diff --git a/.gitlab-ci.R b/.gitlab-ci.R index a1f2f16c0..baaece8f9 100644 --- a/.gitlab-ci.R +++ b/.gitlab-ci.R @@ -37,7 +37,7 @@ gl_update_pkg_all <- function(repos = "https://cran.rstudio.com", devtools::install_dev_deps(repos = repos, quiet = quiet, upgrade = TRUE) - cat("\nINSTALLED:\n\n") + cat("INSTALLED:\n") instld <- as.data.frame(installed.packages()) rownames(instld) <- NULL print(instld[, c("Package", "Version")]) diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index a18951cc7..41ae38f71 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -33,14 +33,14 @@ stages: image: debian:buster-slim before_script: - - apt-get -q update + - apt-get -qq update # install dependencies for packages - - apt-get -y -q install libxml2-dev libssl-dev libcurl4-openssl-dev zlib1g-dev pandoc r-base + - apt-get -y -qq install locales libxml2-dev libssl-dev libcurl4-openssl-dev zlib1g-dev pandoc r-base # 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 en_US.UTF-8 + - locale-gen # cache R packages - mkdir -p installed_deps - echo 'R_LIBS="installed_deps"' > .Renviron @@ -49,8 +49,6 @@ before_script: #- Rscript -e '.libPaths()' # install missing and outdated packages - Rscript -e 'source(".gitlab-ci.R"); gl_update_pkg_all(repos = "https://cran.rstudio.com", quiet = TRUE, install_pkgdown = TRUE)' - #- Rscript -e 'install.packages(c("devtools", "rlang"), repos = "https://cran.rstudio.com", quiet = TRUE)' - #- Rscript -e 'devtools::install_dev_deps(repos = "https://cran.rstudio.com", quiet = TRUE)' cache: key: "$CI_COMMIT_REF_SLUG" @@ -62,10 +60,11 @@ R 3: allow_failure: true script: # remove vignettes folder and get VignetteBuilder field out of DESCRIPTION file - - rm -rf vignettes - - Rscript -e 'd <- read.dcf("DESCRIPTION"); d[, colnames(d) == "VignetteBuilder"] <- NA; write.dcf(d, "DESCRIPTION")' + # - rm -rf vignettes + # - Rscript -e 'd <- read.dcf("DESCRIPTION"); d[, colnames(d) == "VignetteBuilder"] <- NA; write.dcf(d, "DESCRIPTION")' # build package - - R CMD build . --no-build-vignettes --no-manual + # - R CMD build . --no-build-vignettes --no-manual + - R CMD build . --no-manual - PKG_FILE_NAME=$(ls -1t *.tar.gz | head -n 1) - R CMD check "${PKG_FILE_NAME}" --no-build-vignettes --no-manual --as-cran artifacts: diff --git a/docs/news/index.html b/docs/news/index.html index f9eb0469b..d0166294e 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -592,7 +592,7 @@
n_rsi
to count cases where antibiotic test results were available, to be used in conjunction with dplyr::summarise
, see ?rsin_rsi
to count cases where antibiotic test results were available, to be used in conjunction with dplyr::summarise
, see ?rsiguess_bactid
to determine the ID of a microorganism based on genus/species or known abbreviations like MRSAguess_atc
to determine the ATC of an antibiotic based on name, trade name, or known abbreviationsfreq
to create frequency tables, with additional info in a header