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.gitlab-ci.yml
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.gitlab-ci.yml
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variables:
CI_TOOLS: "https://svn.r-project.org/R/branches/tools4pkgs/src/library/tools/R/packages.R"
CRAN_MIRROR: "https://cloud.r-project.org"
BIOC_MIRROR: "https://bioconductor.org/packages/3.4/bioc"
_R_CHECK_FORCE_SUGGESTS_: "FALSE"
stages:
- dependencies
- build
- test
- integration
- deploy
mirror-packages:
stage: dependencies
tags:
- linux
image: docker.io/jangorecki/r-base-dev
script:
- mkdir -p bus/$CI_BUILD_NAME/cran/src/contrib
# mirror R dependencies
- Rscript -e 'source(Sys.getenv("CI_TOOLS")); mirror.packages(packages.dcf("DESCRIPTION", "all"), repos=c(Sys.getenv("CRAN_MIRROR"), Sys.getenv("BIOC_MIRROR")), repodir="bus/mirror-packages/cran")'
#- Rscript -e 'source(Sys.getenv("CI_TOOLS")); mirror.packages(type="win.binary", packages.dcf("DESCRIPTION", "all"), repos=c(Sys.getenv("CRAN_MIRROR"), Sys.getenv("BIOC_MIRROR")), repodir="bus/mirror-packages/cran")'
artifacts:
expire_in: 2 weeks
paths:
- bus
build:
stage: build
tags:
- linux
image: docker.io/jangorecki/r-builder
dependencies:
- mirror-packages
script:
- Rscript -e 'install.packages("knitr", repos=file.path("file:",normalizePath("bus/mirror-packages/cran")))'
- rm -r bus
- R CMD build .
- mkdir -p bus/$CI_BUILD_NAME/cran/src/contrib
- mv $(ls -1t data.table_*.tar.gz | head -n 1) bus/$CI_BUILD_NAME/cran/src/contrib/.
- Rscript -e 'tools::write_PACKAGES(contrib.url("bus/build/cran"), addFiles=TRUE)'
artifacts:
expire_in: 2 weeks
paths:
- bus
test-r-release: # R-release most comprehensive tests, force all suggests
stage: test
tags:
- linux
variables: # unlike CRAN
_R_CHECK_CRAN_INCOMING_: "FALSE"
_R_CHECK_CRAN_INCOMING_REMOTE_: "FALSE"
_R_CHECK_FORCE_SUGGESTS_: "TRUE"
OPENBLAS_MAIN_FREE: "1"
image: docker.io/jangorecki/r-builder
dependencies:
- mirror-packages
- build
script:
- mkdir -p bus/$CI_BUILD_NAME
- Rscript -e 'source(Sys.getenv("CI_TOOLS")); if (length(pkgs<-packages.dcf("DESCRIPTION", "all"))) install.packages(pkgs, repos=file.path("file:",normalizePath("bus/mirror-packages/cran")))'
- cd bus/$CI_BUILD_NAME
- Rscript -e 'file.copy(download.packages("data.table", repos=file.path("file:",normalizePath("../build/cran")))[,2], ".")'
- R CMD check $(ls -1t data.table_*.tar.gz | head -n 1)
artifacts:
expire_in: 2 weeks
when: always
paths:
- bus
test-r-release-cran: # R-release CRAN check
stage: test
tags:
- linux
image: docker.io/jangorecki/r-builder
variables:
_R_CHECK_CRAN_INCOMING_: "TRUE"
_R_CHECK_CRAN_INCOMING_REMOTE_: "TRUE"
dependencies:
- mirror-packages
- build
script:
- mkdir -p bus/$CI_BUILD_NAME
- Rscript -e 'source(Sys.getenv("CI_TOOLS")); if (length(pkgs<-packages.dcf("DESCRIPTION", "all"))) install.packages(pkgs, repos=file.path("file:",normalizePath("bus/mirror-packages/cran")))'
- cd bus/$CI_BUILD_NAME
- Rscript -e 'file.copy(download.packages("data.table", repos=file.path("file:",normalizePath("../build/cran")))[,2], ".")'
- R CMD check --as-cran $(ls -1t data.table_*.tar.gz | head -n 1)
artifacts:
expire_in: 2 weeks
when: always
paths:
- bus
test-r-devel-cran: # R-devel CRAN check
stage: test
tags:
- linux
image: docker.io/jangorecki/drd-pkg # image could be replaced with ubuntu-based builder, this one is based on rocker/drd which is debian
variables:
_R_CHECK_CRAN_INCOMING_: "TRUE"
_R_CHECK_CRAN_INCOMING_REMOTE_: "TRUE"
dependencies:
- mirror-packages
- build
script:
- mkdir -p bus/$CI_BUILD_NAME
- RDscript -e 'source(Sys.getenv("CI_TOOLS")); if (length(pkgs<-packages.dcf("DESCRIPTION", "all"))) install.packages(pkgs, repos=file.path("file:",normalizePath("bus/mirror-packages/cran")))'
- cd bus/$CI_BUILD_NAME
- Rscript -e 'file.copy(download.packages("data.table", repos=file.path("file:",normalizePath("../build/cran")))[,2], ".")'
