From a2fcfdff94c8725ab1517f49d40371a3246159b1 Mon Sep 17 00:00:00 2001 From: pat-s Date: Sat, 10 Aug 2024 13:23:39 +0200 Subject: [PATCH] don't install package in dockerfile --- .woodpecker/build.yaml | 12 ++++++------ docker/Dockerfile-redhat-8 | 1 - docker/Dockerfile-redhat-9 | 1 - docker/Dockerfile-ubuntu-2204 | 1 - docker/Dockerfile-ubuntu-2404 | 1 - 5 files changed, 6 insertions(+), 10 deletions(-) diff --git a/.woodpecker/build.yaml b/.woodpecker/build.yaml index fec0562..8689caf 100644 --- a/.woodpecker/build.yaml +++ b/.woodpecker/build.yaml @@ -6,13 +6,13 @@ skip_clone: true matrix: include: - PLATFORM: redhat-9 - BLOCK: 8302:18000 + BLOCK: 10265:18000 - PLATFORM: redhat-8 - BLOCK: 8107:18000 + BLOCK: 10147:18000 - PLATFORM: ubuntu-2404 - BLOCK: 8576:18000 + BLOCK: 10254:18000 - PLATFORM: ubuntu-2204 - BLOCK: 8723:18000 + BLOCK: 10337:18000 steps: - name: 'Build binaries (${PLATFORM}: ${BLOCK})' secrets: [red_hat_dev_pw, aws_access_key_id, aws_secret_access_key, pgpass, git_ro_token, GITHUB_PAT] @@ -32,7 +32,7 @@ steps: # download latest package version (avoid having to rebuild image every time) # rscript_startup arg: required to pass down global option to future workers https://github.com/HenrikBengtsson/future/issues/134#issuecomment-2245666169 - git clone https://pat-s:$$git_ro_token@git.devxy.io/devxy/arm64-r-binaries.git . - - rm -rf /mnt/cache/R-pkgs/00LOCK-arm64-r-binaries + - rm -rf /mnt/cache/R-pkgs/00LOCK-arm64-r-binaries /mnt/cache/R-pkgs/00LOCK-rBinaries - R -q -e 'pak::pak("dyfanjones/s3fs")' - R -q -e 'devtools::install(); packageVersion("rBinaries")' - mkdir -p /root/.R && /bin/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' @@ -42,7 +42,7 @@ steps: # more complicated system dependencies which pak cannot resolve - mkdir -p /mnt/cache/pkgcache /mnt/cache/R-pkgs /mnt/cache/ccache /mnt/cache/packages # set additional repos: important as otherwise some packages cannot be resolved (e.g. INLA). Also: setting our own binary repos so we can make use of them for dep installation at some point - - R -q -e 'options(crayon.enabled = TRUE, Ncpus = 4, future.globals.onReference = "error", repos = structure(c(getOption("repos"),INLA="https://inla.r-inla-download.org/R/stable"))); pkgs = tools::CRAN_package_db()[[1]][${BLOCK}]; pkgs = setdiff(pkgs, c("biplotbootGUI", "cncaGUI", "dynBiplotGUI", "ade4TkGUI", "BlockmodelingGUI", "cncaGUI", "EventDetectGUI", "irtGUI", "KappaGUI", "magickGUI", "miniGUI", "multibiplotGUI", "TextMiningGUI")); library(rBinaries); future::plan("multisession", workers = 4, rscript_startup = quote(options(crayon.enabled = TRUE))); foo = lapply(pkgs, function(x) build_binary_package(x, build_for_minor=FALSE, debug = FALSE, force = TRUE, platform = "${PLATFORM}"))' + - R -q -e 'options(crayon.enabled = TRUE, Ncpus = 4, future.globals.onReference = "error", repos = structure(c(getOption("repos"),INLA="https://inla.r-inla-download.org/R/stable"))); pkgs = tools::CRAN_package_db()[[1]][${BLOCK}]; pkgs = setdiff(pkgs, c("biplotbootGUI", "cncaGUI", "dynBiplotGUI", "ade4TkGUI", "BlockmodelingGUI", "cncaGUI", "EventDetectGUI", "irtGUI", "KappaGUI", "magickGUI", "miniGUI", "multibiplotGUI", "TextMiningGUI", "later")); library(rBinaries); future::plan("multisession", workers = 4, rscript_startup = quote(options(crayon.enabled = TRUE))); foo = lapply(pkgs, function(x) build_binary_package(x, build_for_minor=FALSE, debug = FALSE, force = T, platform = "${PLATFORM}"))' backend_options: kubernetes: ### PROD diff --git a/docker/Dockerfile-redhat-8 b/docker/Dockerfile-redhat-8 index 2f74740..c5bba9a 100644 --- a/docker/Dockerfile-redhat-8 +++ b/docker/Dockerfile-redhat-8 @@ -16,7 +16,6 @@ RUN R -q -e 'install.packages("pak", repos = sprintf("https://r-lib.github.io/p/ COPY . . RUN R -q -e 'Sys.setenv(PKG_SYSREQS = TRUE, PKG_SYSREQS_VERBOSE = TRUE, PKG_SYSREQS_PLATFORM = "redhat-8"); pak::pak()' -RUN R CMD INSTALL . RUN rm -rf arm-binaries-r CMD ["/bin/bash"] \ No newline at end of file diff --git a/docker/Dockerfile-redhat-9 b/docker/Dockerfile-redhat-9 index e80a955..e2e3ede 100644 --- a/docker/Dockerfile-redhat-9 +++ b/docker/Dockerfile-redhat-9 @@ -21,7 +21,6 @@ RUN R -q -e 'install.packages("pak", repos = sprintf("https://r-lib.github.io/p/ COPY . . RUN R -q -e 'Sys.setenv(PKG_SYSREQS = TRUE, PKG_SYSREQS_VERBOSE = TRUE, PKG_SYSREQS_PLATFORM = "redhat-9"); pak::pak()' -RUN R CMD INSTALL . RUN rm -rf arm-binaries-r CMD ["/bin/bash"] \ No newline at end of file diff --git a/docker/Dockerfile-ubuntu-2204 b/docker/Dockerfile-ubuntu-2204 index e2b841f..49419a2 100644 --- a/docker/Dockerfile-ubuntu-2204 +++ b/docker/Dockerfile-ubuntu-2204 @@ -13,7 +13,6 @@ RUN R -q -e 'install.packages("pak", repos = sprintf("https://r-lib.github.io/p/ COPY . . RUN R -q -e 'Sys.setenv(PKG_SYSREQS = TRUE, PKG_SYSREQS_VERBOSE = TRUE, PKG_SYSREQS_PLATFORM = "ubuntu-24.04"); pak::pak()' -RUN R CMD INSTALL . RUN rm -rf arm-binaries-r CMD ["/bin/bash"] \ No newline at end of file diff --git a/docker/Dockerfile-ubuntu-2404 b/docker/Dockerfile-ubuntu-2404 index 89e8ccf..c9f651c 100644 --- a/docker/Dockerfile-ubuntu-2404 +++ b/docker/Dockerfile-ubuntu-2404 @@ -13,7 +13,6 @@ RUN R -q -e 'install.packages("pak", repos = sprintf("https://r-lib.github.io/p/ COPY . . RUN R -q -e 'Sys.setenv(PKG_SYSREQS = TRUE, PKG_SYSREQS_VERBOSE = TRUE, PKG_SYSREQS_PLATFORM = "ubuntu-24.04"); pak::pak()' -RUN R CMD INSTALL . RUN rm -rf arm-binaries-r CMD ["/bin/bash"] \ No newline at end of file