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	(v1.7.1.9041) new GH actions, branches rename
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							| @@ -23,16 +23,14 @@ | |||||||
| # how to conduct AMR data analysis: https://msberends.github.io/AMR/   # | # how to conduct AMR data analysis: https://msberends.github.io/AMR/   # | ||||||
| # ==================================================================== # | # ==================================================================== # | ||||||
|  |  | ||||||
| # This GitHub Actions file runs without ANY dependency, so works on all versions of R since R-3.0. |  | ||||||
|  |  | ||||||
| on: | on: | ||||||
|   push: |   push: | ||||||
|     branches: |     branches: | ||||||
|       - premaster |       - development | ||||||
|       - master |       - main | ||||||
|   pull_request: |   pull_request: | ||||||
|     branches: |     branches: | ||||||
|       - master |       - main | ||||||
|   schedule: |   schedule: | ||||||
|     # run a schedule everyday at 1 AM. |     # run a schedule everyday at 1 AM. | ||||||
|     # this is to check that all dependencies are still available (see R/zzz.R) |     # this is to check that all dependencies are still available (see R/zzz.R) | ||||||
| @@ -81,44 +79,34 @@ jobs: | |||||||
|           - {os: windows-latest, r: '3.2',     allowfail: false} |           - {os: windows-latest, r: '3.2',     allowfail: false} | ||||||
|  |  | ||||||
|     env: |     env: | ||||||
|       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true |       R_REMOTES_NO_ERRORS_FROM_WARNINGS: false | ||||||
|       RSPM: ${{ matrix.config.rspm }} |       RSPM: ${{ matrix.config.rspm }} | ||||||
|       R_REPOSITORIES: "https://cran.rstudio.com" |       R_REPOSITORIES: "https://cran.rstudio.com" | ||||||
|  |       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | ||||||
|  |       R_KEEP_PKG_SOURCE: yes | ||||||
|  |       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 | ||||||
|  |       # during 'R CMD check', R_LIBS_USER will be overwritten, so: | ||||||
|  |       R_LIBS_USER_GH_ACTIONS: ${{ env.R_LIBS_USER }} | ||||||
|  |       R_RUN_TINYTEST: true | ||||||
|  |  | ||||||
|     steps: |     steps: | ||||||
|       - uses: actions/checkout@v2 |       - uses: actions/checkout@v2 | ||||||
|  |  | ||||||
|  |       - uses: r-lib/actions/setup-pandoc@v1 | ||||||
|  |  | ||||||
|       - uses: r-lib/actions/setup-r@v1 |       - uses: r-lib/actions/setup-r@v1 | ||||||
|         with: |         with: | ||||||
|           r-version: ${{ matrix.config.r }} |           r-version: ${{ matrix.config.r }} | ||||||
|  |           http-user-agent: ${{ matrix.config.http-user-agent }} | ||||||
|  |           use-public-rspm: true | ||||||
|  |  | ||||||
|       - name: Install Linux dependencies |       - uses: r-lib/actions/setup-r-dependencies@v1 | ||||||
|         if: runner.os == 'Linux' |  | ||||||
|         # update the below with sysreqs::sysreqs("DESCRIPTION") and check the "DEB" entries (for Ubuntu). |  | ||||||
|         # we don't want to depend on the sysreqs pkg here, as it requires quite a recent R version |  | ||||||
|         # as of May 2021: https://sysreqs.r-hub.io/pkg/AMR,R,cleaner,curl,dplyr,ggplot2,ggtext,knitr,microbenchmark,pillar,readxl,rmarkdown,rstudioapi,rvest,skimr,tidyr,tinytest,xml2,backports,crayon,rlang,vctrs,evaluate,highr,markdown,stringr,yaml,xfun,cli,ellipsis,fansi,lifecycle,utf8,glue,mime,magrittr,stringi,generics,R6,tibble,tidyselect,pkgconfig,purrr,digest,gtable,isoband,MASS,mgcv,scales,withr,nlme,Matrix,farver,labeling,munsell,RColorBrewer,viridisLite,lattice,colorspace,gridtext,Rcpp,RCurl,png,jpeg,bitops,cellranger,progress,rematch,hms,prettyunits,htmltools,jsonlite,tinytex,base64enc,httr,selectr,openssl,askpass,sys,repr,cpp11 |  | ||||||
