diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml
index f68e56c5..29053e10 100644
--- a/.github/workflows/check.yaml
+++ b/.github/workflows/check.yaml
@@ -144,6 +144,7 @@ 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 }}
run: |
tar -xf data-raw/AMR_latest.tar.gz
rm -rf AMR/vignettes
@@ -158,10 +159,11 @@ 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 }}
run: |
tar -xf data-raw/AMR_latest.tar.gz
rm -rf AMR/vignettes
- R CMD check AMR --no-manual --as-cran --no-vignettes --library='/Users/runner/work/_temp/Library'
+ R CMD check AMR --no-manual --no-vignettes
shell: bash
- name: Show testthat output
diff --git a/DESCRIPTION b/DESCRIPTION
index f0d58ecb..85711e99 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,5 +1,5 @@
Package: AMR
-Version: 1.6.0.9028
+Version: 1.6.0.9030
Date: 2021-05-13
Title: Antimicrobial Resistance Data Analysis
Authors@R: c(
diff --git a/NEWS.md b/NEWS.md
index cc8b053d..465c8846 100755
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-# `AMR` 1.6.0.9028
+# `AMR` 1.6.0.9030
## Last updated: 13 May 2021
### New
diff --git a/data-raw/AMR_latest.tar.gz b/data-raw/AMR_latest.tar.gz
index bbb90353..c6468c07 100644
Binary files a/data-raw/AMR_latest.tar.gz and b/data-raw/AMR_latest.tar.gz differ
diff --git a/docs/404.html b/docs/404.html
index 2965cacd..33f02b6c 100644
--- a/docs/404.html
+++ b/docs/404.html
@@ -81,7 +81,7 @@
AMR (for R)
- 1.6.0.9028
+ 1.6.0.9030
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
index b6137c4d..425aa90d 100644
--- a/docs/LICENSE-text.html
+++ b/docs/LICENSE-text.html
@@ -81,7 +81,7 @@
AMR (for R)
- 1.6.0.9028
+ 1.6.0.9030
diff --git a/docs/articles/index.html b/docs/articles/index.html
index 0fffc9dc..1ae9f88a 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -81,7 +81,7 @@
AMR (for R)
- 1.6.0.9028
+ 1.6.0.9030
diff --git a/docs/authors.html b/docs/authors.html
index 6ed6a3c1..a726d9f2 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -81,7 +81,7 @@
AMR (for R)
- 1.6.0.9028
+ 1.6.0.9030
diff --git a/docs/index.html b/docs/index.html
index 06280279..8ea1630f 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -42,7 +42,7 @@
AMR (for R)
- 1.6.0.9028
+ 1.6.0.9030
diff --git a/docs/news/index.html b/docs/news/index.html
index 8a6912f1..5f95edd0 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -81,7 +81,7 @@
AMR (for R)
- 1.6.0.9028
+ 1.6.0.9030
@@ -236,9 +236,9 @@
Source: NEWS.md
-
-
+
+
Last updated: 13 May 2021
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 75389aea..f0c65a8b 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -12,7 +12,7 @@ articles:
datasets: datasets.html
resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html
-last_built: 2021-05-13T20:43Z
+last_built: 2021-05-13T21:04Z
urls:
reference: https://msberends.github.io/AMR//reference
article: https://msberends.github.io/AMR//articles
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 03e9e9c3..0996b8d7 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -81,7 +81,7 @@
AMR (for R)
- 1.6.0.9028
+ 1.6.0.9030
diff --git a/docs/survey.html b/docs/survey.html
index 2c068b0d..f52d7b9b 100644
--- a/docs/survey.html
+++ b/docs/survey.html
@@ -81,7 +81,7 @@
AMR (for R)
- 1.6.0.9028
+ 1.6.0.9030
diff --git a/tests/testthat.R b/tests/testthat.R
index bd43bc4c..42c8134b 100755
--- a/tests/testthat.R
+++ b/tests/testthat.R
@@ -27,7 +27,10 @@
# able to install it. Yet, we want basic R CMD CHECK's in those R versions
# as well, so only run unit tests in later R versions:
if (require("testthat", warn.conflicts = FALSE)) {
- library(testthat)
library(AMR)
+ # print non-base packages
+ print(as.data.frame(utils::installed.packages())[which(is.na(as.data.frame(utils::installed.packages())$Priority)),
+ "Version",
+ drop = FALSE])
test_check("AMR")
}
diff --git a/tests/testthat/test-mdro.R b/tests/testthat/test-mdro.R
index e17141b5..51698e29 100755
--- a/tests/testthat/test-mdro.R
+++ b/tests/testthat/test-mdro.R
@@ -119,7 +119,7 @@ test_that("mdro works", {
pza = sample_rsi(),
MFX = sample_rsi(),
KAN = sample_rsi())
- expect_gt(n_distinct(mdr_tb(x)), 2)
+ expect_gt(length(unique(mdr_tb(x))), 2)
# check the guideline by Magiorakos et al. (2012), the default guideline
stau <- data.frame(mo = c("S. aureus", "S. aureus", "S. aureus", "S. aureus"),
diff --git a/tests/testthat/test-resistance_predict.R b/tests/testthat/test-resistance_predict.R
index 87041d80..9b7f751e 100644
--- a/tests/testthat/test-resistance_predict.R
+++ b/tests/testthat/test-resistance_predict.R
@@ -48,10 +48,12 @@ test_that("prediction of rsi works", {
info = TRUE)))
pdf(NULL) # prevent Rplots.pdf being created
expect_silent(plot(x))
- expect_silent(ggplot_rsi_predict(x))
- expect_silent(ggplot(x))
- expect_error(ggplot_rsi_predict(example_isolates))
-
+ if (suppressWarnings(require("ggplot2"))) {
+ expect_silent(ggplot_rsi_predict(x))
+ expect_silent(ggplot(x))
+ expect_error(ggplot_rsi_predict(example_isolates))
+ }
+
expect_output(rsi_predict(x = subset(example_isolates, mo == "B_ESCHR_COLI"),
model = "binomial",
col_ab = "AMX",