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debian locale-gen

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dr. M.S. (Matthijs) Berends 2019-01-05 20:39:20 +01:00
parent 74ef20359a
commit 4324337508
3 changed files with 9 additions and 10 deletions
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2
.gitlab-ci.R
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@ -37,7 +37,7 @@ gl_update_pkg_all <- function(repos = "https://cran.rstudio.com",
devtools::install_dev_deps(repos = repos, quiet = quiet, upgrade = TRUE) devtools::install_dev_deps(repos = repos, quiet = quiet, upgrade = TRUE)
cat("\nINSTALLED:\n\n") cat("INSTALLED:\n")
instld <- as.data.frame(installed.packages()) instld <- as.data.frame(installed.packages())
rownames(instld) <- NULL rownames(instld) <- NULL
print(instld[, c("Package", "Version")]) print(instld[, c("Package", "Version")])

15
.gitlab-ci.yml
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@ -33,14 +33,14 @@ stages:
image: debian:buster-slim image: debian:buster-slim
before_script: before_script:
- apt-get -q update - apt-get -qq update
# install dependencies for packages # 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 # 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
- echo "LANG=en_US.UTF-8" > /etc/locale.conf - echo "LANG=en_US.UTF-8" > /etc/locale.conf
- locale-gen en_US.UTF-8 - locale-gen
# cache R packages # cache R packages
- mkdir -p installed_deps - mkdir -p installed_deps
- echo 'R_LIBS="installed_deps"' > .Renviron - echo 'R_LIBS="installed_deps"' > .Renviron
@ -49,8 +49,6 @@ before_script:
#- Rscript -e '.libPaths()' #- Rscript -e '.libPaths()'
# install missing and outdated packages # install missing and outdated packages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 '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: cache:
key: "$CI_COMMIT_REF_SLUG" key: "$CI_COMMIT_REF_SLUG"
@ -62,10 +60,11 @@ 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
artifacts: artifacts:

2
docs/news/index.html
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@ -592,7 +592,7 @@
<ul> <ul>
<li>Full support for Windows, Linux and macOS</li> <li>Full support for Windows, Linux and macOS</li>
<li>Full support for old R versions, only R-3.0.0 (April 2013) or later is needed (needed packages may have other dependencies)</li> <li>Full support for old R versions, only R-3.0.0 (April 2013) or later is needed (needed packages may have other dependencies)</li>
<li>Function <code>n_rsi</code> to count cases where antibiotic test results were available, to be used in conjunction with <code><a href="http://dplyr.tidyverse.org/reference/summarise.html">dplyr::summarise</a></code>, see ?rsi</li> <li>Function <code>n_rsi</code> to count cases where antibiotic test results were available, to be used in conjunction with <code><a href="https://www.rdocumentation.org/packages/dplyr/topics/summarise">dplyr::summarise</a></code>, see ?rsi</li>
<li>Function <code>guess_bactid</code> to <strong>determine the ID</strong> of a microorganism based on genus/species or known abbreviations like MRSA</li> <li>Function <code>guess_bactid</code> to <strong>determine the ID</strong> of a microorganism based on genus/species or known abbreviations like MRSA</li>
<li>Function <code>guess_atc</code> to <strong>determine the ATC</strong> of an antibiotic based on name, trade name, or known abbreviations</li> <li>Function <code>guess_atc</code> to <strong>determine the ATC</strong> of an antibiotic based on name, trade name, or known abbreviations</li>
<li>Function <code>freq</code> to create <strong>frequency tables</strong>, with additional info in a header</li> <li>Function <code>freq</code> to create <strong>frequency tables</strong>, with additional info in a header</li>