|         run: | |  | ||||||
|           sudo apt install -y libssl-dev pandoc pandoc-citeproc libxml2-dev libicu-dev libcurl4-openssl-dev libpng-dev libudunits2-dev |  | ||||||
|  |  | ||||||
|       - name: Query dependencies |  | ||||||
|         # this will change every day (i.e. at scheduled night run of GitHub Action), so it will cache dependency updates |  | ||||||
|         run: | |  | ||||||
|           writeLines(paste0(format(Sys.Date(), "%Y%m%d"), sprintf("-R-%i.%i", getRversion()$major, getRversion()$minor)), ".github/daily-R-bundle") |  | ||||||
|         shell: Rscript {0} |  | ||||||
|          |  | ||||||
|       - name: Restore cached R packages |  | ||||||
|         # this step will add the step 'Post Restore cached R packages' on a succesful run |  | ||||||
|         uses: actions/cache@v2 |  | ||||||
|         with: |         with: | ||||||
|           path: ${{ env.R_LIBS_USER }} |           extra-packages: rcmdcheck | ||||||
|           key: ${{ matrix.config.os }}-${{ hashFiles('.github/daily-R-bundle') }}-v4 |  | ||||||
|  |  | ||||||
|       - name: Unpack AMR and install R dependencies |  | ||||||
|         if: always() |  | ||||||
|         run: | |  | ||||||
|           tar -xf data-raw/AMR_latest.tar.gz |  | ||||||
|           Rscript -e "source('data-raw/_install_deps.R')" |  | ||||||
|         shell: bash |  | ||||||
|            |            | ||||||
|       - name: Show session info |       - name: Show session info | ||||||
|         if: always() |         if: always() | ||||||
| @@ -128,30 +116,16 @@ jobs: | |||||||
|           as.data.frame(utils::installed.packages())[, "Version", drop = FALSE] |           as.data.frame(utils::installed.packages())[, "Version", drop = FALSE] | ||||||
|         shell: Rscript {0} |         shell: Rscript {0} | ||||||
|  |  | ||||||
|       - name: Run R CMD check |       - uses: r-lib/actions/check-r-package@v1 | ||||||
|         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 |  | ||||||
|           # during 'R CMD check', R_LIBS_USER will be overwritten, so: |  | ||||||
|           R_LIBS_USER_GH_ACTIONS: ${{ env.R_LIBS_USER }} |  | ||||||
|           R_RUN_TINYTEST: true |  | ||||||
|         run: | |  | ||||||
|           R CMD check --no-manual --run-donttest --run-dontrun AMR |  | ||||||
|         shell: bash |  | ||||||
|  |  | ||||||
|       - name: Show unit tests output |       - name: Show unit tests output | ||||||
|         if: always() |         if: always() | ||||||
|         run: | |         run: find check -name 'tinytest.Rout*' -exec cat '{}' \; || true | ||||||
|           find . -name 'tinytest.Rout*' -exec cat '{}' \; || true |  | ||||||
|         shell: bash |         shell: bash | ||||||
|  |  | ||||||
|       - name: Upload artifacts |       - name: Upload check results | ||||||
|         if: always() |         if: always() | ||||||
|         uses: actions/upload-artifact@v2 |         uses: actions/upload-artifact@main | ||||||
|         with: |         with: | ||||||
|           name: ${{ matrix.config.os }}-r-${{ matrix.config.r }}-artifacts |           name: ${{ matrix.config.os }}-r-${{ matrix.config.r }}-artifacts | ||||||
|           path: AMR.Rcheck |           path: check | ||||||
|   | |||||||
							
