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CI - test also on r-devel
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4
.gitignore
vendored
4
.gitignore
vendored
@ -18,8 +18,6 @@ vignettes/*.R
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.DS_Store
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.Rprofile
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^CRAN-RELEASE$
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git_premaster.sh
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git_merge.sh
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git_siteonly.sh
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git_*.sh
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packrat/lib*/
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packrat/src/
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@ -30,7 +30,7 @@ image: debian:buster-slim
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before_script:
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- apt-get update -qq
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# install dependencies for packages
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- apt-get install -y wget locales libxml2-dev libssl-dev libcurl4-openssl-dev zlib1g-dev r-base > /dev/null
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- apt-get install -y wget locales libxml2-dev libssl-dev libcurl4-openssl-dev zlib1g-dev > /dev/null
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# recent pandoc
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- wget --quiet https://github.com/jgm/pandoc/releases/download/2.6/pandoc-2.6-1-amd64.deb
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- dpkg -i pandoc*.deb
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@ -49,19 +49,41 @@ before_script:
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- echo 'LANGUAGE="en_US.utf8"' >> .Renviron
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- echo 'LANG="en_US.utf8"' >> .Renviron
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- echo 'LANGUAGE="en_US.utf8"' > ~/.Renviron
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- Rscript -e 'sessionInfo()'
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# install missing and outdated packages
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- Rscript -e 'source(".gitlab-ci.R"); gl_update_pkg_all(repos = "https://cran.rstudio.com", quiet = TRUE, install_pkgdown = TRUE)'
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cache:
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key: "$CI_COMMIT_REF_SLUG"
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paths:
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- installed_deps/
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R:
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R-release:
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stage: build
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image: debian:buster-slim
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allow_failure: false
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script:
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- apt-get install r-base > /dev/null
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- Rscript -e 'sessionInfo()'
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# install missing and outdated packages
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- Rscript -e 'source(".gitlab-ci.R"); gl_update_pkg_all(repos = "https://cran.rstudio.com", quiet = TRUE, install_pkgdown = TRUE)'
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# remove vignettes folder and get VignetteBuilder field out of DESCRIPTION file
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- rm -rf vignettes
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- Rscript -e 'd <- read.dcf("DESCRIPTION"); d[, colnames(d) == "VignetteBuilder"] <- NA; write.dcf(d, "DESCRIPTION")'
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# build package
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- R CMD build . --no-build-vignettes --no-manual
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- PKG_FILE_NAME=$(ls -1t *.tar.gz | head -n 1)
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- R CMD check "${PKG_FILE_NAME}" --no-build-vignettes --no-manual --as-cran
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artifacts:
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paths:
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- '*.Rcheck/*'
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expire_in: '1 month'
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R-devel:
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stage: build
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image: rocker:r-devel
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allow_failure: true
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script:
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- Rscript -e 'sessionInfo()'
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# install missing and outdated packages
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- Rscript -e 'source(".gitlab-ci.R"); gl_update_pkg_all(repos = "https://cran.rstudio.com", quiet = TRUE, install_pkgdown = TRUE)'
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# remove vignettes folder and get VignetteBuilder field out of DESCRIPTION file
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- rm -rf vignettes
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- Rscript -e 'd <- read.dcf("DESCRIPTION"); d[, colnames(d) == "VignetteBuilder"] <- NA; write.dcf(d, "DESCRIPTION")'
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@ -76,7 +98,12 @@ R:
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coverage:
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stage: test
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image: debian:buster-slim
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allow_failure: true
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script:
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- apt-get install r-base > /dev/null
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# install missing and outdated packages
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- Rscript -e 'source(".gitlab-ci.R"); gl_update_pkg_all(repos = "https://cran.rstudio.com", quiet = TRUE, install_pkgdown = TRUE)'
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when: on_success
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only:
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- premaster
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@ -89,6 +116,11 @@ coverage:
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pages:
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stage: deploy
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image: debian:buster-slim
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script:
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- apt-get install r-base > /dev/null
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# install missing and outdated packages
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- Rscript -e 'source(".gitlab-ci.R"); gl_update_pkg_all(repos = "https://cran.rstudio.com", quiet = TRUE, install_pkgdown = TRUE)'
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when: always
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only:
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- master
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@ -1,6 +1,6 @@
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Package: AMR
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Version: 0.6.1
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Date: 2019-03-28
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Version: 0.6.1.9001
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Date: 2019-03-29
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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person(
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