From df583bcf375ef24d32f2f6544436df58d7b2d55b Mon Sep 17 00:00:00 2001 From: pat-s Date: Sat, 14 Sep 2024 17:43:45 +0200 Subject: [PATCH] use pak devel, test platform auto-detection --- .woodpecker/warm_up_process_cran_updates.yaml | 2 +- R/install-deps.R | 12 ++++++------ docker/Dockerfile-alpine-320 | 3 ++- docker/Dockerfile-redhat-8 | 2 +- docker/Dockerfile-redhat-9 | 2 +- docker/Dockerfile-ubuntu-2204 | 2 +- docker/Dockerfile-ubuntu-2404 | 2 +- 7 files changed, 13 insertions(+), 12 deletions(-) diff --git a/.woodpecker/warm_up_process_cran_updates.yaml b/.woodpecker/warm_up_process_cran_updates.yaml index 1c0a04b..09edc75 100644 --- a/.woodpecker/warm_up_process_cran_updates.yaml +++ b/.woodpecker/warm_up_process_cran_updates.yaml @@ -30,7 +30,7 @@ steps: image: busybox:latest failure: ignore commands: - - sleep 200 + - sleep 10 - echo "Warmed Up" backend_options: diff --git a/R/install-deps.R b/R/install-deps.R index c0833fb..4d5184c 100644 --- a/R/install-deps.R +++ b/R/install-deps.R @@ -22,15 +22,15 @@ install_package_system_dependencies <- function(package_name, } cli::cli_alert("{.fun install_package_system_dependencies}: Installing R package dependencies for {.pkg {package_name[1]}} with tag {.field {tail(tag, 1)}}.") - Sys.setenv(PKG_SYSREQS_PLATFORM = platform) + # Sys.setenv(PKG_SYSREQS_PLATFORM = platform) Sys.setenv(PKG_SYSREQS = TRUE) Sys.setenv(PKG_SYSREQS_VERBOSE = TRUE) # FIXME: https://github.com/r-lib/pak/issues/610 - if (grepl("rhel-9", pak::system_r_platform())) { - Sys.setenv(PKG_SYSREQS_PLATFORM = "redhat-9") - } else if (grepl("rhel-9", pak::system_r_platform())) { - Sys.setenv(PKG_SYSREQS_PLATFORM = "redhat-8") - } + # if (grepl("rhel-9", pak::system_r_platform())) { + # Sys.setenv(PKG_SYSREQS_PLATFORM = "redhat-9") + # } else if (grepl("rhel-9", pak::system_r_platform())) { + # Sys.setenv(PKG_SYSREQS_PLATFORM = "redhat-8") + # } if (deps_verbose) { pak::local_install_deps(sprintf("%s", local_clone_dir_single)) } else { diff --git a/docker/Dockerfile-alpine-320 b/docker/Dockerfile-alpine-320 index 109c5f9..961ecf9 100644 --- a/docker/Dockerfile-alpine-320 +++ b/docker/Dockerfile-alpine-320 @@ -33,7 +33,8 @@ RUN apk add -q --no-cache R-dev curl ca-certificates bash g++ tzdata openjdk17 t # https://github.com/RcppCore/Rcpp/issues/448#issuecomment-220148774 # LDFLAGS+=-fPIC -> arrow (https://github.com/r-hub/r-minimal/blob/main/examples/arrow/Dockerfile) # dbarts: CFLAGS += -flax-vector-conversions (https://github.com/vdorie/dbarts/issues/66) -RUN mkdir -p /root/.R && bash -c 'echo -e "CXX_STD = CXX14\nCFLAGS += -flax-vector-conversions\nLDFLAGS+=-fPIC\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' +# CXXFLAGS: -> Rcpp +RUN mkdir -p /root/.R && bash -c 'echo -e "CXX_STD = CXX14\nCXXFLAGS=-D__MUSL__\nCPPFLAGS=-D__MUSL__\nCFLAGS += -flax-vector-conversions\nLDFLAGS+=-fPIC\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' # R repos RUN bash -c 'echo -e "options(crayon.enabled = TRUE, Ncpus = ${NCPUS}, future.globals.onReference = NULL, repos = structure(c(CRAN = \"https://cloud.r-project.org\", INLA = \"https://inla.r-inla-download.org/R/stable\")))" > /root/.Rprofile' diff --git a/docker/Dockerfile-redhat-8 b/docker/Dockerfile-redhat-8 index 8220709..c995572 100644 --- a/docker/Dockerfile-redhat-8 +++ b/docker/Dockerfile-redhat-8 @@ -28,7 +28,7 @@ RUN curl -q -L -O https://sourceforge.net/projects/mcmc-jags/files/JAGS/4.x/Sour ### INSTALL R RUN curl -O "https://devxy-r-builds.s3.eu-central-2.amazonaws.com/el8/R-${R_VERSION}-1-1.