(v1.1.0.9002) CI fix

.gitlab-ci.yml

@@ -23,6 +23,7 @@
 # chck <- rhub::check(devtools::build(), platform = rhub::platforms()[!is.na(rhub::platforms()$`cran-name`), 'name'])
 
 stages:
+  - test
   - check
   - lint
   - website
@@ -53,9 +54,25 @@ before_script:
   - echo 'LANG="en_US.utf8"' >> .Renviron
   - echo 'LANGUAGE="en_US.utf8"' > ~/.Renviron
 
+R-release-test-only:
+  stage: test
+  when: always
+  allow_failure: false
+  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+    # install missing and outdated packages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,  install_lintr = TRUE)'
+    - Rscript -e 'devtools::test(stop_on_failure = FALSE)'
+  cache:
+    key: release_4_0
+    paths:
+      - installed_deps/
+    policy: pull # no uploading after run
+      
 R-release:
   stage: check
-  allow_failure: false
+  when: on_success
+  allow_failure: true
   script:
     - Rscript -e 'sessionInfo()'
     # install missing and outdated packages
@@ -80,6 +97,7 @@ R-release:
 
 R-devel:
   stage: check
+  when: on_success
   image: rocker/r-devel
   allow_failure: true
   script:
@@ -107,7 +125,7 @@ R-devel:
 lintr:
   stage: lint
   allow_failure: true
-  when: on_success
+  when: always
   cache:
     key: release_4_0
     paths:
@@ -122,6 +140,7 @@ lintr:
 
 pages:
   stage: website
+  allow_failure: true
   when: always
   only:
     - master
@@ -134,7 +153,7 @@ pages:
 codecovr:
   stage: coverage
   allow_failure: true
-  when: on_success
+  when: always
   cache:
     key: release_4_0
     paths:

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 1.1.0.9000
+Version: 1.1.0.9002
 Date: 2020-04-30
 Title: Antimicrobial Resistance Analysis
 Authors@R: c(

NEWS.md

@@ -1,4 +1,4 @@
-# AMR 1.1.0.9000
+# AMR 1.1.0.9002
 ## <small>Last updated: 30-Apr-2020</small>
 
 ### Changed

appveyor.yml

@@ -51,7 +51,7 @@ matrix:
   - R_VERSION: "devel"
   
 build_script:
-  - travis_tool.sh clean_library # turn off for caching, turn on for release of new R versions
+  # - travis_tool.sh clean_library # turn off for caching, turn on for release of new R versions
   - travis_tool.sh install_deps
 
 test_script:

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">1.1.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9002</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">1.1.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9002</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">1.1.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9002</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">1.1.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9002</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">1.1.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9002</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">1.1.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9002</span>
       </span>
     </div>
 
@@ -229,9 +229,9 @@
       <small>Source: <a href='https://gitlab.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
     </div>
 
-    <div id="amr-1-1-0-9000" class="section level1">
+    <div id="amr-1-1-0-9002" class="section level1">
-<h1 class="page-header" data-toc-text="1.1.0.9000">
+<h1 class="page-header" data-toc-text="1.1.0.9002">
-<a href="#amr-1-1-0-9000" class="anchor"></a>AMR 1.1.0.9000<small> Unreleased </small>
+<a href="#amr-1-1-0-9002" class="anchor"></a>AMR 1.1.0.9002<small> Unreleased </small>
 </h1>
 <div id="last-updated-30-apr-2020" class="section level2">
 <h2 class="hasAnchor">

docs/pkgdown.yml

@@ -10,7 +10,7 @@ articles:
   WHONET: WHONET.html
   benchmarks: benchmarks.html
   resistance_predict: resistance_predict.html
-last_built: 2020-04-30T07:04Z
+last_built: 2020-04-30T16:46Z
 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">1.1.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.1.0.9002</span>
       </span>
     </div>
 

git_premaster.sh

@@ -63,21 +63,20 @@ if [ -z "$3" ]; then
   # no version number set, so get latest tags to create it
   git pull --tags --quiet
   current_tag=`git describe --tags --abbrev=0 | sed 's/v//'`
-
-# current_commit=`git describe --tags | sed 's/.*-\(.*\)-.*/\1/'`
   if [ -z "current_tag" ]; then
     echo "FATAL - could not determine current tag"
     exit 1
   fi
-  current_tag_dots=`echo $current_tag | grep -o "[.]" | wc -l`
+  current_tag_full=`git describe --tags | sed 's/v//'`
-  if (( "$current_tag_dots" < 3 )); then
+  current_tag_dashes=`echo $current_tag_full | grep -o "[-]" | wc -l`
-    # contains two dots, so version number is like "1.0.0", commit nr is 0
+  if (( "$current_tag_dashes" < 1 )); then
+    # so version number is like "1.0.0", commit nr is 0
     current_commit=0
     echo "---------------"
     echo "Mind NEWS.md! Assuming sequence number 9000."
     echo "---------------"
   else
-    current_commit=`git describe --tags | sed 's/.*[.]//'`
+    current_commit=`git describe --tags | sed 's/.*-\(.*\)-.*/\1/'`
   fi
   if [ -z "current_commit" ]; then
     echo "FATAL - could not determine last commit index number"