From f01d62ee5dfabd005f8a9bf66a0e3c69ecaf3b28 Mon Sep 17 00:00:00 2001 From: "Matthijs S. Berends" 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 ~/.Renviron #- Rscript -e '.libPaths()' # install missing and outdated packages - - Rscript -e 'Sys.setlocale("LC_ALL", "en_US.UTF-8"); sessionInfo()' - Rscript -e 'sessionInfo()' - Rscript -e 'source(".gitlab-ci.R");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(