mirror of https://github.com/msberends/AMR
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82 lines
4.6 KiB
82 lines
4.6 KiB
# ==================================================================== # |
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# TITLE # |
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# Antimicrobial Resistance (AMR) Data Analysis for R # |
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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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# LICENCE # |
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# (c) 2018-2021 Berends MS, Luz CF et al. # |
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# Developed at the University of Groningen, the Netherlands, in # |
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# collaboration with non-profit organisations Certe Medical # |
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# Diagnostics & Advice, and University Medical Center Groningen. # |
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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("data-raw/AMR_latest.tar.gz", dependencies = FALSE) |
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pkg_suggests <- gsub("[^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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split = ", ?"))) |
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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$OS.type != "unix") { |
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# no compiling on Windows here |
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options(install.packages.compile.from.source = FALSE) |
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} |
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to_install <- pkg_suggests[!pkg_suggests %in% rownames(utils::installed.packages())] |
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if (length(to_install) == 0) { |
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message("\nNothing to install\n") |
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} |
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for (i in seq_len(length(to_install))) { |
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cat("Installing package", to_install[i], "\n") |
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tryCatch(install.packages(to_install[i], |
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type = "source", |
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repos = "https://cran.rstudio.com/", |
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dependencies = c("Depends", "Imports", "LinkingTo"), |
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quiet = FALSE), |
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# message = function(m) invisible(), |
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warning = function(w) message(w$message), |
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error = function(e) message(e$message)) |
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if (.Platform$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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# 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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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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cat("Updated to '", to_update[i], "' v", as.character(packageVersion(to_update[i])), "\n", sep = "") |
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}
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