diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml index 31c01c61..64b8f0d1 100644 --- a/.github/workflows/check.yaml +++ b/.github/workflows/check.yaml @@ -77,36 +77,40 @@ jobs: - {os: windows-latest, r: '3.4', allowfail: false} - {os: windows-latest, r: '3.3', allowfail: false} - {os: windows-latest, r: '3.2', allowfail: false} - env: R_REMOTES_NO_ERRORS_FROM_WARNINGS: true RSPM: ${{ matrix.config.rspm }} R_REPOSITORIES: "https://cran.rstudio.com" - GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} - R_KEEP_PKG_SOURCE: yes - + steps: - uses: actions/checkout@v2 - - uses: r-lib/actions/setup-pandoc@v1 - - uses: r-lib/actions/setup-r@v1 with: r-version: ${{ matrix.config.r }} - http-user-agent: ${{ matrix.config.http-user-agent }} - use-public-rspm: true - - - name: show file list - run: ls -lh - shell: bash - - - name: Install dependencies + + - name: Install Linux dependencies + if: runner.os == 'Linux' + # update the below with sysreqs::sysreqs("DESCRIPTION") and check the "DEB" entries (for Ubuntu). + # we don't want to depend on the sysreqs pkg here, as it requires quite a recent R version + # as of May 2021: https://sysreqs.r-hub.io/pkg/AMR,R,cleaner,curl,dplyr,ggplot2,ggtext,knitr,microbenchmark,pillar,readxl,rmarkdown,rstudioapi,rvest,skimr,tidyr,tinytest,xml2,backports,crayon,rlang,vctrs,evaluate,highr,markdown,stringr,yaml,xfun,cli,ellipsis,fansi,lifecycle,utf8,glue,mime,magrittr,stringi,generics,R6,tibble,tidyselect,pkgconfig,purrr,digest,gtable,isoband,MASS,mgcv,scales,withr,nlme,Matrix,farver,labeling,munsell,RColorBrewer,viridisLite,lattice,colorspace,gridtext,Rcpp,RCurl,png,jpeg,bitops,cellranger,progress,rematch,hms,prettyunits,htmltools,jsonlite,tinytex,base64enc,httr,selectr,openssl,askpass,sys,repr,cpp11 + run: | + sudo apt install -y libssl-dev pandoc pandoc-citeproc libxml2-dev libicu-dev libcurl4-openssl-dev libpng-dev + - 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: + path: ${{ env.R_LIBS_USER }} + key: ${{ matrix.config.os }}-r-${{ matrix.config.r }}-v4 + + - name: Unpack AMR and install R dependencies if: always() run: | - install.packages("remotes", repos = c("https://cloud.r-project.org", "https://cran.rstudio.com")) - remotes::install_local("data-raw/AMR_latest.tar.gz", dependencies = TRUE) - shell: Rscript {0} - + tar -xf data-raw/AMR_latest.tar.gz + Rscript -e "source('data-raw/_install_deps.R')" + shell: bash + - name: Show session info if: always() run: | @@ -114,26 +118,43 @@ jobs: utils::sessionInfo() as.data.frame(utils::installed.packages())[, "Version", drop = FALSE] shell: Rscript {0} - - - uses: r-lib/actions/check-r-package@v1 + + # # - name: Only keep vignettes on release version + # - name: Remove vignettes + # # if: matrix.config.r != 'release' + # if: always() + # # writing to DESCRIPTION2 and then moving to DESCRIPTION is required for R < 3.3 as writeLines() cannot overwrite + # run: | + # rm -rf AMR/vignettes + # Rscript -e "writeLines(readLines('AMR/DESCRIPTION')[!grepl('VignetteBuilder', readLines('AMR/DESCRIPTION'))], 'AMR/DESCRIPTION2')" + # rm AMR/DESCRIPTION + # mv AMR/DESCRIPTION2 AMR/DESCRIPTION + # shell: bash + + - name: Run R CMD check + if: always() env: _R_CHECK_CRAN_INCOMING_: false _R_CHECK_FORCE_SUGGESTS_: false _R_CHECK_DEPENDS_ONLY_: true _R_CHECK_LENGTH_1_CONDITION_: verbose _R_CHECK_LENGTH_1_LOGIC2_: verbose - R_RUN_TINYTEST: true # during 'R CMD check', R_LIBS_USER will be overwritten, so: R_LIBS_USER_GH_ACTIONS: ${{ env.R_LIBS_USER }} - - - name: Show unit tests output - if: always() - run: find check -name 'tinytest.Rout*' -exec cat '{}' \; || true + R_RUN_TINYTEST: true + run: | + R CMD check --no-manual --run-donttest --run-dontrun AMR shell: bash - - name: Upload check results + - name: Show unit tests output if: always() - uses: actions/upload-artifact@main + run: | + find . -name 'tinytest.Rout*' -exec cat '{}' \; || true + shell: bash + + - name: Upload artifacts + if: always() + uses: actions/upload-artifact@v2 with: - name: ${{ matrix.config.os }}-r-${{ matrix.config.r }}-artifacts - path: check + name: artifacts-${{ matrix.config.os }}-r${{ matrix.config.r }} + path: AMR.Rcheck diff --git a/DESCRIPTION b/DESCRIPTION index 24564087..c5a7b19d 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: AMR -Version: 1.7.1.9045 -Date: 2021-09-29 +Version: 1.7.1.9046 +Date: 2021-10-03 Title: Antimicrobial Resistance Data Analysis Description: Functions to simplify and standardise antimicrobial resistance (AMR) data analysis and to work with microbial and antimicrobial properties by diff --git a/NEWS.md b/NEWS.md index fc912cd3..61e9d4d8 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,5 @@ -# `AMR` 1.7.1.9045 -## Last updated: 29 September 2021 +# `AMR` 1.7.1.9046 +## Last updated: 3 October 2021 ### Breaking changes * Removed `p_symbol()` and all `filter_*()` functions (except for `filter_first_isolate()`), which were all deprecated in a previous package version diff --git a/data-raw/AMR_latest.tar.gz b/data-raw/AMR_latest.tar.gz index ecdb35b2..41eb9178 100644 Binary files a/data-raw/AMR_latest.tar.gz and b/data-raw/AMR_latest.tar.gz differ diff --git a/docs/articles/datasets.html b/docs/articles/datasets.html index ace6dfb1..b87b0c55 100644 --- a/docs/articles/datasets.html +++ b/docs/articles/datasets.html @@ -44,7 +44,7 @@ AMR (for R) - 1.7.1.9045 + 1.7.1.9046 @@ -190,7 +190,7 @@

