(v1.1.0.9003) CI fix

.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

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: AMR
-Version: 1.1.0.9002
+Version: 1.1.0.9003
-Date: 2020-04-30
+Date: 2020-05-01
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(
     person(role = c("aut", "cre"), 

NEWS.md

@@ -1,5 +1,5 @@
-# AMR 1.1.0.9002
+# AMR 1.1.0.9003
-## <small>Last updated: 30-Apr-2020</small>
+## <small>Last updated: 01-May-2020</small>
 
 ### Changed
 * Small fix for some text input that could not be coerced as valid MIC values 

docs/404.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="https://msberends.gitlab.io/AMR/index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9002</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9003</span>
       </span>
     </div>
 

docs/LICENSE-text.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9002</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9003</span>
       </span>
     </div>
 

docs/articles/index.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9002</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9003</span>
       </span>
     </div>
 

docs/authors.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9002</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9003</span>
       </span>
     </div>
 

docs/index.html

@@ -43,7 +43,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9002</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9003</span>
       </span>
     </div>
 

docs/news/index.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9002</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9003</span>
       </span>
     </div>
 
@@ -229,13 +229,13 @@
       <small>Source: <a href='https://gitlab.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
     </div>
 
-    <div id="amr-1-1-0-9002" class="section level1">
+    <div id="amr-1-1-0-9003" class="section level1">
-<h1 class="page-header" data-toc-text="1.1.0.9002">
+<h1 class="page-header" data-toc-text="1.1.0.9003">
-<a href="#amr-1-1-0-9002" class="anchor"></a>AMR 1.1.0.9002<small> Unreleased </small>
+<a href="#amr-1-1-0-9003" class="anchor"></a>AMR 1.1.0.9003<small> Unreleased </small>
 </h1>
-<div id="last-updated-30-apr-2020" class="section level2">
+<div id="last-updated-01-may-2020" class="section level2">
 <h2 class="hasAnchor">
-<a href="#last-updated-30-apr-2020" class="anchor"></a><small>Last updated: 30-Apr-2020</small>
+<a href="#last-updated-01-may-2020" class="anchor"></a><small>Last updated: 01-May-2020</small>
 </h2>
 <div id="changed" class="section level3">
 <h3 class="hasAnchor">

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

docs/reference/index.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9002</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9003</span>
       </span>
     </div>
 

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")
-  
 })