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51 lines
3.2 KiB
R
51 lines
3.2 KiB
R
# ==================================================================== #
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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 CODE: #
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# https://github.com/msberends/AMR #
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# #
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# PLEASE CITE THIS SOFTWARE AS: #
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# Berends MS, Luz CF, Friedrich AW, et al. (2022). #
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# AMR: An R Package for Working with Antimicrobial Resistance Data. #
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# Journal of Statistical Software, 104(3), 1-31. #
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# https://doi.org/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://amr-for-r.org #
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# ==================================================================== #
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# Runs all unit tests from source, see run_tests.sh. Quits with status 1 on any failure or error, and with status 2 if the tests could not be run at all.
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# Every top-level error must end in quit(), since an interactive session would otherwise continue reading "1" from stdin.
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status <- tryCatch(
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{
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if (identical(Sys.getenv("AMR_TEST_INTERACTIVE"), "true") && !interactive()) {
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stop("AMR_TEST_INTERACTIVE is set, but this R session is not interactive")
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}
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cat("Interactive:", interactive(), "| LANG:", Sys.getenv("LANG"), "| AMR options:", paste(names(options())[grepl("^AMR_", names(options()))], collapse = ", "), "\n")
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# report all failures, not only the first 10
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options(warn = 1, testthat.summary.max_reports = Inf, testthat.progress.max_fails = Inf)
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res <- as.data.frame(testthat::test_local(Sys.getenv("AMR_TEST_PKG_DIR", "."), reporter = "summary", stop_on_failure = FALSE))
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cat("\nFiles:", length(unique(res$file)), "| failed:", sum(res$failed), "| errors:", sum(res$error), "| skipped:", sum(res$skipped), "| passed:", sum(res$passed), "\n")
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as.integer(sum(res$failed) > 0 || any(res$error))
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},
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error = function(e) {
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cat("Tests could not be run:", conditionMessage(e), "\n")
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2L
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}
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)
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quit(save = "no", status = status)
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