								
								
									
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							| @@ -0,0 +1,157 @@ | |||||||
|  | # ==================================================================== # | ||||||
|  | # TITLE                                                                # | ||||||
|  | # Antimicrobial Resistance (AMR) Data Analysis for R                   # | ||||||
|  | #                                                                      # | ||||||
|  | # SOURCE                                                               # | ||||||
|  | # https://github.com/msberends/AMR                                     # | ||||||
|  | #                                                                      # | ||||||
|  | # LICENCE                                                              # | ||||||
|  | # (c) 2018-2021 Berends MS, Luz CF et al.                              # | ||||||
|  | # Developed at the University of Groningen, the Netherlands, in        # | ||||||
|  | # collaboration with non-profit organisations Certe Medical            # | ||||||
|  | # Diagnostics & Advice, and University Medical Center Groningen.       #  | ||||||
|  | #                                                                      # | ||||||
|  | # This R package is free software; you can freely use and distribute   # | ||||||
|  | # it for both personal and commercial purposes under the terms of the  # | ||||||
|  | # GNU General Public License version 2.0 (GNU GPL-2), as published by  # | ||||||
|  | # the Free Software Foundation.                                        # | ||||||
|  | # We created this package for both routine data analysis and academic  # | ||||||
|  | # research and it was publicly released in the hope that it will be    # | ||||||
|  | # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              # | ||||||
|  | #                                                                      # | ||||||
|  | # Visit our website for the full manual and a complete tutorial about  # | ||||||
|  | # how to conduct AMR data analysis: https://msberends.github.io/AMR/   # | ||||||
|  | # ==================================================================== # | ||||||
|  |  | ||||||
|  | # This GitHub Actions file runs without ANY dependency, so works on all versions of R since R-3.0. | ||||||
|  |  | ||||||
|  | on: | ||||||
|  |   push: | ||||||
|  |     branches: | ||||||
|  |       - premaster | ||||||
|  |       - master | ||||||
|  |   pull_request: | ||||||
|  |     branches: | ||||||
|  |       - master | ||||||
|  |   schedule: | ||||||
|  |     # run a schedule everyday at 1 AM. | ||||||
|  |     # this is to check that all dependencies are still available (see R/zzz.R) | ||||||
|  |     - cron:  '0 1 * * *' | ||||||
|  |  | ||||||
|  | name: R-code-check | ||||||
|  |  | ||||||
|  | jobs: | ||||||
|  |   R-code-check: | ||||||
|  |     runs-on: ${{ matrix.config.os }} | ||||||
|  |      | ||||||
|  |     continue-on-error: ${{ matrix.config.allowfail }} | ||||||
|  |  | ||||||
|  |     name: ${{ matrix.config.os }} (R-${{ matrix.config.r }}) | ||||||
|  |  | ||||||
|  |     strategy: | ||||||
|  |       fail-fast: false | ||||||
|  |       matrix: | ||||||
|  |         config: | ||||||
|  |           # test all systems against all released versions of R >= 3.0, we support them all! | ||||||
|  |           - {os: macOS-latest,   r: 'devel',   allowfail: true} | ||||||
|  |           - {os: macOS-latest,   r: '4.1',     allowfail: false} | ||||||
|  |           - {os: macOS-latest,   r: '4.0',     allowfail: false} | ||||||
|  |           - {os: macOS-latest,   r: '3.6',     allowfail: false} | ||||||
|  |           - {os: macOS-latest,   r: '3.5',     allowfail: false} | ||||||
|  |           - {os: macOS-latest,   r: '3.4',     allowfail: false} | ||||||
|  |           - {os: macOS-latest,   r: '3.3',     allowfail: false} | ||||||
|  |           - {os: macOS-latest,   r: '3.2',     allowfail: false} | ||||||
|  |           - {os: ubuntu-20.04,   r: 'devel',   allowfail: true,  rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} | ||||||
|  |           - {os: ubuntu-20.04,   r: '4.1',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} | ||||||
|  |           - {os: ubuntu-20.04,   r: '4.0',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} | ||||||
|  |           - {os: ubuntu-20.04,   r: '3.6',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} | ||||||
|  |           - {os: ubuntu-20.04,   r: '3.5',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} | ||||||
|  |           - {os: ubuntu-20.04,   r: '3.4',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} | ||||||
