From 4324337508be575b61aba07521bf448309d03411 Mon Sep 17 00:00:00 2001
From: "Matthijs S. Berends" <m.s.berends@umcg.nl>
Date: Sat, 5 Jan 2019 20:39:20 +0100
Subject: [PATCH] debian locale-gen

---
 .gitlab-ci.R         |  2 +-
 .gitlab-ci.yml       | 15 +++++++--------
 docs/news/index.html |  2 +-
 3 files changed, 9 insertions(+), 10 deletions(-)

diff --git a/.gitlab-ci.R b/.gitlab-ci.R
index a1f2f16c..baaece8f 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 a18951cc..41ae38f7 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   # install missing and outdated packages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 f9eb0469..d0166294 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -592,7 +592,7 @@
 <ul>
 <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>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_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>