 @@
FROM devxygmbh/r-alpine:4.4-3.20 AS build
# ARG GITHUB_PAT
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()$arch))'
RUN R -q -e 'install.packages("pak", repos = sprintf("https://r-lib.github.io/p/pak/stable/%s/%s/%s", .Platform$pkgType, R.Version()$os, R.Version()$arch))'
COPY --link ./DESCRIPTION .
COPY --link ./R ./R

6
docker/Containerfile-ubuntu-2204
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@ -29,18 +29,18 @@ RUN apt-get install -y software-properties-common && \
### INSTALL R
RUN curl -O "https://devxy-r-builds.s3.eu-central-2.amazonaws.com/2204/r-${R_VERSION}_1_$(dpkg --print-architecture).deb"
RUN gdebi -n -qq "r-${R_VERSION}_1_$(dpkg --print-architecture).deb" && rm "r-${R_VERSION}_1_$(dpkg --print-architecture).deb"
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()$arch))'
RUN R -q -e 'install.packages("pak", repos = sprintf("https://r-lib.github.io/p/pak/stable/%s/%s/%s", .Platform$pkgType, R.Version()$os, R.Version()$arch))'
### Makevars
# dbarts: CFLAGS += -flax-vector-conversions (https://github.com/vdorie/dbarts/issues/66)
# can't set ccache for gfortran because of https://gitlab.com/roigrp/solver/highs/-/issues/4
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'
RUN R -q -e "options(Ncpus = ${NCPUS}); packageVersion('pak'); pak::repo_get(); pak::pak(c('DBI', 'R6', 'RPostgres', 'Rcpp', 'askpass', 'base64enc', 'bit64', 'bit', 'blob', 'callr', 'cli', 'credentials', 'curl', 'data.table', 'desc', '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', 'cranlike', 'RSQLite', 'cachem', 'crayon', 'debugme', 'fastmap', 'memoise', 'progress', 'future.callr', 'dbplyr'))"
# R repos
RUN bash -c 'echo -e "options(encoding = \"UTF-8\", pkg.sysreqs_verbose = TRUE, crayon.enabled = TRUE, Ncpus = ${NCPUS}, future.globals.onReference = NULL, repos = structure(c(CRAN = \"https://cloud.r-project.org\", INLA = \"https://inla.r-inla-download.org/R/stable\")))" > ~/.Rprofile'
RUN R -q -e 'pak::pak(c("DBI", "R6", "RPostgres", "Rcpp", "askpass", "base64enc", "bit64", "bit", "blob", "callr", "cli", "credentials", "curl", "data.table", "desc", "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", "cranlike", "RSQLite", "cachem", "crayon", "debugme", "fastmap", "memoise", "progress", "future.callr", "dbplyr"))'
COPY --link . .
# remove secrets from COPY
RUN touch /.Renviron /.envrc && rm /.Renviron /.envrc

2
docker/Containerfile-ubuntu-2404
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@ -29,7 +29,7 @@ RUN apt-get install -y software-properties-common && \
### INSTALL R
RUN curl -O "https://devxy-r-builds.s3.eu-central-2.amazonaws.com/2404/r-${R_VERSION}_1_$(dpkg --print-architecture).deb"
RUN gdebi -n -qq "r-${R_VERSION}_1_$(dpkg --print-architecture).deb" && rm "r-${R_VERSION}_1_$(dpkg --print-architecture).deb"
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()$arch))'
RUN R -q -e 'install.packages("pak", repos = sprintf("https://r-lib.github.io/p/pak/stable/%s/%s/%s", .Platform$pkgType, R.Version()$os, R.Version()$arch))'
### Makevars
# dbarts: CFLAGS += -flax-vector-conversions (https://github.com/vdorie/dbarts/issues/66)