|  |           - {os: ubuntu-20.04,   r: '3.3',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} | ||||||
|  |           - {os: ubuntu-20.04,   r: '3.2',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} | ||||||
|  |           - {os: ubuntu-20.04,   r: '3.1',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} | ||||||
|  |           - {os: ubuntu-20.04,   r: '3.0',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} | ||||||
|  |           - {os: windows-latest, r: 'devel',   allowfail: true} | ||||||
|  |           - {os: windows-latest, r: '4.1',     allowfail: false} | ||||||
|  |           - {os: windows-latest, r: '4.0',     allowfail: false} | ||||||
|  |           - {os: windows-latest, r: '3.6',     allowfail: false} | ||||||
|  |           - {os: windows-latest, r: '3.5',     allowfail: false} | ||||||
|  |           - {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" | ||||||
|  |      | ||||||
|  |     steps: | ||||||
|  |       - uses: actions/checkout@v2 | ||||||
|  |  | ||||||
|  |       - uses: r-lib/actions/setup-r@v1 | ||||||
|  |         with: | ||||||
|  |           r-version: ${{ matrix.config.r }} | ||||||
|  |  | ||||||
|  |       - name: Install Linux dependencies | ||||||
|  |         if: runner.os == 'Linux' | ||||||
|  |         # update the below with sysreqs::sysreqs("DESCRIPTION") and check the "DEB" entries (for Ubuntu). | ||||||
|  |         # we don't want to depend on the sysreqs pkg here, as it requires quite a recent R version | ||||||
|  |         # as of May 2021: https://sysreqs.r-hub.io/pkg/AMR,R,cleaner,curl,dplyr,ggplot2,ggtext,knitr,microbenchmark,pillar,readxl,rmarkdown,rstudioapi,rvest,skimr,tidyr,tinytest,xml2,backports,crayon,rlang,vctrs,evaluate,highr,markdown,stringr,yaml,xfun,cli,ellipsis,fansi,lifecycle,utf8,glue,mime,magrittr,stringi,generics,R6,tibble,tidyselect,pkgconfig,purrr,digest,gtable,isoband,MASS,mgcv,scales,withr,nlme,Matrix,farver,labeling,munsell,RColorBrewer,viridisLite,lattice,colorspace,gridtext,Rcpp,RCurl,png,jpeg,bitops,cellranger,progress,rematch,hms,prettyunits,htmltools,jsonlite,tinytex,base64enc,httr,selectr,openssl,askpass,sys,repr,cpp11 | ||||||
|  |         run: | | ||||||
|  |           sudo apt install -y libssl-dev pandoc pandoc-citeproc libxml2-dev libicu-dev libcurl4-openssl-dev libpng-dev libudunits2-dev | ||||||
|  |  | ||||||
|  |       - name: Query dependencies | ||||||
|  |         # this will change every day (i.e. at scheduled night run of GitHub Action), so it will cache dependency updates | ||||||
|  |         run: | | ||||||
|  |           writeLines(paste0(format(Sys.Date(), "%Y%m%d"), sprintf("-R-%i.%i", getRversion()$major, getRversion()$minor)), ".github/daily-R-bundle") | ||||||
|  |         shell: Rscript {0} | ||||||
|  |          | ||||||
|  |       - name: Restore cached R packages | ||||||
|  |         # this step will add the step 'Post Restore cached R packages' on a succesful run | ||||||
|  |         uses: actions/cache@v2 | ||||||
|  |         with: | ||||||
|  |           path: ${{ env.R_LIBS_USER }} | ||||||
|  |           key: ${{ matrix.config.os }}-${{ hashFiles('.github/daily-R-bundle') }}-v4 | ||||||
|  |  | ||||||
|  |       - name: Unpack AMR and install R dependencies | ||||||
|  |         if: always() | ||||||
|  |         run: | | ||||||
|  |           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: | | ||||||
|  |           options(width = 100) | ||||||
|  |           utils::sessionInfo() | ||||||
|  |           as.data.frame(utils::installed.packages())[, "Version", drop = FALSE] | ||||||
|  |         shell: Rscript {0} | ||||||
|  |          | ||||||
|  |       - 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 | ||||||
|  |           # during 'R CMD check', R_LIBS_USER will be overwritten, so: | ||||||
|  |           R_LIBS_USER_GH_ACTIONS: ${{ env.R_LIBS_USER }} | ||||||
|  |           R_RUN_TINYTEST: true | ||||||
|  |         run: | | ||||||
|  |           R CMD check --no-manual --run-donttest --run-dontrun AMR | ||||||
|  |         shell: bash | ||||||
|  |  | ||||||
|  |       - name: Show unit tests output | ||||||
|  |         if: always() | ||||||
|  |         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: AMR.Rcheck | ||||||
| @@ -1,5 +1,5 @@ | |||||||
| Package: AMR | Package: AMR | ||||||
| Version: 1.7.1.9040 | Version: 1.7.1.9041 | ||||||
| Date: 2021-09-29 | Date: 2021-09-29 | ||||||
| Title: Antimicrobial Resistance Data Analysis | Title: Antimicrobial Resistance Data Analysis | ||||||
| Description: Functions to simplify and standardise antimicrobial resistance (AMR) | Description: Functions to simplify and standardise antimicrobial resistance (AMR) | ||||||
|   | |||||||
							
