mirror of
https://github.com/msberends/AMR.git
synced 2024-12-24 18:46:14 +01:00
unit test fix
This commit is contained in:
parent
0d67db4f32
commit
71db246d5c
3
.github/workflows/check-pr.yaml
vendored
3
.github/workflows/check-pr.yaml
vendored
@ -32,6 +32,9 @@ name: R-code-check-PR
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jobs:
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jobs:
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R-code-check-PR:
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R-code-check-PR:
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# do not run if we are the authors - the other checks will already run
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if: ${{ github.event.comment.author_association != 'MEMBER' && github.event.comment.author_association != 'OWNER' }}
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runs-on: ${{ matrix.config.os }}
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runs-on: ${{ matrix.config.os }}
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continue-on-error: ${{ matrix.config.allowfail }}
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continue-on-error: ${{ matrix.config.allowfail }}
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1
.github/workflows/check.yaml
vendored
1
.github/workflows/check.yaml
vendored
@ -131,6 +131,7 @@ jobs:
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_R_CHECK_LENGTH_1_LOGIC2_: verbose
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_R_CHECK_LENGTH_1_LOGIC2_: verbose
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# during 'R CMD check', R_LIBS_USER will be overwritten, so:
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# during 'R CMD check', R_LIBS_USER will be overwritten, so:
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R_LIBS_USER_GH_ACTIONS: ${{ env.R_LIBS_USER }}
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R_LIBS_USER_GH_ACTIONS: ${{ env.R_LIBS_USER }}
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# this is a required value to run the unit tests:
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R_RUN_TINYTEST: true
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R_RUN_TINYTEST: true
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run: |
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run: |
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cd ..
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cd ..
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42
.github/workflows/codecovr.yaml
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42
.github/workflows/codecovr.yaml
vendored
@ -33,54 +33,30 @@ name: code-coverage
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jobs:
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jobs:
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code-coverage:
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code-coverage:
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runs-on: macOS-latest
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runs-on: ubuntu-latest
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env:
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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CODECOV_TOKEN: ${{secrets.CODECOV_TOKEN}}
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steps:
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steps:
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- uses: actions/checkout@v3
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- uses: actions/checkout@v3
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- uses: r-lib/actions/setup-pandoc@v2
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- uses: r-lib/actions/setup-r@v2
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- uses: r-lib/actions/setup-r@v2
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with:
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with:
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r-version: release
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r-version: release
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# use RStudio Package Manager to quickly install packages
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- uses: r-lib/actions/setup-pandoc@v2
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use-public-rspm: true
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# with:
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# pandoc-version: '2.7.3' # The pandoc version to download (if necessary) and use.
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- name: Query dependencies
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- uses: r-lib/actions/setup-r-dependencies@v2
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# this will change once a week, so it will cache dependency updates
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run: |
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writeLines(paste(format(Sys.Date(), "week %V %Y"), sprintf("R-%i.%i", getRversion()$major, getRversion()$minor)), ".github/week-R-version")
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shell: Rscript {0}
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- name: Restore cached R packages
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# this step will add the step 'Post Restore cached R packages' on a succesful run
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uses: actions/cache@v2
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with:
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with:
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path: ${{ env.R_LIBS_USER }}
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extra-packages: any::covr
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key: ${{ matrix.config.os }}-${{ hashFiles('.github/week-R-version') }}-v4
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- name: Unpack AMR and install R dependencies
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run: |
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tar -xf data-raw/AMR_latest.tar.gz
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Rscript -e "source('data-raw/_install_deps.R')"
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shell: bash
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- name: Show session info
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run: |
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options(width = 100)
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utils::sessionInfo()
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as.data.frame(utils::installed.packages())[, "Version", drop = FALSE]
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shell: Rscript {0}
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- name: Test coverage
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- name: Test coverage
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env:
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env:
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CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
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R_LIBS_USER_GH_ACTIONS: ${{ env.R_LIBS_USER }}
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R_RUN_TINYTEST: true
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R_RUN_TINYTEST: true
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run: |
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run: |
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install.packages("covr", repos = "https://cran.rstudio.com/")
