diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml
index cbdc6067..2d49ae61 100644
--- a/.github/workflows/check.yaml
+++ b/.github/workflows/check.yaml
@@ -84,13 +84,7 @@ jobs:
R_REPOSITORIES: "https://cran.rstudio.com"
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
R_KEEP_PKG_SOURCE: yes
- R_CHECK_CRAN_INCOMING: false
- R_CHECK_FORCE_SUGGESTS: false
- R_CHECK_DEPENDS_ONLY: true
- R_CHECK_LENGTH_1_CONDITION: verbose
- R_CHECK_LENGTH_1_LOGIC2: verbose
- R_RUN_TINYTEST: true
-
+
steps:
- uses: actions/checkout@v2
@@ -101,11 +95,18 @@ jobs:
r-version: ${{ matrix.config.r }}
http-user-agent: ${{ matrix.config.http-user-agent }}
use-public-rspm: true
-
- - uses: r-lib/actions/setup-r-dependencies@v1
- with:
- extra-packages: rcmdcheck
+ - name: show file list
+ run: ls -lh
+ shell: bash
+
+ - name: Install dependencies
+ if: always()
+ run: |
+ install.packages("remotes")
+ remotes::install_local("data-raw/AMR_latest.tar.gz", dependencies = TRUE)
+ shell: Rscript {0}
+
- name: Show session info
if: always()
run: |
@@ -116,10 +117,15 @@ jobs:
- uses: r-lib/actions/check-r-package@v1
env:
+ _R_CHECK_CRAN_INCOMING_: false
+ _R_CHECK_FORCE_SUGGESTS_: false
+ _R_CHECK_DEPENDS_ONLY_: true
+ _R_CHECK_LENGTH_1_CONDITION_: verbose
+ _R_CHECK_LENGTH_1_LOGIC2_: verbose
+ R_RUN_TINYTEST: true
# during 'R CMD check', R_LIBS_USER will be overwritten, so:
R_LIBS_USER_GH_ACTIONS: ${{ env.R_LIBS_USER }}
-
- name: Show unit tests output
if: always()
run: find check -name 'tinytest.Rout*' -exec cat '{}' \; || true
diff --git a/.github/workflows/codecovr.yaml b/.github/workflows/codecovr.yaml
index 6dd0afaa..51c0205f 100644
--- a/.github/workflows/codecovr.yaml
+++ b/.github/workflows/codecovr.yaml
@@ -26,11 +26,11 @@
on:
push:
branches:
- - premaster
- - master
+ - development
+ - main
pull_request:
branches:
- - master
+ - main
name: code-coverage
diff --git a/.github/workflows/lintr.yaml b/.github/workflows/lintr.yaml
index eb42cd50..ed1acee1 100644
--- a/.github/workflows/lintr.yaml
+++ b/.github/workflows/lintr.yaml
@@ -26,11 +26,11 @@
on:
push:
branches:
- - premaster
- - master
+ - development
+ - main
pull_request:
branches:
- - master
+ - main
name: lintr
diff --git a/DESCRIPTION b/DESCRIPTION
index 00695030..bc50c7af 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,5 +1,5 @@
Package: AMR
-Version: 1.7.1.9041
+Version: 1.7.1.9043
Date: 2021-09-29
Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR)
diff --git a/NEWS.md b/NEWS.md
index 30cbbd0b..f32b55f6 100755
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-# `AMR` 1.7.1.9041
+# `AMR` 1.7.1.9043
## Last updated: 29 September 2021
### Breaking changes
diff --git a/data-raw/AMR_latest.tar.gz b/data-raw/AMR_latest.tar.gz
index fc4f27c6..0e736f6e 100644
Binary files a/data-raw/AMR_latest.tar.gz and b/data-raw/AMR_latest.tar.gz differ
diff --git a/docs/articles/datasets.html b/docs/articles/datasets.html
index 0ff18c37..9b7bd9e3 100644
--- a/docs/articles/datasets.html
+++ b/docs/articles/datasets.html
@@ -44,7 +44,7 @@
NEWS.md
-
AMR
1.7.1.9041AMR
1.7.1.9043