								
								
									
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								NEWS.md
									
									
									
									
									
								
							| @@ -1,4 +1,4 @@ | |||||||
| # `AMR` 1.7.1.9040 | # `AMR` 1.7.1.9041 | ||||||
| ## <small>Last updated: 29 September 2021</small> | ## <small>Last updated: 29 September 2021</small> | ||||||
|  |  | ||||||
| ### Breaking changes | ### Breaking changes | ||||||
|   | |||||||
										
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							| @@ -31,7 +31,10 @@ pkg_suggests <- gsub("[^a-zA-Z0-9]+", "", | |||||||
|                      unlist(strsplit(unlist(packageDescription("AMR", |                      unlist(strsplit(unlist(packageDescription("AMR", | ||||||
|                                                                fields = c("Suggests", "Enhances", "LinkingTo"))), |                                                                fields = c("Suggests", "Enhances", "LinkingTo"))), | ||||||
|                                      split = ", ?"))) |                                      split = ", ?"))) | ||||||
|  | pkg_suggests <- unname(pkg_suggests[!is.na(pkg_suggests)]) | ||||||
|  | cat("################################################\n") | ||||||
| cat("Packages listed in Suggests/Enhances:", paste(pkg_suggests, collapse = ", "), "\n") | cat("Packages listed in Suggests/Enhances:", paste(pkg_suggests, collapse = ", "), "\n") | ||||||
|  | cat("################################################\n") | ||||||
|  |  | ||||||
| if (.Platform$OS.type != "unix") { | if (.Platform$OS.type != "unix") { | ||||||
|   # no compiling on Windows here |   # no compiling on Windows here | ||||||
| @@ -52,6 +55,16 @@ for (i in seq_len(length(to_install))) { | |||||||
|            # message = function(m) invisible(), |            # message = function(m) invisible(), | ||||||
|            warning = function(w) message(w$message), |            warning = function(w) message(w$message), | ||||||
|            error = function(e) message(e$message)) |            error = function(e) message(e$message)) | ||||||
|  |   if (.Platform$OS.type != "unix" && !to_install[i] %in% rownames(utils::installed.packages())) { | ||||||
|  |     tryCatch(install.packages(to_install[i], | ||||||
|  |                               type = "binary", | ||||||
|  |                               repos = "https://cran.rstudio.com/", | ||||||
|  |                               dependencies = c("Depends", "Imports", "LinkingTo"), | ||||||
|  |                               quiet = FALSE), | ||||||
|  |              # message = function(m) invisible(), | ||||||
|  |              warning = function(w) message(w$message), | ||||||
|  |              error = function(e) message(e$message)) | ||||||
|  |   } | ||||||
| } | } | ||||||
|  |  | ||||||
| to_update <- as.data.frame(utils::old.packages(repos = "https://cran.rstudio.com/"), stringsAsFactors = FALSE) | to_update <- as.data.frame(utils::old.packages(repos = "https://cran.rstudio.com/"), stringsAsFactors = FALSE) | ||||||
|   | |||||||
| @@ -44,7 +44,7 @@ | |||||||
|       </button> |       </button> | ||||||
|       <span class="navbar-brand"> |       <span class="navbar-brand"> | ||||||
|         <a class="navbar-link" href="../index.html">AMR (for R)</a> |         <a class="navbar-link" href="../index.html">AMR (for R)</a> | ||||||
|         <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9040</span> |         <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9041</span> | ||||||
|       </span> |       </span> | ||||||
|     </div> |     </div> | ||||||
|  |  | ||||||
|   | |||||||
| @@ -92,7 +92,7 @@ | |||||||
|       </button> |       </button> | ||||||
|       <span class="navbar-brand"> |       <span class="navbar-brand"> | ||||||
|         <a class="navbar-link" href="../index.html">AMR (for R)</a> |         <a class="navbar-link" href="../index.html">AMR (for R)</a> | ||||||
|         <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9040</span> |         <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9041</span> | ||||||
|       </span> |       </span> | ||||||
|     </div> |     </div> | ||||||
|  |  | ||||||
| @@ -240,9 +240,9 @@ | |||||||
|       <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small> |       <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small> | ||||||
|     </div> |     </div> | ||||||
|  |  | ||||||
|     <div id="amr-1719040" class="section level1"> |     <div id="amr-1719041" class="section level1"> | ||||||
| <h1 class="page-header" data-toc-text="1.7.1.9040"> | <h1 class="page-header" data-toc-text="1.7.1.9041"> | ||||||
| <a href="#amr-1719040" class="anchor" aria-hidden="true"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9040</h1> | <a href="#amr-1719041" class="anchor" aria-hidden="true"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9041</h1> | ||||||
| <div id="last-updated-29-september-2021" class="section level2"> | <div id="last-updated-29-september-2021" class="section level2"> | ||||||
| <h2 class="hasAnchor"> | <h2 class="hasAnchor"> | ||||||
| <a href="#last-updated-29-september-2021" class="anchor" aria-hidden="true"></a><small>Last updated: 29 September 2021</small> | <a href="#last-updated-29-september-2021" class="anchor" aria-hidden="true"></a><small>Last updated: 29 September 2021</small> | ||||||
|   | |||||||
| @@ -24,26 +24,26 @@ | |||||||
