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6-utils.R
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6-utils.R
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# msg <- function(..., startup = FALSE) {
# if (startup) {
# if (!isTRUE(getOption("masstools.quiet"))) {
# packageStartupMessage(text_col(...))
# }
# } else {
# message(text_col(...))
# }
# }
# text_col <- function(x) {
# # If RStudio not available, messages already printed in black
# if (!rstudioapi::isAvailable()) {
# return(x)
# }
#
# if (!rstudioapi::hasFun("getThemeInfo")) {
# return(x)
# }
#
# theme <- rstudioapi::getThemeInfo()
#
# if (isTRUE(theme$dark)) {
# crayon::white(x)
# } else {
# crayon::black(x)
# }
# }
#' List all packages in the masstools
#'
#' @param include_self Include masstools in the list?
#' @export
#' @return masstools packages
#' @examples
#' masstools_packages()
masstools_packages <- function(include_self = TRUE) {
raw <- utils::packageDescription("masstools")$Imports
imports <- strsplit(raw, ",")[[1]]
parsed <- gsub("^\\s+|\\s+$", "", imports)
names <-
vapply(strsplit(parsed, "\\s+"), "[[", 1, FUN.VALUE = character(1))
if (include_self) {
names <- c(names, "masstools")
}
names
}
invert <- function(x) {
if (length(x) == 0) {
return()
}
stacked <- utils::stack(x)
tapply(as.character(stacked$ind), stacked$values, list)
}
style_grey <- function(level, ...) {
crayon::style(paste0(...),
crayon::make_style(grDevices::grey(level), grey = TRUE))
}
# # NOTE: keep in sync with install-patRoon version
# findPWizPath <- function() {
# # try to find ProteoWizard
# # order: options --> win registry --> PATH
# # the PATH is searched last because
# OpenMS might have added its own old version.
#
# path <- getOption("patRoon.path.pwiz")
# if (!is.null(path) & nzchar(path))
# return(path)
#
# if (Sys.info()[["sysname"]] == "Windows")
# {
# # Inspired by scan_registry_for_rtools() from pkgload
# key <- "Directory\\shell\\Open with SeeMS\\command"
# reg <-
# tryCatch(
# utils::readRegistry(key, "HCR"),
# error = function(e)
# NULL
# )
#
# # not sure if this might occur
# if (is.null(reg))
# reg <-
# tryCatch(
# utils::readRegistry(key, "HLM"),
# error = function(e)
# NULL
# )
#
# if (!is.null(reg))
# {
# path <-
# tryCatch(
# dirname(sub("\"([^\"]*)\".*", "\\1", reg[[1]])),
# error = function(e)
# NULL
# )
# if (!is.null(path) &
# file.exists(file.path(path, "msconvert.exe")))
# # extra check: see if msconvert is there
# return(path)
# }
# }
#
# # check PATH
# msc <-
# if (Sys.info()[["sysname"]] == "Windows")
# "msconvert.exe"
# else
# "msconvert"
# path <- dirname(Sys.which(msc))
# if (nzchar(path))
# return(path)
#
# return(NULL)
# }
#' @title show_progresser
#' @description show_progresser
#' @author Xiaotao Shen
#' \email{shenxt1990@@outlook.com}
#' @param index index for loop
#' @param progresser progresser
#' @return A data.frame
#' @importFrom magrittr %>%
#' @importFrom dplyr case_when everything select filter
#' @importFrom purrr map map2 walk
#' @importFrom crayon green
#' @export
show_progresser <-
function(index = 1:1000,
progresser = c(1, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100)) {
idx <-
seq(
from = 1,
to = max(index),
length.out = length(progresser)
) %>%
round()
data.frame(idx = idx,
progresser = paste0(progresser, "%"))
}
#' @title install_fastgit
#' @description install packages from fastgit. Credit to Shixiang Wang
#' @author Xiaotao Shen
#' \email{shenxt1990@@outlook.com}
#' @param pkg pkg name from github, gitlab or gitee, "name/repo" format
#' @param from gitlab, github or gitee.
#' @param ... Other parameters for install_git
#' @return NULL
#' @export
install_fastgit <-
function(pkg,
from = c("gitee", "gitlab", "github"),
...) {
from <- match.arg(from)
if (from == "gitee") {
if (!grepl("/", pkg)) {
stop("Invalid package name, should in 'name/repo' format.")
}
remotes::install_git(paste0("https://gitee.com/", pkg), ...)
} else {
if (any(grepl(":", pkg))) {
remotes::install_git(pkg, ...)
} else {
if (any(grepl("/", pkg))) {
tryCatch(
remotes::install_git(paste0("https://hub.fastgit.org/", pkg)),
error = function(e) {
message("Install error when use GitHub mirror, roll back to official GitHub.")
remotes::install_github(pkg)
}
)
}
}
}
}