From f01d62ee5dfabd005f8a9bf66a0e3c69ecaf3b28 Mon Sep 17 00:00:00 2001
From: "Matthijs S. Berends" <m.s.berends@umcg.nl>
Date: Sat, 5 Jan 2019 21:51:48 +0100
Subject: [PATCH] language

---
 .gitlab-ci.yml | 14 +++++---------
 DESCRIPTION    |  2 +-
 2 files changed, 6 insertions(+), 10 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 08439903..f7c6160b 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -30,7 +30,7 @@ image: debian:buster-slim
 before_script:
   - apt-get update -qq
   # 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
   - echo "LC_ALL=en_US.UTF-8" >> /etc/environment
   - 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_SITE="installed_deps"' >> .Renviron
   - echo 'LANGUAGE="en_US.utf8"' >> .Renviron
-  - echo 'LANG="en_US.utf8"' >> .Renviron
   - echo 'LANGUAGE="en_US.utf8"' > ~/.Renviron
   #- Rscript -e '.libPaths()'
   # install missing and outdated packages
-  - Rscript -e 'Sys.setlocale("LC_ALL", "en_US.UTF-8"); sessionInfo()'
   - Rscript -e 'sessionInfo()'
   - 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
   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-manual
+    - R CMD build . --no-build-vignettes --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
-    - R CMD check "${PKG_FILE_NAME}" --no-manual --as-cran
+    - R CMD check "${PKG_FILE_NAME}" --no-build-vignettes --no-manual --as-cran
   artifacts:
     paths:
       - '*.Rcheck/*'
diff --git a/DESCRIPTION b/DESCRIPTION
index e77a924e..f4327adc 100755
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: AMR
 Version: 0.5.0.9009
-Date: 2019-01-02
+Date: 2019-01-05
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(
     person(