| # ==================================================================== # | # ==================================================================== # | ||||||
| 
 | 
 | ||||||
| ######################################################################## | ######################################################################## | ||||||
| # `git_premaster.sh` takes 3 parameters:                               # | # `git_development.sh` takes 3 parameters:                             # | ||||||
| #   1. Commit message (character) [mandatory]                          # | #   1. Commit message (character) [mandatory]                          # | ||||||
| #   2. Lazy website generation (logical), with TRUE only changed       # | #   2. Lazy website generation (logical), with TRUE only changed       # | ||||||
| #      files will be processed [defaults to TRUE]                      # | #      files will be processed [defaults to TRUE]                      # | ||||||
| #   3. Version number to be used in DESCRIPTION and NEWS.md            # | #   3. Version number to be used in DESCRIPTION and NEWS.md            # | ||||||
| #      [defaults to current tag and last commit number + 9000]         # | #      [defaults to current tag and last commit number + 9000]         # | ||||||
| #                                                                      # | #                                                                      # | ||||||
| # To push new commits to the premaster branch, run:                    # | # To push new commits to the development branch, run:                  # | ||||||
| # bash git_premaster.sh "commit message"                               # | # bash git_development.sh "commit message"                             # | ||||||
| # This creates auto version numbering in DESCRIPTION and NEWS.md.      # | # This creates auto version numbering in DESCRIPTION and NEWS.md.      # | ||||||
| #                                                                      # | #                                                                      # | ||||||
| # After successful test checks, merge it to the master branch with:    # | # After successful test checks, merge it to the main branch with:      # | ||||||
| # bash git_merge.sh                                                    # | # bash git_merge.sh                                                    # | ||||||
| #                                                                      # | #                                                                      # | ||||||
| # To prerelease a new version number, run:                             # | # To prerelease a new version number, run:                             # | ||||||
| # bash git_premaster.sh "v1.x.x" FALSE "1.x.x"                         # | # bash git_development.sh "v1.x.x" FALSE "1.x.x"                       # | ||||||
| #                                                                      # | #                                                                      # | ||||||
| # To only update the website, run:                                     # | # To only update the website, run:                                     # | ||||||
| # bash git_siteonly.sh                                                 # | # bash git_siteonly.sh                                                 # | ||||||
| # (which is short for 'bash git_premaster.sh "website update" FALSE')  # | # (which is short for 'bash git_development.sh "website update" FALSE')# | ||||||
| ######################################################################## | ######################################################################## | ||||||
| 
 | 
 | ||||||
| if [ -z "$1" ]; then | if [ -z "$1" ]; then | ||||||
| @@ -56,8 +56,8 @@ else | |||||||
|   lazy=$2 |   lazy=$2 | ||||||
| fi | fi | ||||||
| 
 | 
 | ||||||
| # be sure to be on premaster branch | # be sure to be on development branch | ||||||
| git checkout premaster --quiet | git checkout development --quiet | ||||||
| 
 | 
 | ||||||
| echo "••••••••••••••••••••••••••••••••••••••••••••" | echo "••••••••••••••••••••••••••••••••••••••••••••" | ||||||
| echo "• Updating package date and version number •" | echo "• Updating package date and version number •" | ||||||
| @@ -127,7 +127,7 @@ echo "••••••••••••••••••••" | |||||||
| echo "• Building package •" | echo "• Building package •" | ||||||
| echo "••••••••••••••••••••" | echo "••••••••••••••••••••" | ||||||
| echo "• Building 'data-raw/AMR_latest.tar.gz'..." | echo "• Building 'data-raw/AMR_latest.tar.gz'..." | ||||||
| Rscript -e "x <- devtools::build(path = 'data-raw', vignettes = FALSE, manual = FALSE, binary = FALSE, quiet = TRUE)" | Rscript -e "x <- devtools::build(path = 'data-raw', vignettes = TRUE, manual = TRUE, binary = FALSE, quiet = TRUE)" | ||||||
| rm data-raw/AMR_latest.tar.gz | rm data-raw/AMR_latest.tar.gz | ||||||
| mv data-raw/AMR_*.tar.gz data-raw/AMR_latest.tar.gz | mv data-raw/AMR_*.tar.gz data-raw/AMR_latest.tar.gz | ||||||
| 
 | 
 | ||||||
| @@ -193,7 +193,7 @@ git add . | |||||||
| git commit -a -m "(v${new_version}) $1" --quiet | git commit -a -m "(v${new_version}) $1" --quiet | ||||||
| git push --quiet | git push --quiet | ||||||
| echo "Comparison:" | echo "Comparison:" | ||||||
| echo "https://github.com/msberends/AMR/compare/master...premaster?view=inline" | echo "https://github.com/msberends/AMR/compare/main...development?view=inline" | ||||||
| 
 | 
 | ||||||
| echo | echo | ||||||
| echo "•••••••••" | echo "•••••••••" | ||||||
							