- RD CMD check --as-cran --no-manual $(ls -1t data.table_*.tar.gz | head -n 1) # remove --no-manual when own image provided
artifacts:
expire_in: 2 weeks
when: always
paths:
- bus
allow_failure: true
test-r-release-vanilla: # check minimal installation, no suggested deps, no vignettes or manuals
stage: test
tags:
- linux
image: docker.io/jangorecki/r-base-dev
dependencies:
- mirror-packages
- build
script:
- mkdir -p bus/$CI_BUILD_NAME
- Rscript -e 'source(Sys.getenv("CI_TOOLS")); if (length(pkgs<-packages.dcf("DESCRIPTION"))) install.packages(pkgs, repos=file.path("file:",normalizePath("bus/mirror-packages/cran")))'
- cd bus/$CI_BUILD_NAME
- Rscript -e 'file.copy(download.packages("data.table", repos=file.path("file:",normalizePath("../build/cran")))[,2], ".")'
- R CMD check --no-manual --ignore-vignettes $(ls -1t data.table_*.tar.gz | head -n 1)
artifacts:
expire_in: 2 weeks
when: always
paths:
- bus
test-r-3.1.0-cran:
stage: test
tags:
- linux
image: docker.io/jangorecki/r-3.1.0
variables:
_R_CHECK_CRAN_INCOMING_: "TRUE"
_R_CHECK_CRAN_INCOMING_REMOTE_: "TRUE"
dependencies:
- mirror-packages
- build
script:
- mkdir -p bus/$CI_BUILD_NAME
- curl -O $CI_TOOLS
- R3script -e 'source("packages.R"); if (length(pkgs<-packages.dcf("DESCRIPTION", "all"))) install.packages(pkgs, repos=file.path("file:",normalizePath("bus/mirror-packages/cran")))'
- cd bus/$CI_BUILD_NAME
- R3script -e 'file.copy(download.packages("data.table", repos=file.path("file:",normalizePath("../build/cran")))[,2], ".")'
- R3 CMD check --no-manual --as-cran $(ls -1t data.table_*.tar.gz | head -n 1)
artifacts:
expire_in: 2 weeks
when: always
paths:
- bus
.test-r-release-windows:
stage: test
tags:
- windows # TODO provide machine
script: # TODO win scripts
- mkdir -p bus/$CI_BUILD_NAME
- Rscript -e 'source(Sys.getenv("CI_TOOLS")); if (length(pkgs<-packages.dcf("DESCRIPTION", "all"))) install.packages(pkgs, repos=file.path("file:",normalizePath("bus/mirror-packages/cran")))'
- cd bus/$CI_BUILD_NAME
- Rscript -e 'file.copy(download.packages("data.table", repos=file.path("file:",normalizePath("../build/cran")))[,2], ".")'
- R CMD build --no-manual --no-build-vignettes .
- R CMD check --no-manual --ignore-vignettes data.table_X.zip
# build windows binaries
- R CMD INSTALL --build data.table_X.zip
artifacts:
expire_in: 2 weeks
when: always
paths:
- bus
integration: # merging all artifacts so multiple deploy jobs can build same repo
stage: integration
tags:
- linux
only:
- gl-ci-upgrade
- master
image: docker.io/jangorecki/r-builder
dependencies:
- mirror-packages
- build
- test-r-release
- test-r-release-cran
- test-r-devel-cran
- test-r-release-vanilla
- test-r-3.1.0-cran
script:
- mkdir -p bus/$CI_BUILD_NAME
# integration helpers, not in tools4pkgs branch, for multi pkgs use: pkg<-strsplit(job, "-", fixed=TRUE)[[1L]][2L]
- echo 'test.jobs<-c("test-r-release"="data.table","test-r-release-cran"="data.table","test-r-devel-cran"="data.table","test-r-release-vanilla"="data.table","test-r-3.1.0-cran"="data.table")' > integration.R
- echo 'lib.copy<-function(lib.from, repodir="bus/integration/cran"){ pkgs.from<-list.dirs(lib.from, recursive=FALSE); pkgs.to<-list.dirs(lib.to<-file.path(repodir,"library"), recursive=FALSE); pkg.copy<-function(pkg.from, lib.to){ pkg<-basename(pkg.from); dir.create(file.path(lib.to, pkg), recursive=TRUE); lib.dirs<-intersect(c("html","doc"), all.lib.dirs<-list.dirs(pkg.from, full.names=FALSE)); ans1<-setNames(file.copy(file.path(pkg.from, lib.dirs), file.path(lib.to, pkg), recursive=TRUE), lib.dirs); lib.files<-setdiff(list.files(pkg.from), all.lib.dirs); ans2<-setNames(file.copy(file.path(pkg.from, lib.files), file.path(lib.to, pkg)), lib.files); all(ans1, ans2)}; pkgs.from.new<-pkgs.from[!basename(pkgs.from) %in% basename(pkgs.to)]; setNames(sapply(pkgs.from.new, pkg.copy, lib.to=lib.to), basename(pkgs.from.new)) }' >> integration.R