Data sets for download / own use

-

29 September 2021

+

03 October 2021

Source: vignettes/datasets.Rmd diff --git a/docs/news/index.html b/docs/news/index.html index f2a49b7f..9a94dbb4 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -92,7 +92,7 @@ AMR (for R) - 1.7.1.9045 + 1.7.1.9046
@@ -240,12 +240,12 @@ Source: NEWS.md -
-

- Unreleased AMR 1.7.1.9045

-
+
+

+ Unreleased AMR 1.7.1.9046

+

-Last updated: 29 September 2021 +Last updated: 3 October 2021

diff --git a/git_development.sh b/git_development.sh index 9f7bd22c..87e648b4 100755 --- a/git_development.sh +++ b/git_development.sh @@ -127,7 +127,7 @@ echo "••••••••••••••••••••" echo "• Building package •" echo "••••••••••••••••••••" echo "• Building 'data-raw/AMR_latest.tar.gz'..." -Rscript -e "x <- devtools::build(path = 'data-raw', vignettes = TRUE, manual = TRUE, binary = FALSE, quiet = TRUE)" +Rscript -e "x <- devtools::build(path = 'data-raw', vignettes = TRUE, manual = FALSE, binary = FALSE, quiet = TRUE)" rm data-raw/AMR_latest.tar.gz mv data-raw/AMR_*.tar.gz data-raw/AMR_latest.tar.gz