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library(AMR)
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library(tinytest)
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x <- covr::codecov(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"))
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x <- covr::codecov(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"))
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print(x)
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print(x)
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shell: Rscript {0}
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shell: Rscript {0}
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29
.github/workflows/lintr.yaml
vendored
29
.github/workflows/lintr.yaml
vendored
@ -33,34 +33,23 @@ name: lintr
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jobs:
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jobs:
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lintr:
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lintr:
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runs-on: macOS-latest
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runs-on: ubuntu-latest
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env:
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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steps:
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steps:
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- uses: actions/checkout@v3
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- uses: actions/checkout@v3
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- uses: r-lib/actions/setup-pandoc@v2
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- uses: r-lib/actions/setup-r@v2
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- uses: r-lib/actions/setup-r@v2
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- name: Query dependencies
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run: |
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install.packages('remotes')
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saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
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writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
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shell: Rscript {0}
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- name: Cache R packages
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uses: actions/cache@v2
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with:
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with:
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path: ${{ env.R_LIBS_USER }}
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r-version: release
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key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
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# use RStudio Package Manager to quickly install packages
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restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
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use-public-rspm: true
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- name: Install dependencies
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- uses: r-lib/actions/setup-r-dependencies@v2
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run: |
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with:
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install.packages(c("remotes"))
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extra-packages: any::lintr
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remotes::install_deps(dependencies = TRUE)
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remotes::install_cran("lintr")
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shell: Rscript {0}
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- name: Lint
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- name: Lint
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run: lintr::lint_package(linters = lintr::with_defaults(line_length_linter = NULL, trailing_whitespace_linter = NULL, object_name_linter = NULL, cyclocomp_linter = NULL, object_length_linter = lintr::object_length_linter(length = 50L)), exclusions = list("R/aa_helper_pm_functions.R"))
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run: lintr::lint_package(linters = lintr::with_defaults(line_length_linter = NULL, trailing_whitespace_linter = NULL, object_name_linter = NULL, cyclocomp_linter = NULL, object_length_linter = lintr::object_length_linter(length = 50L)), exclusions = list("R/aa_helper_pm_functions.R"))
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@ -1,5 +1,5 @@
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Package: AMR
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Package: AMR
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Version: 1.8.1.9034
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Version: 1.8.1.9039
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Date: 2022-08-28
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Date: 2022-08-28
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Title: Antimicrobial Resistance Data Analysis
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Title: Antimicrobial Resistance Data Analysis
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Description: Functions to simplify and standardise antimicrobial resistance (AMR)
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Description: Functions to simplify and standardise antimicrobial resistance (AMR)
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@ -42,7 +42,7 @@ Suggests:
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rvest,
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rvest,
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tinytest,
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tinytest,
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xml2
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xml2
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VignetteBuilder: knitr
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VignetteBuilder: knitr,rmarkdown
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URL: https://msberends.github.io/AMR/, https://github.com/msberends/AMR
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URL: https://msberends.github.io/AMR/, https://github.com/msberends/AMR
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BugReports: https://github.com/msberends/AMR/issues
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BugReports: https://github.com/msberends/AMR/issues
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License: GPL-2 | file LICENSE
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License: GPL-2 | file LICENSE
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2
NEWS.md
2
NEWS.md
@ -1,4 +1,4 @@
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# AMR 1.8.1.9034
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# AMR 1.8.1.9039
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### New
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### New
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* EUCAST 2022 and CLSI 2022 guidelines have been added for `as.rsi()`. EUCAST 2022 is now the new default guideline for all MIC and disks diffusion interpretations.
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* EUCAST 2022 and CLSI 2022 guidelines have been added for `as.rsi()`. EUCAST 2022 is now the new default guideline for all MIC and disks diffusion interpretations.