- echo 'doc.copy<-function(repodir="bus/integration/cran"){ cp1<-c("COPYING","AUTHORS","THANKS"); ans1<-setNames(file.copy(file.path(R.home("doc"), cp1), file.path(repodir, "doc", cp1)), cp1); cp2<-c("html","manual"); ans2<-setNames(file.copy(file.path(R.home("doc"), cp2), file.path(repodir,"doc"), recursive=TRUE), cp2); c(ans1, ans2) }' >> integration.R
- echo 'check.copy<-function(job, repodir="bus/integration/cran"){ dir.create(job.checks<-file.path(repodir, "web", "checks", pkg<-"data.table", job), recursive=TRUE); all(file.copy(file.path("bus", sprintf("%s/%s.Rcheck", job, pkg), c("00install.out","00check.log")), job.checks)) }' >> integration.R
- echo 'pdf.copy<-function(job, repodir="bus/integration/cran"){ dir.create(pkg.to<-file.path(repodir,"web","packages",pkg<-"data.table"), recursive=TRUE); file.copy(file.path("bus", job, sprintf("%s.Rcheck", pkg), sprintf("%s-manual.pdf",pkg)), to=file.path(pkg.to, sprintf("%s.pdf",pkg))) }' >> integration.R
- echo 'check.test<-function(job) { check<-readLines(file.path("bus", job, sprintf("%s.Rcheck", pkg<-"data.table"), "00check.log")); check[length(check)] }' >> integration.R
#- echo '' >> integration.R
# TODO: testing CRAN check results raise error so deploy wont start if there are check issues
- Rscript -e 'source("integration.R"); sapply(names(test.jobs), check.test, simplify=FALSE)'
# merge mirror-packages and R devel packages
- cp -R bus/mirror-packages/cran bus/$CI_BUILD_NAME/
- mkdir -p bus/$CI_BUILD_NAME/cran/library bus/$CI_BUILD_NAME/cran/doc
- mv $(ls -1t bus/build/cran/src/contrib/data.table_*.tar.gz | head -n 1) bus/$CI_BUILD_NAME/cran/src/contrib
- Rscript -e 'tools::write_PACKAGES(contrib.url("bus/integration/cran"), addFiles=TRUE)'
# install all pkgs to render html and double check successful installation of all devel packages
- mkdir -p /tmp/opencran/library /tmp/opencran/doc/html
- Rscript -e 'install.packages("data.table", dependencies=TRUE, lib="/tmp/opencran/library", repos=file.path("file:",normalizePath("bus/integration/cran")), INSTALL_opts="--html", quiet=TRUE)'
- Rscript -e 'sapply("data.table", packageVersion, lib.loc="/tmp/opencran/library", simplify=FALSE)'
# R docs, html, css, icons
- Rscript -e 'source("integration.R"); doc.copy(repodir="/tmp/opencran")'
# Update packages.html, rewrite file:/ to relative path
- Rscript -e 'setwd("/tmp/opencran/doc/html"); make.packages.html(lib.loc="../../library", docdir="/tmp/opencran/doc"); tmp<-readLines(f<-"/tmp/opencran/doc/html/packages.html"); writeLines(gsub("file:///../../library","../../library", tmp, fixed=TRUE), f)'
- mv /tmp/opencran/doc bus/integration/cran/
# library
- Rscript -e 'source("integration.R"); lib.copy(lib.from="/tmp/opencran/library")'
# web/checks/$pkg/$job: 00install.out, 00check.log
- Rscript -e 'source("integration.R"); sapply(names(test.jobs), check.copy)'
# web/packages - here is only single package
#- Rscript -e 'source("integration.R"); sapply(sprintf("test-%s-r-release", unique(test.jobs)), pdf.copy)'
- Rscript -e 'source("integration.R"); pdf.copy("test-r-release")'
# TODO: web/checks/check_results_$pkg.html
# https://github.com/wch/r-source/blob/trunk/src/library/tools/R/CRANtools.R
# TODO: web/packages/$pkg/index.html
artifacts:
expire_in: 2 weeks
paths:
- bus
pages:
stage: deploy
environment: production
tags:
- linux
only:
- gl-ci-upgrade
- master
image: docker.io/ubuntu
dependencies:
- integration
script:
- mkdir -p public
- cp -r bus/integration/cran/* public
- cat public/src/contrib/PACKAGES
artifacts:
expire_in: 2 weeks
paths:
- public