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use pak devel, test platform auto-detection

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This commit is contained in:
Patrick Schratz 2024-09-14 17:43:45 +02:00
commit df583bcf37
Signed by: pat-s
GPG key ID: 3C6318841EF78925
7 changed files with 13 additions and 12 deletions
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2
.woodpecker/warm_up_process_cran_updates.yaml
View file

@ -30,7 +30,7 @@ steps:
image: busybox:latest
failure: ignore
commands:
- sleep 200
- sleep 10
- echo "Warmed Up"
backend_options:

12
R/install-deps.R
View file

@ -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 {

3
docker/Dockerfile-alpine-320
View file

@ -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'

2
docker/Dockerfile-redhat-8
View file

@ -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)

2
docker/Dockerfile-redhat-9
View file

@ -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)

2
docker/Dockerfile-ubuntu-2204
View file

@ -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)

2
docker/Dockerfile-ubuntu-2404
View file

@ -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)