From b2a08d056b548e2d26e2c68379fb1762635b42c2 Mon Sep 17 00:00:00 2001 From: "Matthijs S. Berends" Date: Fri, 11 Oct 2019 19:16:49 +0200 Subject: [PATCH] (v0.7.1.9103) add lintr to CI --- .gitlab-ci.yml | 22 +++++++++++++--------- DESCRIPTION | 2 +- NEWS.md | 2 +- docs/404.html | 2 +- docs/LICENSE-text.html | 2 +- docs/articles/index.html | 2 +- docs/authors.html | 2 +- docs/index.html | 2 +- docs/news/index.html | 8 ++++---- docs/reference/index.html | 2 +- git_merge.sh | 3 +-- 11 files changed, 26 insertions(+), 23 deletions(-) diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 356bbc8b..d6ec3501 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -19,8 +19,8 @@ # Visit our website for more info: https://msberends.gitlab.io/AMR. # # ==================================================================== # -# to check with R-Hub: -# chck <- rhub::check_for_cran(devtools::build(args = c('--no-build-vignettes'))) +# to do a full CRAN check with R-Hub: +# chck <- rhub::check(devtools::build(), platform = c('debian-clang-devel', 'debian-gcc-devel', 'fedora-clang-devel', 'fedora-gcc-devel', 'windows-x86_64-devel', 'debian-gcc-patched', 'solaris-x86-patched', 'debian-gcc-release', 'windows-x86_64-release', 'macos-elcapitan-release', 'windows-x86_64-oldrel')) stages: - build @@ -59,7 +59,7 @@ R-release: script: - Rscript -e 'sessionInfo()' # install missing and outdated packages - - Rscript -e 'source(".gitlab-ci.R"); gl_update_pkg_all(repos = "https://cran.rstudio.com", quiet = TRUE, install_pkgdown = TRUE)' + - Rscript -e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, install_lintr = TRUE)' # 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")' @@ -80,11 +80,11 @@ R-release: R-devel: stage: build image: rocker/r-devel - allow_failure: true + allow_failure: false script: - Rscriptdevel -e 'sessionInfo()' # install missing and outdated packages - - Rscriptdevel -e 'source(".gitlab-ci.R"); gl_update_pkg_all(repos = "https://cran.rstudio.com", quiet = TRUE, install_pkgdown = TRUE)' + - Rscriptdevel -e 'source(".gitlab-ci.R"); gl_update_pkg_all(repos = "https://cran.rstudio.com", quiet = TRUE)' # remove vignettes folder and get VignetteBuilder field out of DESCRIPTION file - rm -rf vignettes - Rscriptdevel -e 'd <- read.dcf("DESCRIPTION"); d[, colnames(d) == "VignetteBuilder"] <- NA; write.dcf(d, "DESCRIPTION")' @@ -116,8 +116,6 @@ coverage: - master script: - apt-get install --yes git - # install missing and outdated packages - - Rscript -e 'source(".gitlab-ci.R"); gl_update_pkg_all(repos = "https://cran.rstudio.com", quiet = TRUE, install_pkgdown = FALSE)' # codecov token is set in https://gitlab.com/msberends/AMR/settings/ci_cd - Rscript -e "cc <- covr::package_coverage(); covr::codecov(coverage = cc, token = '$codecov'); cat('Code coverage:', covr::percent_coverage(cc))" coverage: '/Code coverage: \d+\.\d+/' @@ -136,8 +134,14 @@ pages: lintr: stage: lint when: on_success + cache: + key: r350 + paths: + - installed_deps/ + policy: pull # no uploading after run + only: + - premaster + - master script: - # install missing and outdated packages - - Rscript -e 'source(".gitlab-ci.R"); gl_update_pkg_all(repos = "https://cran.rstudio.com", quiet = TRUE, install_pkgdown = FALSE, install_lintr = TRUE)' # check all syntax with lintr - Rscript -e 'lintr::lint_package()' diff --git a/DESCRIPTION b/DESCRIPTION index b480b8fc..d25d3fb6 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 0.7.1.9102 +Version: 0.7.1.9103 Date: 2019-10-11 Title: Antimicrobial Resistance Analysis Authors@R: c( diff --git a/NEWS.md b/NEWS.md index 0dc01b35..c21587b0 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 0.7.1.9102 +# AMR 0.7.1.9103 Last updated: 11-Oct-2019 ### Breaking diff --git a/docs/404.html b/docs/404.html index 88fba41a..f5f2c53d 100644 --- a/docs/404.html +++ b/docs/404.html @@ -84,7 +84,7 @@ AMR (for R) - 0.7.1.9102 + 0.7.1.9103 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 40cb0929..4e983b33 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -84,7 +84,7 @@ AMR (for R) - 0.7.1.9102 + 0.7.1.9103 diff --git a/docs/articles/index.html b/docs/articles/index.html index 0f541830..c2e28a27 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -84,7 +84,7 @@ AMR (for R) - 0.7.1.9102 + 0.7.1.9103 diff --git a/docs/authors.html b/docs/authors.html index 11e7a8fb..89a90bd4 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -84,7 +84,7 @@ AMR (for R) - 0.7.1.9102 + 0.7.1.9103 diff --git a/docs/index.html b/docs/index.html index 4adf543d..3fd71501 100644 --- a/docs/index.html +++ b/docs/index.html @@ -43,7 +43,7 @@ AMR (for R) - 0.7.1.9102 + 0.7.1.9103 diff --git a/docs/news/index.html b/docs/news/index.html index 371c8785..398a7995 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -84,7 +84,7 @@ AMR (for R) - 0.7.1.9102 + 0.7.1.9103 @@ -231,9 +231,9 @@ -
+

-AMR 0.7.1.9102 Unreleased +AMR 0.7.1.9103 Unreleased

Last updated: 11-Oct-2019

@@ -1292,7 +1292,7 @@ Using as.mo(..., allow_uncertain = 3)

Contents

    -
  • 0.7.1.9102
    • +
  • 0.7.1.9103
  • 0.7.1
  • 0.7.0
  • 0.6.1
    • diff --git a/docs/reference/index.html b/docs/reference/index.html index c2304aa4..f872d64f 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -84,7 +84,7 @@ AMR (for R) - 0.7.1.9102 + 0.7.1.9103
diff --git a/git_merge.sh b/git_merge.sh index 436f6552..027f15bc 100755 --- a/git_merge.sh +++ b/git_merge.sh @@ -30,8 +30,7 @@ case "$choice" in y|Y|j|J ) ;; * ) exit 1;; esac -Rscript -e "rhub::check(devtools::build(), platform = c('debian-clang-devel', 'debian-gcc-devel', 'fedora-clang-devel', 'fedora-gcc-devel', 'windows-x86_64-devel', 'debian-gcc-patched', 'solaris-x86-patched', 'debian-gcc-release', 'windows-x86_64-release', 'macos-elcapitan-release', -'windows-x86_64-oldrel'))" +Rscript -e "rhub::check(devtools::build(), platform = c('debian-clang-devel', 'debian-gcc-devel', 'fedora-clang-devel', 'fedora-gcc-devel', 'windows-x86_64-devel', 'debian-gcc-patched', 'solaris-x86-patched', 'debian-gcc-release', 'windows-x86_64-release', 'macos-elcapitan-release', 'windows-x86_64-oldrel'))" echo # and get stashed changes back