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@ -529,7 +529,7 @@ first_isolate <- function(x = NULL,
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}
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}
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if (!is.null(col_icu)) {
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if (!is.null(col_icu)) {
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if (icu_exclude == TRUE) {
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if (icu_exclude == TRUE) {
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message_("Excluding ", format(sum(!col_icu, na.rm = TRUE), big.mark = ","), " isolates from ICU.",
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message_("Excluding ", format(sum(col_icu, na.rm = TRUE), big.mark = ","), " isolates from ICU.",
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add_fn = font_black,
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add_fn = font_black,
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as_note = FALSE
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as_note = FALSE
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)
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)
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12
R/mo.R
12
R/mo.R
@ -204,12 +204,12 @@ as.mo <- function(x,
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))
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))
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}
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}
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reference_df <- repair_reference_df(reference_df)
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if (!is.null(reference_df) &&
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if (!is.null(reference_df) &&
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check_validity_mo_source(reference_df) &&
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check_validity_mo_source(reference_df) &&
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isFALSE(Becker) &&
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isFALSE(Becker) &&
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isFALSE(Lancefield) &&
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isFALSE(Lancefield) &&
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all(x %in% unlist(reference_df), na.rm = TRUE)) {
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all(x %in% reference_df[, 1, drop = TRUE], na.rm = TRUE)) {
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reference_df <- repair_reference_df(reference_df)
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suppressWarnings(
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suppressWarnings(
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y <- data.frame(x = x, stringsAsFactors = FALSE) %pm>%
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y <- data.frame(x = x, stringsAsFactors = FALSE) %pm>%
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pm_left_join(reference_df, by = "x") %pm>%
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pm_left_join(reference_df, by = "x") %pm>%
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@ -221,6 +221,7 @@ as.mo <- function(x,
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y <- x
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y <- x
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} else {
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} else {
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# will be checked for mo class in validation and uses exec_as.mo internally if necessary
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# will be checked for mo class in validation and uses exec_as.mo internally if necessary
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y <- mo_validate(
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y <- mo_validate(
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x = x, property = "mo",
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x = x, property = "mo",
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Becker = Becker, Lancefield = Lancefield,
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Becker = Becker, Lancefield = Lancefield,
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@ -420,7 +421,7 @@ exec_as.mo <- function(x,
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}
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}
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# all empty
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# all empty
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if (all(identical(trimws(x_input), "") | is.na(x_input) | length(x) == 0)) {
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if (all(identical(trimws(x_input), "") | is.na(x_input) | length(x) == 0, na.rm = TRUE)) {
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if (property == "mo") {
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if (property == "mo") {
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return(set_clean_class(rep(NA_character_, length(x_input)),
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return(set_clean_class(rep(NA_character_, length(x_input)),
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new_class = c("mo", "character")
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new_class = c("mo", "character")
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@ -428,7 +429,7 @@ exec_as.mo <- function(x,
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} else {
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} else {
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return(rep(NA_character_, length(x_input)))
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return(rep(NA_character_, length(x_input)))
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}
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}
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} else if (all(x %in% reference_df[, 1, drop = TRUE][[1]])) {
