From 9fce546901d16ead803366197f68cce939d8f9da Mon Sep 17 00:00:00 2001 From: "Matthijs S. Berends" Date: Fri, 1 May 2020 09:14:32 +0200 Subject: [PATCH] (v1.1.0.9003) CI fix --- .gitlab-ci.yml | 27 +++++++++++++-------------- DESCRIPTION | 4 ++-- NEWS.md | 4 ++-- 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 | 12 ++++++------ docs/pkgdown.yml | 2 +- docs/reference/index.html | 2 +- tests/testthat/test-mo.R | 6 ------ 12 files changed, 30 insertions(+), 37 deletions(-) diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 31258517..afecc0cc 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -64,10 +64,9 @@ R-release-test-only: - Rscript -e 'source(".gitlab-ci.R"); gl_update_pkg_all(repos = "https://cran.rstudio.com", quiet = TRUE, install_pkgdown = TRUE, install_lintr = TRUE)' - Rscript -e 'devtools::test(stop_on_failure = FALSE)' cache: - key: release_4_0 + key: release paths: - installed_deps/ - policy: pull # no uploading after run R-release: stage: check @@ -91,7 +90,7 @@ R-release: - '*.Rcheck/*' expire_in: '1 month' cache: - key: release_4_0 + key: release paths: - installed_deps/ @@ -118,7 +117,7 @@ R-devel: - '*.Rcheck/*' expire_in: '1 month' cache: - key: devel_4_1 + key: devel paths: - installed_deps/ @@ -126,17 +125,17 @@ lintr: stage: lint allow_failure: true when: always - cache: - key: release_4_0 - paths: - - installed_deps/ - policy: pull # no uploading after run only: - premaster - master script: # check all syntax with lintr - Rscript -e 'lintr::lint_package()' + cache: + key: release + paths: + - installed_deps/ + policy: pull # no uploading after run pages: stage: website @@ -154,11 +153,6 @@ codecovr: stage: coverage allow_failure: true when: always - cache: - key: release_4_0 - paths: - - installed_deps/ - policy: pull # no uploading after run only: - premaster - master @@ -168,3 +162,8 @@ codecovr: # Sys.setenv(NOT_CRAN = 'true'), because otherwise skip_on_cran() will be applied on Covr too, resulting in extremely low coverage percentages - Rscript -e "Sys.setenv(NOT_CRAN = 'true'); cc <- covr::package_coverage(line_exclusions = list('R/atc_online.R', 'R/mo_history.R', 'R/mo_source.R', 'R/resistance_predict.R')); covr::codecov(coverage = cc, token = '$codecov'); cat('Code coverage:', covr::percent_coverage(cc))" coverage: '/Code coverage: \d+\.\d+/' + cache: + key: release + paths: + - installed_deps/ + policy: pull # no uploading after run diff --git a/DESCRIPTION b/DESCRIPTION index 5ec4f71f..a6f94aa7 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: AMR -Version: 1.1.0.9002 -Date: 2020-04-30 +Version: 1.1.0.9003 +Date: 2020-05-01 Title: Antimicrobial Resistance Analysis Authors@R: c( person(role = c("aut", "cre"), diff --git a/NEWS.md b/NEWS.md index 7e426054..1bab1f02 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,5 @@ -# AMR 1.1.0.9002 -## Last updated: 30-Apr-2020 +# AMR 1.1.0.9003 +## Last updated: 01-May-2020 ### Changed * Small fix for some text input that could not be coerced as valid MIC values diff --git a/docs/404.html b/docs/404.html index 0e9338be..e5e24707 100644 --- a/docs/404.html +++ b/docs/404.html @@ -81,7 +81,7 @@ AMR (for R) - 1.1.0.9002 + 1.1.0.9003 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 17bd49df..0e47b032 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -81,7 +81,7 @@ AMR (for R) - 1.1.0.9002 + 1.1.0.9003 diff --git a/docs/articles/index.html b/docs/articles/index.html index 9b8fee54..cf817da6 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.1.0.9002 + 1.1.0.9003 diff --git a/docs/authors.html b/docs/authors.html index e8f16353..0d136c18 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -81,7 +81,7 @@ AMR (for R) - 1.1.0.9002 + 1.1.0.9003 diff --git a/docs/index.html b/docs/index.html index 530bb727..d5bdb5d9 100644 --- a/docs/index.html +++ b/docs/index.html @@ -43,7 +43,7 @@ AMR (for R) - 1.1.0.9002 + 1.1.0.9003 diff --git a/docs/news/index.html b/docs/news/index.html index b3cb1c6b..750b6c1c 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.1.0.9002 + 1.1.0.9003 @@ -229,13 +229,13 @@ Source: NEWS.md -
-

-AMR 1.1.0.9002 Unreleased +
+

+AMR 1.1.0.9003 Unreleased

-
+

-Last updated: 30-Apr-2020 +Last updated: 01-May-2020

diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 80a4b612..ea06d7a7 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -10,7 +10,7 @@ articles: WHONET: WHONET.html benchmarks: benchmarks.html resistance_predict: resistance_predict.html -last_built: 2020-04-30T16:46Z +last_built: 2020-05-01T07:13Z urls: reference: https://msberends.gitlab.io/AMR/reference article: https://msberends.gitlab.io/AMR/articles diff --git a/docs/reference/index.html b/docs/reference/index.html index e237a3ad..f64c1dd6 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.1.0.9002 + 1.1.0.9003

diff --git a/tests/testthat/test-mo.R b/tests/testthat/test-mo.R index 9bdf8c7f..1e37f0dc 100644 --- a/tests/testthat/test-mo.R +++ b/tests/testthat/test-mo.R @@ -288,10 +288,4 @@ test_that("as.mo works", { expect_warning(x[[1]] <- "invalid code") expect_warning(c(x[1], "test")) - # joining on mo class - expect_identical(class(bind_rows(example_isolates, - example_isolates, - example_isolates)$mo), - "mo") - })