mirror of
https://github.com/msberends/AMR.git
synced 2024-12-26 06:46:11 +01:00
103 lines
3.9 KiB
YAML
103 lines
3.9 KiB
YAML
# ==================================================================== #
|
|
# TITLE #
|
|
# Antimicrobial Resistance (AMR) Analysis #
|
|
# #
|
|
# SOURCE #
|
|
# https://gitlab.com/msberends/AMR #
|
|
# #
|
|
# LICENCE #
|
|
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
|
# #
|
|
# This R package is free software; you can freely use and distribute #
|
|
# it for both personal and commercial purposes under the terms of the #
|
|
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
|
|
# the Free Software Foundation. #
|
|
# #
|
|
# This R package was created for academic research and was publicly #
|
|
# released in the hope that it will be useful, but it comes WITHOUT #
|
|
# ANY WARRANTY OR LIABILITY. #
|
|
# Visit our website for more info: https://msberends.gitab.io/AMR. #
|
|
# ==================================================================== #
|
|
|
|
stages:
|
|
- build
|
|
- test
|
|
- deploy
|
|
|
|
# debian stretch only contains R 3.3...
|
|
image: debian:buster-slim
|
|
|
|
before_script:
|
|
- apt-get update -qq
|
|
# install dependencies for packages
|
|
- apt-get install -y wget locales libxml2-dev libssl-dev libcurl4-openssl-dev zlib1g-dev r-base > /dev/null
|
|
# recent pandoc
|
|
- wget --quiet https://github.com/jgm/pandoc/releases/download/2.6/pandoc-2.6-1-amd64.deb
|
|
- dpkg -i pandoc*.deb
|
|
- rm pandoc*.deb
|
|
# set R system language
|
|
- echo "LC_ALL=en_US.UTF-8" >> /etc/environment
|
|
- echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen
|
|
- echo "LANG=en_US.UTF-8" > /etc/locale.conf
|
|
- locale-gen
|
|
# cache R packages
|
|
- mkdir -p installed_deps
|
|
- echo 'R_LIBS="installed_deps"' > .Renviron
|
|
- echo 'R_LIBS_USER="installed_deps"' >> .Renviron
|
|
- echo 'R_LIBS_SITE="installed_deps"' >> .Renviron
|
|
# set language
|
|
- echo 'LANGUAGE="en_US.utf8"' >> .Renviron
|
|
- echo 'LANG="en_US.utf8"' >> .Renviron
|
|
- echo 'LANGUAGE="en_US.utf8"' > ~/.Renviron
|
|
- Rscript -e 'sessionInfo()'
|
|
# install missing and outdated packages
|
|
- Rscript -e 'source(".gitlab-ci.R"); gl_update_pkg_all(repos = "https://cran.rstudio.com", quiet = TRUE, install_pkgdown = TRUE)'
|
|
|
|
cache:
|
|
key: "$CI_COMMIT_REF_SLUG"
|
|
paths:
|
|
- installed_deps/
|
|
|
|
R:
|
|
stage: build
|
|
allow_failure: false
|
|
variables:
|
|
WARNINGS_ARE_ERRORS: 1
|
|
script:
|
|
- export WARNINGS_ARE_ERRORS=1
|
|
# remove vignettes folder and get VignetteBuilder field out of DESCRIPTION file
|
|
- rm -rf vignettes
|
|
- Rscript -e 'd <- read.dcf("DESCRIPTION"); d[, colnames(d) == "VignetteBuilder"] <- NA; write.dcf(d, "DESCRIPTION")'
|
|
# build package
|
|
- R CMD build . --no-build-vignettes --no-manual
|
|
- PKG_FILE_NAME=$(ls -1t *.tar.gz | head -n 1)
|
|
- R CMD check "${PKG_FILE_NAME}" --no-build-vignettes --no-manual --as-cran
|
|
artifacts:
|
|
paths:
|
|
- '*.Rcheck/*'
|
|
expire_in: '1 month'
|
|
|
|
coverage:
|
|
stage: test
|
|
allow_failure: true
|
|
when: on_success
|
|
only:
|
|
- premaster
|
|
- master
|
|
script:
|
|
- apt-get install --yes git
|
|
- Rscript -e 'cc <- covr::package_coverage(); covr::codecov(coverage = cc, token = "50ffa0aa-fee0-4f8b-a11d-8c7edc6d32ca"); cat("Code coverage:", covr::percent_coverage(cc))'
|
|
coverage: '/Code coverage: \d+\.\d+/'
|
|
|
|
pages:
|
|
stage: deploy
|
|
when: always
|
|
only:
|
|
- master
|
|
script:
|
|
- Rscript -e "devtools::install(build = TRUE, upgrade = FALSE)"
|
|
- R -e "pkgdown::build_site(examples = FALSE, lazy = TRUE, override = list(destination = 'public'))"
|
|
artifacts:
|
|
paths:
|
|
- public
|