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 @@ AMR (for R) - 1.6.0.9058 + 1.6.0.9060 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index b9c388b0..d4050696 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -81,7 +81,7 @@ AMR (for R) - 1.6.0.9058 + 1.6.0.9060 diff --git a/docs/articles/datasets.html b/docs/articles/datasets.html index 473fffcc..be882ebb 100644 --- a/docs/articles/datasets.html +++ b/docs/articles/datasets.html @@ -39,7 +39,7 @@ AMR (for R) - 1.6.0.9058 + 1.6.0.9060 diff --git a/docs/articles/index.html b/docs/articles/index.html index 1adb1c9f..8c887e27 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.6.0.9058 + 1.6.0.9060 diff --git a/docs/authors.html b/docs/authors.html index 00a672e0..a96e8a77 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -81,7 +81,7 @@ AMR (for R) - 1.6.0.9058 + 1.6.0.9060 diff --git a/docs/index.html b/docs/index.html index 2ab72e55..39cb1286 100644 --- a/docs/index.html +++ b/docs/index.html @@ -42,7 +42,7 @@ AMR (for R) - 1.6.0.9058 + 1.6.0.9060 diff --git a/docs/news/index.html b/docs/news/index.html index 6d2e74f2..675accf7 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.6.0.9058 + 1.6.0.9060 @@ -236,9 +236,9 @@ Source: NEWS.md -
-

- Unreleased AMR 1.6.0.9058

+
+

+ Unreleased AMR 1.6.0.9060

Last updated: 22 May 2021 diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 14230cba..74046425 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: 2021-05-22T06:56Z +last_built: 2021-05-22T07:53Z 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 2012c6e5..3b5e745f 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.6.0.9058 + 1.6.0.9060

diff --git a/docs/survey.html b/docs/survey.html index 1ebc72cf..fb15c1df 100644 --- a/docs/survey.html +++ b/docs/survey.html @@ -81,7 +81,7 @@ AMR (for R) - 1.6.0.9058 + 1.6.0.9060