diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml
index 21b07c41..b9756395 100644
--- a/.github/workflows/check.yaml
+++ b/.github/workflows/check.yaml
@@ -89,18 +89,10 @@ jobs:
steps:
- uses: actions/checkout@v2
- - uses: r-lib/actions/setup-r@master
+ - uses: r-lib/actions/setup-r@v1
with:
r-version: ${{ matrix.config.r }}
- # - uses: r-lib/actions/setup-pandoc@master
-
- # - name: Query dependencies
- # if: matrix.config.r != '3.0'
- # run: |
- # saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
- # shell: Rscript {0}
-
- name: Install Linux dependencies
if: runner.os == 'Linux'
# update the below with sysreqs::sysreqs("DESCRIPTION") and check the "DEB" entries (for Ubuntu).
@@ -108,7 +100,8 @@ jobs:
run: |
sudo apt install -y libssl-dev pandoc pandoc-citeproc libxml2-dev libicu-dev libcurl4-openssl-dev
- - name: Cache R packages
+ - name: Restore cached R packages
+ # this step will add the step 'Post Restore cached R packages' on a succesful run
if: runner.os != 'Windows'
uses: actions/cache@v1
with:
@@ -122,7 +115,7 @@ jobs:
source("data-raw/_install_deps.R")
shell: Rscript {0}
- - name: Session info
+ - name: Show session info
run: |
options(width = 100)
utils::sessionInfo()
@@ -137,8 +130,9 @@ jobs:
_R_CHECK_DEPENDS_ONLY_: true
_R_CHECK_LENGTH_1_CONDITION_: verbose
_R_CHECK_LENGTH_1_LOGIC2_: verbose
- R_LIBS_USER: ${{ env.R_LIBS_USER }}
- R_TINYTEST: true
+ # during 'R CMD check', R_LIBS_USER will be overwritten, so:
+ R_LIBS_USER_GH_ACTIONS: ${{ env.R_LIBS_USER }}
+ R_RUN_TINYTEST: true
run: |
tar -xf data-raw/AMR_latest.tar.gz
rm -rf AMR/vignettes
@@ -153,8 +147,9 @@ jobs:
_R_CHECK_DEPENDS_ONLY_: true
_R_CHECK_LENGTH_1_CONDITION_: verbose
_R_CHECK_LENGTH_1_LOGIC2_: verbose
- R_LIBS_USER: ${{ env.R_LIBS_USER }}
- R_TINYTEST: true
+ # during 'R CMD check', R_LIBS_USER will be overwritten, so:
+ R_LIBS_USER_GH_ACTIONS: ${{ env.R_LIBS_USER }}
+ R_RUN_TINYTEST: true
run: |
tar -xf data-raw/AMR_latest.tar.gz
rm -rf AMR/vignettes
@@ -167,9 +162,9 @@ jobs:
find . -name 'tinytest.Rout*' -exec cat '{}' \; || true
shell: bash
- - name: Upload check results
- if: failure()
- uses: actions/upload-artifact@master
+ - name: Upload artifacts
+ if: always()
+ uses: actions/upload-artifact@v2
with:
- name: ${{ matrix.config.os }}-r${{ matrix.config.r }}-results
+ name: artifacts-${{ matrix.config.os }}-r${{ matrix.config.r }}
path: AMR.Rcheck
diff --git a/DESCRIPTION b/DESCRIPTION
index bd559c48..c73af0a0 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
Package: AMR
-Version: 1.6.0.9038
-Date: 2021-05-15
+Version: 1.6.0.9040
+Date: 2021-05-16
Title: Antimicrobial Resistance Data Analysis
Authors@R: c(
person(role = c("aut", "cre"),
@@ -57,7 +57,7 @@ Suggests:
skimr,
tidyr,
tinytest,
- xml2,
+ xml2
VignetteBuilder: knitr,rmarkdown
URL: https://msberends.github.io/AMR/, https://github.com/msberends/AMR
BugReports: https://github.com/msberends/AMR/issues
diff --git a/NEWS.md b/NEWS.md
index 12307163..1e0ddd7c 100755
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,5 +1,5 @@
-# `AMR` 1.6.0.9035
-## Last updated: 15 May 2021
+# `AMR` 1.6.0.9040
+## Last updated: 16 May 2021
### New
* Function `custom_eucast_rules()` that brings support for custom AMR rules in `eucast_rules()`
diff --git a/data-raw/AMR_latest.tar.gz b/data-raw/AMR_latest.tar.gz
index c7458b63..30419455 100644
Binary files a/data-raw/AMR_latest.tar.gz and b/data-raw/AMR_latest.tar.gz differ
diff --git a/data-raw/_install_deps.R b/data-raw/_install_deps.R
index a0c9c7d3..45101a3f 100644
--- a/data-raw/_install_deps.R
+++ b/data-raw/_install_deps.R
@@ -43,5 +43,3 @@ for (i in seq_len(length(to_update))) {
warning = function(w) message(w$message),
error = function(e) message(e$message))
}
-
-# saveRDS(to_update, ".github/depends.Rds", version = 2)
diff --git a/docs/404.html b/docs/404.html
index 6f3df78c..c233e496 100644
--- a/docs/404.html
+++ b/docs/404.html
@@ -81,7 +81,7 @@
AMR (for R)
- 1.6.0.9031
+ 1.6.0.9040
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
index e5c16bd8..585a1a73 100644
--- a/docs/LICENSE-text.html
+++ b/docs/LICENSE-text.html
@@ -81,7 +81,7 @@
AMR (for R)
- 1.6.0.9031
+ 1.6.0.9040
diff --git a/docs/articles/datasets.html b/docs/articles/datasets.html
index 83a910ce..14460448 100644
--- a/docs/articles/datasets.html
+++ b/docs/articles/datasets.html
@@ -39,7 +39,7 @@
AMR (for R)
- 1.6.0.9011
+ 1.6.0.9040
@@ -47,14 +47,14 @@