don't install package in dockerfile

.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

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"]

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"]

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"]

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"]