								
								
									
										30
									
								
								git_merge.sh
									
									
									
									
									
								
							
							
						
						
									
										30
									
								
								git_merge.sh
									
									
									
									
									
								
							| @@ -24,44 +24,44 @@ | |||||||
| # ==================================================================== # | # ==================================================================== # | ||||||
|  |  | ||||||
| ######################################################################## | ######################################################################## | ||||||
| # `git_premaster.sh` takes 3 parameters:                               # | # `git_development.sh` takes 3 parameters:                             # | ||||||
| #   1. Commit message (character) [mandatory]                          # | #   1. Commit message (character) [mandatory]                          # | ||||||
| #   2. Lazy website generation (logical), with TRUE only changed       # | #   2. Lazy website generation (logical), with TRUE only changed       # | ||||||
| #      files will be processed [defaults to TRUE]                      # | #      files will be processed [defaults to TRUE]                      # | ||||||
| #   3. Version number to be used in DESCRIPTION and NEWS.md            # | #   3. Version number to be used in DESCRIPTION and NEWS.md            # | ||||||
| #      [defaults to current tag and last commit number + 9000]         # | #      [defaults to current tag and last commit number + 9000]         # | ||||||
| #                                                                      # | #                                                                      # | ||||||
| # To push new commits to the premaster branch, run:                    # | # To push new commits to the development branch, run:                  # | ||||||
| # bash git_premaster.sh "commit message"                               # | # bash git_development.sh "commit message"                             # | ||||||
| # This creates auto version numbering in DESCRIPTION and NEWS.md.      # | # This creates auto version numbering in DESCRIPTION and NEWS.md.      # | ||||||
| #                                                                      # | #                                                                      # | ||||||
| # After successful test checks, merge it to the master branch with:    # | # After successful test checks, merge it to the main branch with:      # | ||||||
| # bash git_merge.sh                                                    # | # bash git_merge.sh                                                    # | ||||||
| #                                                                      # | #                                                                      # | ||||||
| # To prerelease a new version number, run:                             # | # To prerelease a new version number, run:                             # | ||||||
| # bash git_premaster.sh "v1.x.x" FALSE "1.x.x"                         # | # bash git_development.sh "v1.x.x" FALSE "1.x.x"                       # | ||||||
| #                                                                      # | #                                                                      # | ||||||
| # To only update the website, run:                                     # | # To only update the website, run:                                     # | ||||||
| # bash git_siteonly.sh                                                 # | # bash git_siteonly.sh                                                 # | ||||||
| # (which is short for 'bash git_premaster.sh "website update" FALSE')  # | # (which is short for 'bash git_development.sh "website update" FALSE')# | ||||||
| ######################################################################## | ######################################################################## | ||||||
|  |  | ||||||
| # stash current changes | # stash current changes | ||||||
| # git stash --quiet | # git stash --quiet | ||||||
|  |  | ||||||
| # go to master | # go to main | ||||||
| git checkout master --quiet | git checkout main --quiet | ||||||
| echo "• changed branch to master" | echo "• changed branch to main" | ||||||
|  |  | ||||||
| # import everything from premaster | # import everything from development | ||||||
| git merge premaster --quiet | git merge development --quiet | ||||||
| # and send it to git | # and send it to git | ||||||
| git push --quiet | git push --quiet | ||||||
| echo "• pushed changes to master" | echo "• pushed changes to main" | ||||||
|  |  | ||||||
