diff --git a/.github/workflows/codecovr.yaml b/.github/workflows/codecovr.yaml
index b43576f9..b4784214 100644
--- a/.github/workflows/codecovr.yaml
+++ b/.github/workflows/codecovr.yaml
@@ -60,7 +60,6 @@ jobs:
run: |
tar -xf data-raw/AMR_latest.tar.gz
Rscript -e "source('data-raw/_install_deps.R')"
- Rscript -e "install.packages('covr')"
shell: bash
- name: Show session info
@@ -76,10 +75,11 @@ jobs:
run: |
library(AMR)
library(tinytest)
+ library(covr)
source_files <- list.files("AMR/R", pattern = ".R$", full.names = TRUE)
test_files <- list.files("AMR/inst/tinytest", full.names = TRUE)
- cov <- covr::file_coverage(source_files = source_files, test_files = test_files, parent_env = asNamespace("AMR"), line_exclusions = list("R/atc_online.R", "R/mo_source.R", "R/translate.R", "R/resistance_predict.R", "R/aa_helper_functions.R", "R/aa_helper_pm_functions.R", "R/zzz.R"))
+ cov <- file_coverage(source_files = source_files, test_files = test_files, parent_env = asNamespace("AMR"), line_exclusions = list("AMR/R/atc_online.R", "AMR/R/mo_source.R", "AMR/R/translate.R", "AMR/R/resistance_predict.R", "AMR/R/aa_helper_functions.R", "AMR/R/aa_helper_pm_functions.R", "AMR/R/zzz.R"))
print(cov)
- attr(cov, which = "package") <- list(path = "") # until https://github.com/r-lib/covr/issues/478 is solved
- covr::codecov(cov, quiet = FALSE)
+ attr(cov, which = "package") <- list(path = ".") # until https://github.com/r-lib/covr/issues/478 is solved
+ codecov(coverage = cov, quiet = FALSE)
shell: Rscript {0}
diff --git a/DESCRIPTION b/DESCRIPTION
index ff5281d4..cb09bf45 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,5 +1,5 @@
Package: AMR
-Version: 1.6.0.9058
+Version: 1.6.0.9060
Date: 2021-05-22
Title: Antimicrobial Resistance Data Analysis
Authors@R: c(
@@ -43,6 +43,7 @@ Depends:
R (>= 3.0.0)
Suggests:
cleaner,
+ covr,
curl,
dplyr,
ggplot2,
diff --git a/NEWS.md b/NEWS.md
index 7e1e13fe..8a36c740 100755
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-# `AMR` 1.6.0.9058
+# `AMR` 1.6.0.9060
## Last updated: 22 May 2021
### Breaking change
diff --git a/data-raw/AMR_latest.tar.gz b/data-raw/AMR_latest.tar.gz
index 83595fab..4f2c044c 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 a783790a..41d76d4f 100644
--- a/data-raw/_install_deps.R
+++ b/data-raw/_install_deps.R
@@ -32,7 +32,7 @@ cat("Packages listed in Suggests:", paste(pkg_suggests, collapse = ", "), "\n")
to_install <- pkg_suggests[!pkg_suggests %in% rownames(utils::installed.packages())]
if (length(to_install) == 0) {
- message("Nothing to install")
+ message("\nNothing to install\n")
}
for (i in seq_len(length(to_install))) {
cat("Installing package", to_install[i], "\n")
@@ -45,7 +45,7 @@ for (i in seq_len(length(to_install))) {
to_update <- as.data.frame(utils::old.packages(repos = "https://cran.rstudio.com/"), stringsAsFactors = FALSE)
to_update <- to_update[which(to_update$Package %in% pkg_suggests), "Package", drop = TRUE]
if (length(to_update) == 0) {
- message("Nothing to update")
+ message("\nNothing to update\n")
}
for (i in seq_len(length(to_update))) {
cat("Updating package", to_update[i], "\n")
diff --git a/docs/404.html b/docs/404.html
index 59d99bde..99ba4b0d 100644
--- a/docs/404.html
+++ b/docs/404.html
@@ -81,7 +81,7 @@
NEWS.md
-
AMR
1.6.0.9058AMR
1.6.0.9060