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https://github.com/msberends/AMR.git
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unit tests
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parent
8a0a0d4682
commit
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34
.github/workflows/check-old.yaml
vendored
34
.github/workflows/check-old.yaml
vendored
@ -47,7 +47,9 @@ jobs:
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matrix:
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config:
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# Test all old versions of R >= 3.0, we support them all!
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# For recent R versions, see check-recent.yaml (r-lib supports the latest 5 major R versions)
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# For these old versions, dependencies will not be installed and checked.
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# For recent R versions, see check-recent.yaml (r-lib and tidyverse support the latest 5 major R versions).
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- {os: ubuntu-22.04, r: '3.4', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
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- {os: ubuntu-22.04, r: '3.3', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
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- {os: ubuntu-22.04, r: '3.2', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
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- {os: ubuntu-22.04, r: '3.1', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
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@ -67,26 +69,10 @@ jobs:
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- uses: r-lib/actions/setup-pandoc@v2
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- name: Install Linux dependencies
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if: runner.os == 'Linux'
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# update the below with sysreqs::sysreqs("DESCRIPTION") and check the "DEB" entries (for Ubuntu).
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# we don't want to depend on the sysreqs pkg here, as it requires quite a recent R version
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# as of May 2021: https://sysreqs.r-hub.io/pkg/AMR,R,cleaner,curl,dplyr,ggplot2,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
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- name: Install tinytest
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run: |
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sudo apt install -y libssl-dev libxml2-dev libcurl4-openssl-dev
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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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path: ${{ env.R_LIBS_USER }}
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key: ${{ matrix.config.os }}-r-${{ matrix.config.r }}-v5
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- name: Install R dependencies
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if: always()
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run: |
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Rscript -e "source('data-raw/_install_deps.R')"
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shell: bash
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install.packages("tinytest")
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shell: Rscript {0}
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- name: Show session info
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if: always()
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@ -135,11 +121,3 @@ jobs:
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cd ../AMR.Rcheck
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find . -name 'tinytest.Rout*' -exec cat '{}' \; || true
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shell: bash
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- name: Upload artifacts
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if: always()
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continue-on-error: true
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uses: actions/upload-artifact@v3
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with:
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name: artifacts-${{ matrix.config.os }}-r${{ matrix.config.r }}
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path: ${{ github.workspace }}.Rcheck
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3
.github/workflows/check-recent.yaml
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3
.github/workflows/check-recent.yaml
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@ -66,8 +66,7 @@ jobs:
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- {os: ubuntu-latest, r: '4.1', allowfail: false}
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- {os: ubuntu-latest, r: '4.0', allowfail: false}
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- {os: ubuntu-latest, r: '3.6', allowfail: false}
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- {os: ubuntu-latest, r: '3.5', allowfail: false}
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- {os: ubuntu-latest, r: '3.4', allowfail: false} # when a new R releases, this one has to move to check-old.yaml
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- {os: ubuntu-latest, r: '3.5', allowfail: false} # when a new R releases, this one has to move to check-old.yaml
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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@ -1,5 +1,5 @@
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Package: AMR
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Version: 1.8.2.9082
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Version: 1.8.2.9083
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Date: 2023-01-06
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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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2
NEWS.md
2
NEWS.md
@ -1,4 +1,4 @@
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# AMR 1.8.2.9082
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# AMR 1.8.2.9083
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*(this beta version will eventually become v2.0! We're happy to reach a new major milestone soon!)*
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@ -1,95 +0,0 @@
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# ==================================================================== #
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# TITLE #
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# AMR: An R Package for Working with Antimicrobial Resistance Data #
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# #
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# SOURCE #
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# https://github.com/msberends/AMR #
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# #
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# CITE AS #
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# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
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# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
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# Data. Journal of Statistical Software, 104(3), 1-31. #
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# doi:10.18637/jss.v104.i03 #
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# #
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# Developed at the University of Groningen and the University Medical #
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# Center Groningen in The Netherlands, in collaboration with many #
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# colleagues from around the world, see our website. #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# We created this package for both routine data analysis and academic #
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# research and it was publicly released in the hope that it will be #
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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# #
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# Visit our website for the full manual and a complete tutorial about #
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# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
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# ==================================================================== #
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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(getwd(), repos = NULL, type = "source")
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pkg_suggests <- gsub(
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"[^a-zA-Z0-9.]+", "",
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unlist(strsplit(unlist(packageDescription("AMR",
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fields = c("Suggests", "Enhances", "LinkingTo")
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)),
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split = ", ?"
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))
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)
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pkg_suggests <- unname(pkg_suggests[!is.na(pkg_suggests)])
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cat("################################################\n")
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cat("Packages listed in Suggests/Enhances:", paste(pkg_suggests, collapse = ", "), "\n")
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cat("################################################\n")
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if (.Platform$OS.type != "unix") {
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# no compiling on Windows here
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options(install.packages.compile.from.source = FALSE)
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}
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to_install <- pkg_suggests[!pkg_suggests %in% rownames(utils::installed.packages())]
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if (length(to_install) == 0) {
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message("\nNothing to install\n")
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}
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for (i in seq_len(length(to_install))) {
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cat("Installing package", to_install[i], "\n")
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tryCatch(install.packages(to_install[i],
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type = "source",
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repos = "https://cran.rstudio.com/",
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dependencies = c("Depends", "Imports", "LinkingTo"),
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quiet = FALSE
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),
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# message = function(m) invisible(),
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warning = function(w) message(w$message),
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error = function(e) message(e$message)
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)
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if (.Platform$OS.type != "unix" && !to_install[i] %in% rownames(utils::installed.packages())) {
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tryCatch(install.packages(to_install[i],
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type = "binary",
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repos = "https://cran.rstudio.com/",
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dependencies = c("Depends", "Imports", "LinkingTo"),
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quiet = FALSE
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),
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# message = function(m) invisible(),
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warning = function(w) message(w$message),
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error = function(e) message(e$message)
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)
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}
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}
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to_update <- as.data.frame(utils::old.packages(repos = "https://cran.rstudio.com/"), stringsAsFactors = FALSE)
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to_update <- to_update[which(to_update$Package %in% pkg_suggests), "Package", drop = TRUE]
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if (length(to_update) == 0) {
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message("\nNothing to update\n")
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}
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for (i in seq_len(length(to_update))) {
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cat("Updating package '", to_update[i], "' v", as.character(packageVersion(to_update[i])), "\n", sep = "")
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tryCatch(update.packages(to_update[i], repos = "https://cran.rstudio.com/", ask = FALSE),
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# message = function(m) invisible(),
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warning = function(w) message(w$message),
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error = function(e) message(e$message)
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)
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cat("Updated to '", to_update[i], "' v", as.character(packageVersion(to_update[i])), "\n", sep = "")
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}
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