| # return to premaster | # return to development | ||||||
| git checkout premaster --quiet | git checkout development --quiet | ||||||
| echo "• changed branch back to premaster" | echo "• changed branch back to development" | ||||||
| git status --short | git status --short | ||||||
| echo | echo | ||||||
|  |  | ||||||
|   | |||||||
| @@ -24,35 +24,35 @@ | |||||||
| # ==================================================================== # | # ==================================================================== # | ||||||
|  |  | ||||||
| ######################################################################## | ######################################################################## | ||||||
| # `git_premaster.sh` takes 3 parameters:                               # | # `git_development.sh` takes 3 parameters:                             # | ||||||
| #   1. Commit message (character) [mandatory]                          # | #   1. Commit message (character) [mandatory]                          # | ||||||
| #   2. Lazy website generation (logical), with TRUE only changed       # | #   2. Lazy website generation (logical), with TRUE only changed       # | ||||||
| #      files will be processed [defaults to TRUE]                      # | #      files will be processed [defaults to TRUE]                      # | ||||||
| #   3. Version number to be used in DESCRIPTION and NEWS.md            # | #   3. Version number to be used in DESCRIPTION and NEWS.md            # | ||||||
| #      [defaults to current tag and last commit number + 9000]         # | #      [defaults to current tag and last commit number + 9000]         # | ||||||
| #                                                                      # | #                                                                      # | ||||||
| # To push new commits to the premaster branch, run:                    # | # To push new commits to the development branch, run:                  # | ||||||
| # bash git_premaster.sh "commit message"                               # | # bash git_development.sh "commit message"                             # | ||||||
| # This creates auto version numbering in DESCRIPTION and NEWS.md.      # | # This creates auto version numbering in DESCRIPTION and NEWS.md.      # | ||||||
| #                                                                      # | #                                                                      # | ||||||
| # After successful test checks, merge it to the master branch with:    # | # After successful test checks, merge it to the main branch with:      # | ||||||
| # bash git_merge.sh                                                    # | # bash git_merge.sh                                                    # | ||||||
| #                                                                      # | #                                                                      # | ||||||
| # To prerelease a new version number, run:                             # | # To prerelease a new version number, run:                             # | ||||||
| # bash git_premaster.sh "v1.x.x" FALSE "1.x.x"                         # | # bash git_development.sh "v1.x.x" FALSE "1.x.x"                       # | ||||||
| #                                                                      # | #                                                                      # | ||||||
| # To only update the website, run:                                     # | # To only update the website, run:                                     # | ||||||
| # bash git_siteonly.sh                                                 # | # bash git_siteonly.sh                                                 # | ||||||
| # (which is short for 'bash git_premaster.sh "website update" FALSE')  # | # (which is short for 'bash git_development.sh "website update" FALSE')# | ||||||
| ######################################################################## | ######################################################################## | ||||||
|  |  | ||||||
| bash git_premaster.sh "website update" FALSE | bash git_development.sh "website update" FALSE | ||||||
|  |  | ||||||
| echo | echo | ||||||
| echo "••••••••••••••••••••••••••••••" | echo "••••••••••••••••••••••••••••" | ||||||
| echo "• Uploading to master branch •" | echo "• Uploading to main branch •" | ||||||
| echo "••••••••••••••••••••••••••••••" | echo "••••••••••••••••••••••••••••" | ||||||
| git checkout master | git checkout main | ||||||
| git merge premaster | git merge development | ||||||
| git push --quiet | git push --quiet | ||||||
| git checkout premaster | git checkout development | ||||||
|   | |||||||
		Reference in New Issue
	
	Block a user