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} else if (all(x %in% reference_df[, 1, drop = TRUE], na.rm = TRUE)) {
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# all in reference df
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# all in reference df
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colnames(reference_df)[1] <- "x"
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colnames(reference_df)[1] <- "x"
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suppressWarnings(
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suppressWarnings(
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@ -2357,6 +2358,9 @@ replace_ignore_pattern <- function(x, ignore_pattern) {
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}
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}
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repair_reference_df <- function(reference_df) {
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repair_reference_df <- function(reference_df) {
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if (is.null(reference_df)) {
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return(NULL)
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}
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# has valid own reference_df
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# has valid own reference_df
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reference_df <- reference_df %pm>%
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reference_df <- reference_df %pm>%
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pm_filter(!is.na(mo))
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pm_filter(!is.na(mo))
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@ -26,7 +26,6 @@
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# some old R instances have trouble installing tinytest, so we ship it too
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# some old R instances have trouble installing tinytest, so we ship it too
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install.packages("data-raw/tinytest_1.3.1.tar.gz", dependencies = c("Depends", "Imports", "LinkingTo"))
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install.packages("data-raw/tinytest_1.3.1.tar.gz", dependencies = c("Depends", "Imports", "LinkingTo"))
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install.packages(getwd(), repos = NULL, type = "source")
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install.packages(getwd(), repos = NULL, type = "source")
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# install.packages("data-raw/AMR_latest.tar.gz", dependencies = FALSE)
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pkg_suggests <- gsub(
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pkg_suggests <- gsub(
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"[^a-zA-Z0-9]+", "",
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"[^a-zA-Z0-9]+", "",
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@ -475,6 +475,11 @@ rm(current_globalenv)
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devtools::load_all(quiet = TRUE)
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devtools::load_all(quiet = TRUE)
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# Update URLs -------------------------------------------------------------
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usethis::ui_info("Checking URLs for redirects")
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invisible(capture.output(urlchecker::url_update()))
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# Document pkg ------------------------------------------------------------
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# Document pkg ------------------------------------------------------------
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usethis::ui_info("Documenting package")
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usethis::ui_info("Documenting package")
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suppressMessages(devtools::document(quiet = TRUE))
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suppressMessages(devtools::document(quiet = TRUE))
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@ -1 +1 @@
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19af89838b60bc8549d4474609629e8d
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b57c9cc7380a233a2616a80e8e904a81
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@ -47,7 +47,7 @@ if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
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expect_warning(AMR:::get_column_abx(rename(example_isolates, thisone = AMX), amox = "thisone", tmp = "thisone", verbose = FALSE))
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expect_warning(AMR:::get_column_abx(rename(example_isolates, thisone = AMX), amox = "thisone", tmp = "thisone", verbose = FALSE))
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}
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}
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# we rely on "grouped_tbl" being a class of grouped tibbles, so implement a test that checks for this:
|
# we rely on "grouped_tbl" being a class of grouped tibbles, so run a test that checks for this:
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if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
|
if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
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expect_true(AMR:::is_null_or_grouped_tbl(example_isolates %>% group_by(ward)))
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expect_true(AMR:::is_null_or_grouped_tbl(example_isolates %>% group_by(ward)))
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}
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}
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@ -68,15 +68,15 @@ expect_true(ab_url("AMX") %like% "whocc.no")
