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| Original file line number | Diff line number | Diff line change |
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| @@ -1,15 +1,21 @@ | ||
| Package: Rseb | ||
| Type: Package | ||
| Title: A package for NGS data managing and visualization | ||
| Version: 0.1.6 | ||
| Version: 0.1.7 | ||
| Author: Sebastian Gregoricchio | ||
| Maintainer: Sebastian Gregoricchio <sebastian.gregoricchio@gmail.com> | ||
| Description: An R-package for daily tasks required to handle biological data as well as avoid re-coding of small functions for quick but necessary data managing. | ||
| License: GNU GENERAL PUBLIC LICENSE version 3 | ||
| Depends: | ||
| R (>= 3.2.0), BiocManager, Biostrings, biomaRt, GO.db, rtracklayer, cowplot, data.table, ggplot2 (>= 3.3.3), ggrepel, matrixStats, plyr, dplyr, purrr, robustbase, stringr, tidyr, tools, labeling, devtools, rvcheck, curl | ||
| R (>= 4.0.0) | ||
| Imports: | ||
| BiocManager, Biostrings, biomaRt, GO.db, rtracklayer, cowplot, data.table, ggplot2 (>= 3.3.3), ggrepel, ggpubr, matrixStats, plyr, dplyr, tidyr, purrr, robustbase, stringr, tools, devtools, rvcheck, curl | ||
| biocViews: | ||
| Encoding: UTF-8 | ||
| LazyData: true | ||
| RoxygenNote: 7.1.1 | ||
| git_url: https://github.com/sebastian-gregoricchio/Rseb/ | ||
| URL: | ||
| https://sebastian-gregoricchio.github.io/Rseb/ | ||
| https://github.com/sebastian-gregoricchio/Rseb/ | ||
| https://sebastian-gregoricchio.github.io/ | ||
| BugReports: https://github.com/sebastian-gregoricchio/Rseb/issues |
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| @@ -1,41 +1,56 @@ | ||
| #' @title \code{Rseb} updates verification | ||
| #' | ||
| #' @description It verifies if \code{Rseb} is up-to-date and installs it when required. | ||
| #' | ||
| #' @param update Logical value to define whether update the \code{Rseb} package. By default \code{TRUE}. | ||
| #' @param verbose Logical value to define whether print messages. By default \code{TRUE}. | ||
| #' @param force Logical value to define whether to force the installation of \code{Rseb} even though already up-to-date. Parameter passed to \code{devtools::install_github()}. By default \code{FALSE}. | ||
| #' | ||
| #' @return Warnings and/or messages. Installation of the latest version of \code{Rseb} if required. | ||
| #' | ||
| #' @details This function will check for internet availability. | ||
| #' | ||
| #' @export actualize | ||
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| actualize = function(update = TRUE, | ||
| verbose = TRUE, | ||
| force = FALSE) { | ||
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| # Check internet connection | ||
| if (isFALSE(curl::has_internet())) {return(invisible(NULL))} | ||
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| # Store Rseb package versions | ||
| check = suppressMessages(rvcheck::check_github("sebastian-gregoricchio/Rseb")) | ||
| # When up-to-date == NA it means that it is a developmental version higher then the last release | ||
| if (is.na(check$up_to_date)) {return(invisible(NULL))} | ||
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| # Check if Rseb is up-to-date | ||
| if (check$up_to_date == FALSE) { | ||
| return(warning(paste("The Rseb package is not up-to-date. Installed version", | ||
| check$installed_version, "-->", check$latest_version, | ||
| "available. \nTo update Rseb type: Rseb::actualize()"))) | ||
| } | ||
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| # Update Rseb if required | ||
| if (check$up_to_date == FALSE & update == TRUE) { | ||
| devtools::install_github("sebastian-gregoricchio/Rseb", force = force) | ||
| } else if (verbose == T) { | ||
| return(message(paste("Rseb's latest version (v", check$installed_version, ") is already installed.", sep = "")))} | ||
|
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| } # END function | ||
| #' @title \code{Rseb} updates verification | ||
| #' | ||
| #' @description It verifies if \code{Rseb} is up-to-date and installs it when required. | ||
| #' | ||
| #' @param update Logical value to define whether update the \code{Rseb} package. By default \code{TRUE}. | ||
| #' @param verbose Logical value to define whether print messages. By default \code{TRUE}. | ||
| #' @param force Logical value to define whether to force the installation of \code{Rseb} even though already up-to-date. Parameter passed to \code{devtools::install_github()}. By default \code{FALSE}. | ||
| #' | ||
| #' @return Warnings and/or messages. Installation of the latest version of \code{Rseb} if required. | ||
| #' | ||
| #' @details This function will check for internet availability. | ||
| #' | ||
| #' @export actualize | ||
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| actualize = function(update = TRUE, | ||
| verbose = TRUE, | ||
| force = FALSE) { | ||
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| # Check internet connection | ||
| if (isFALSE(curl::has_internet())) {return(invisible(NULL))} | ||
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| # Store Rseb package versions | ||
| check = suppressMessages(rvcheck::check_github("sebastian-gregoricchio/Rseb")) | ||
| # When up-to-date == NA it means that it is a developmental version higher then the last release | ||
| if (is.na(check$up_to_date)) {return(invisible(NULL))} | ||
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| # Check if Rseb is up-to-date and return a message if not up-to-date | ||
| if (check$up_to_date == FALSE) { | ||
| message = paste("| The 'Rseb' package is not up-to-date. Installed version", | ||
| check$installed_version, "-->", check$latest_version, | ||
| "available. |") | ||
| command = "| To update Rseb type: Rseb::actualize()" | ||
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| return(message(paste("\033[0;37;44m", | ||
| paste(rep("-", nchar(message)), collapse = ""), | ||
| "\n", message, "\n", | ||
| command, paste(rep(" ", (nchar(message) - nchar(command)) - 1), collapse = ""), "|", | ||
| "\n", paste(rep("-", nchar(message)), collapse = ""), | ||
| "\033[0m", | ||
| sep = ""))) | ||
| } | ||
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| # Update Rseb if required | ||
| if (check$up_to_date == F & update == T) {devtools::install_github("sebastian-gregoricchio/Rseb")} | ||
| else if (check$up_to_date == T) { | ||
| if (force == T) {devtools::install_github("sebastian-gregoricchio/Rseb", force = force)} | ||
| else if (verbose == T) {return(message(paste("Rseb's latest version (v", check$installed_version, ") is already installed.", sep = "")))} | ||
| } | ||
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| } # END function |
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