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dr. M.S. (Matthijs) Berends 2019-01-05 21:51:48 +01:00
parent 2c798547bf
commit f01d62ee5d
2 changed files with 6 additions and 10 deletions
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14
.gitlab-ci.yml
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@ -30,7 +30,7 @@ image: debian:buster-slim
before_script: before_script:
- apt-get update -qq - apt-get update -qq
# install dependencies for packages # install dependencies for packages
- apt-get install -qq locales libxml2-dev libssl-dev libcurl4-openssl-dev zlib1g-dev pandoc r-base - apt-get install -qq locales libxml2-dev libssl-dev libcurl4-openssl-dev zlib1g-dev pandoc pandoc-citeproc r-base
# set R system language # set R system language
- echo "LC_ALL=en_US.UTF-8" >> /etc/environment - echo "LC_ALL=en_US.UTF-8" >> /etc/environment
- echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen - echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen
@ -42,11 +42,9 @@ before_script:
- echo 'R_LIBS_USER="installed_deps"' >> .Renviron - echo 'R_LIBS_USER="installed_deps"' >> .Renviron
- echo 'R_LIBS_SITE="installed_deps"' >> .Renviron - echo 'R_LIBS_SITE="installed_deps"' >> .Renviron
- echo 'LANGUAGE="en_US.utf8"' >> .Renviron - echo 'LANGUAGE="en_US.utf8"' >> .Renviron
- echo 'LANG="en_US.utf8"' >> .Renviron
- echo 'LANGUAGE="en_US.utf8"' > ~/.Renviron - echo 'LANGUAGE="en_US.utf8"' > ~/.Renviron
#- Rscript -e '.libPaths()' #- Rscript -e '.libPaths()'
# install missing and outdated packages # install missing and outdated packages
- Rscript -e 'Sys.setlocale("LC_ALL", "en_US.UTF-8"); sessionInfo()'
- Rscript -e 'sessionInfo()' - Rscript -e 'sessionInfo()'
- Rscript -e 'source(".gitlab-ci.R"); gl_update_pkg_all(repos = "https://cran.rstudio.com", quiet = TRUE, install_pkgdown = TRUE)' - Rscript -e 'source(".gitlab-ci.R"); gl_update_pkg_all(repos = "https://cran.rstudio.com", quiet = TRUE, install_pkgdown = TRUE)'
@ -60,14 +58,12 @@ R 3:
allow_failure: true allow_failure: true
script: script:
# remove vignettes folder and get VignetteBuilder field out of DESCRIPTION file # remove vignettes folder and get VignetteBuilder field out of DESCRIPTION file
# - rm -rf vignettes - rm -rf vignettes
# - Rscript -e 'd <- read.dcf("DESCRIPTION"); d[, colnames(d) == "VignetteBuilder"] <- NA; write.dcf(d, "DESCRIPTION")' - Rscript -e 'd <- read.dcf("DESCRIPTION"); d[, colnames(d) == "VignetteBuilder"] <- NA; write.dcf(d, "DESCRIPTION")'
# build package # build package
# - R CMD build . --no-build-vignettes --no-manual - R CMD build . --no-build-vignettes --no-manual
- R CMD build . --no-manual
- PKG_FILE_NAME=$(ls -1t *.tar.gz | head -n 1) - PKG_FILE_NAME=$(ls -1t *.tar.gz | head -n 1)
# - R CMD check "${PKG_FILE_NAME}" --no-build-vignettes --no-manual --as-cran - R CMD check "${PKG_FILE_NAME}" --no-build-vignettes --no-manual --as-cran
- R CMD check "${PKG_FILE_NAME}" --no-manual --as-cran
artifacts: artifacts:
paths: paths:
- '*.Rcheck/*' - '*.Rcheck/*'

2
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR Package: AMR
Version: 0.5.0.9009 Version: 0.5.0.9009
Date: 2019-01-02 Date: 2019-01-05
Title: Antimicrobial Resistance Analysis Title: Antimicrobial Resistance Analysis
Authors@R: c( Authors@R: c(
person( person(