$(arch).rpm" RUN dnf install -q -y "R-${R_VERSION}-1-1.$(arch).rpm" && rm "R-${R_VERSION}-1-1.$(arch).rpm" -RUN R -q -e 'install.packages("pak", repos = sprintf("https://r-lib.github.io/p/pak/stable/%s/%s/%s", .Platform$pkgType, R.Version()$os, R.Version()$arch))' +RUN R -q -e 'install.packages("pak", repos = sprintf("https://r-lib.github.io/p/pak/devel/%s/%s/%s", .Platform$pkgType, R.Version()$os, R.Version()$arch))' ### Makevars # dbarts: CFLAGS += -flax-vector-conversions (https://github.com/vdorie/dbarts/issues/66) diff --git a/docker/Dockerfile-redhat-9 b/docker/Dockerfile-redhat-9 index 017f440..4f80fba 100644 --- a/docker/Dockerfile-redhat-9 +++ b/docker/Dockerfile-redhat-9 @@ -28,7 +28,7 @@ RUN curl -q -L -O https://sourceforge.net/projects/mcmc-jags/files/JAGS/4.x/Sour ### INSTALL R RUN curl -O "https://devxy-r-builds.s3.eu-central-2.amazonaws.com/el9/R-${R_VERSION}-1-1.$(arch).rpm" RUN dnf install -q -y "R-${R_VERSION}-1-1.$(arch).rpm" && rm "R-${R_VERSION}-1-1.$(arch).rpm" -RUN R -q -e 'install.packages("pak", repos = sprintf("https://r-lib.github.io/p/pak/stable/%s/%s/%s", .Platform$pkgType, R.Version()$os, R.Version()$arch))' +RUN R -q -e 'install.packages("pak", repos = sprintf("https://r-lib.github.io/p/pak/devel/%s/%s/%s", .Platform$pkgType, R.Version()$os, R.Version()$arch))' ### Makevars # dbarts: CFLAGS += -flax-vector-conversions (https://github.com/vdorie/dbarts/issues/66) diff --git a/docker/Dockerfile-ubuntu-2204 b/docker/Dockerfile-ubuntu-2204 index c3e396e..94107d4 100644 --- a/docker/Dockerfile-ubuntu-2204 +++ b/docker/Dockerfile-ubuntu-2204 @@ -25,7 +25,7 @@ RUN curl -q -L -O https://sourceforge.net/projects/mcmc-jags/files/JAGS/4.x/Sour ### INSTALL R RUN curl -O "https://devxy-r-builds.s3.eu-central-2.amazonaws.com/2204/r-${R_VERSION}_1_$(dpkg --print-architecture).deb" RUN gdebi -n -qq "r-${R_VERSION}_1_$(dpkg --print-architecture).deb" && rm "r-${R_VERSION}_1_$(dpkg --print-architecture).deb" -RUN R -q -e 'install.packages("pak", repos = sprintf("https://r-lib.github.io/p/pak/stable/%s/%s/%s", .Platform$pkgType, R.Version()$os, R.Version()$arch))' +RUN R -q -e 'install.packages("pak", repos = sprintf("https://r-lib.github.io/p/pak/devel/%s/%s/%s", .Platform$pkgType, R.Version()$os, R.Version()$arch))' ### Makevars # dbarts: CFLAGS += -flax-vector-conversions (https://github.com/vdorie/dbarts/issues/66) diff --git a/docker/Dockerfile-ubuntu-2404 b/docker/Dockerfile-ubuntu-2404 index b11ae56..fcbedac 100644 --- a/docker/Dockerfile-ubuntu-2404 +++ b/docker/Dockerfile-ubuntu-2404 @@ -25,7 +25,7 @@ RUN curl -q -L -O https://sourceforge.net/projects/mcmc-jags/files/JAGS/4.x/Sour ### INSTALL R RUN curl -O "https://devxy-r-builds.s3.eu-central-2.amazonaws.com/2404/r-${R_VERSION}_1_$(dpkg --print-architecture).deb" RUN gdebi -n -qq "r-${R_VERSION}_1_$(dpkg --print-architecture).deb" && rm "r-${R_VERSION}_1_$(dpkg --print-architecture).deb" -RUN R -q -e 'install.packages("pak", repos = sprintf("https://r-lib.github.io/p/pak/stable/%s/%s/%s", .Platform$pkgType, R.Version()$os, R.Version()$arch))' +RUN R -q -e 'install.packages("pak", repos = sprintf("https://r-lib.github.io/p/pak/devel/%s/%s/%s", .Platform$pkgType, R.Version()$os, R.Version()$arch))' ### Makevars # dbarts: CFLAGS += -flax-vector-conversions (https://github.com/vdorie/dbarts/issues/66)