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expect_warning(ab_url("ASP"))
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expect_warning(ab_url("ASP"))
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|
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expect_identical(
|
expect_identical(
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colnames(set_ab_names(example_isolates[, 20:25])),
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colnames(set_ab_names(example_isolates[, 17:22])),
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c("cefoxitin", "cefotaxime", "ceftazidime", "ceftriaxone", "gentamicin", "tobramycin")
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c("cefoxitin", "cefotaxime", "ceftazidime", "ceftriaxone", "gentamicin", "tobramycin")
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)
|
)
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expect_identical(
|
expect_identical(
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colnames(set_ab_names(example_isolates[, 20:25], language = "nl", snake_case = FALSE)),
|
colnames(set_ab_names(example_isolates[, 17:22], language = "nl", snake_case = FALSE)),
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c("Cefoxitine", "Cefotaxim", "Ceftazidim", "Ceftriaxon", "Gentamicine", "Tobramycine")
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c("Cefoxitine", "Cefotaxim", "Ceftazidim", "Ceftriaxon", "Gentamicine", "Tobramycine")
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)
|
)
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expect_identical(
|
expect_identical(
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colnames(set_ab_names(example_isolates[, 20:25], property = "atc")),
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colnames(set_ab_names(example_isolates[, 17:22], property = "atc")),
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c("J01DC01", "J01DD01", "J01DD02", "J01DD04", "J01GB03", "J01GB01")
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c("J01DC01", "J01DD01", "J01DD02", "J01DD04", "J01GB03", "J01GB01")
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)
|
)
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@ -79,7 +79,7 @@ if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
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combination = count_susceptible(CIP, GEN)
|
combination = count_susceptible(CIP, GEN)
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) %>%
|
) %>%
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pull(combination),
|
pull(combination),
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c(253, 465, 192, 558)
|
c(946, 428, 94)
|
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)
|
)
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|
|
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# count_df
|
# count_df
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|
@ -57,7 +57,6 @@ expect_identical(as.ab(antibiotics$name), antibiotics$ab)
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|||||||
datasets <- data(package = "AMR", envir = asNamespace("AMR"))$results[, "Item", drop = TRUE]
|
datasets <- data(package = "AMR", envir = asNamespace("AMR"))$results[, "Item", drop = TRUE]
|
||||||
for (i in seq_len(length(datasets))) {
|
for (i in seq_len(length(datasets))) {
|
||||||
dataset <- get(datasets[i], envir = asNamespace("AMR"))
|
dataset <- get(datasets[i], envir = asNamespace("AMR"))
|
||||||
expect_identical(class(dataset), "data.frame")
|
|
||||||
expect_identical(AMR:::dataset_UTF8_to_ASCII(dataset), dataset, info = datasets[i])
|
expect_identical(AMR:::dataset_UTF8_to_ASCII(dataset), dataset, info = datasets[i])
|
||||||
}
|
}
|
||||||
|
|
||||||
|
@ -75,7 +75,7 @@ expect_equal(
|
|||||||
),
|
),
|
||||||
na.rm = TRUE
|
na.rm = TRUE
|
||||||
),
|
),
|
||||||
941
|
942
|
||||||
)
|
)
|
||||||
|
|
||||||
# set 1500 random observations to be of specimen type 'Urine'
|
# set 1500 random observations to be of specimen type 'Urine'
|
||||||
@ -160,7 +160,7 @@ if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
|
|||||||
|
|
||||||
# support for WHONET
|
# support for WHONET
|
||||||
expect_message(example_isolates %>%
|
expect_message(example_isolates %>%
|
||||||
select(-patient_id) %>%
|
select(-patient) %>%
|
||||||
mutate(
|
mutate(
|
||||||
`First name` = "test",
|
`First name` = "test",
|
||||||
`Last name` = "test",
|
`Last name` = "test",
|
||||||
|
@ -84,7 +84,7 @@ if (AMR:::pkg_is_available("dplyr", min_version = "1.0.0")) {
|
|||||||
combination_n = n_rsi(CIP, GEN)
|
combination_n = n_rsi(CIP, GEN)
|
||||||
) %>%
|
) %>%
|
||||||
pull(combination_n),
|
pull(combination_n),
|
||||||
c(305, 617, 241, 711)
|
c(1181, 577, 116)
|
||||||
)
|
)
|
||||||
|
|
||||||
# proportion_df
|
# proportion_df
|
||||||
|
@ -27,8 +27,9 @@
|
|||||||
if (identical(Sys.getenv("R_RUN_TINYTEST"), "true")) {
|
if (identical(Sys.getenv("R_RUN_TINYTEST"), "true")) {
|
||||||
# env var 'R_LIBS_USER' got overwritten during 'R CMD check' in GitHub Actions, so:
|
# env var 'R_LIBS_USER' got overwritten during 'R CMD check' in GitHub Actions, so:
|
||||||
.libPaths(c(Sys.getenv("R_LIBS_USER_GH_ACTIONS"), .libPaths()))
|
.libPaths(c(Sys.getenv("R_LIBS_USER_GH_ACTIONS"), .libPaths()))
|
||||||
if (AMR:::pkg_is_available("tinytest")) {
|
if (AMR:::pkg_is_available("tinytest", also_load = TRUE)) {
|
||||||
library(AMR)
|
library(AMR)
|
||||||
|
set_AMR_locale("English")
|
||||||
out <- test_package("AMR",
|
out <- test_package("AMR",
|
||||||
testdir = ifelse(AMR:::dir.exists("inst/tinytest"),
|
testdir = ifelse(AMR:::dir.exists("inst/tinytest"),
|
||||||
"inst/tinytest",
|
"inst/tinytest",
|
||||||
@ -37,7 +38,7 @@ if (identical(Sys.getenv("R_RUN_TINYTEST"), "true")) {
|
|||||||
verbose = 99,
|
verbose = 99,
|
||||||
color = FALSE
|
color = FALSE
|
||||||
)
|
)
|
||||||
cat("SUMMARY:\n")
|
cat("\n\nSUMMARY:\n")
|
||||||
print(summary(out))
|
print(summary(out))
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
Loading…
Reference in New Issue
Block a user