Rprofile

[ShixiangWang]

options(encoding = 'UTF-8')
# options("repos" = c(CRAN="https://mirrors.tuna.tsinghua.edu.cn/CRAN/"))
# options(BioC_mirror="https://mirrors.tuna.tsinghua.edu.cn/bioconductor")
#Sys.setenv(XML_CONFIG="/usr/local/include/libxml2")
Sys.setenv(LANGUAGE = 'en')

options(languageserver.formatting_style = function(options) {
  style <- styler::tidyverse_style(indent_by = options$tabSize)
  style$token$force_assignment_op <- NULL
  style
})


#--------------------------------------------
# Set custom library and temp directory for R
# NOTE: please only change following 2 paths
#   Any Question, please email to
#       Shixiang Wang <w_shixiang@163.com>
#--------------------------------------------
.CUSTOM_LIB = "/Users/wsx/R_library" # set your custom library location
#.TMP = "C:/Tools/R/Rtmp"             # set a temp dir for R running
# please do not add '/' at the end !!!

if (!dir.exists(.CUSTOM_LIB)){
  dir.create(.CUSTOM_LIB)
}

.libPaths(c(.CUSTOM_LIB, .libPaths()))
message("Using library: ", .libPaths()[1])


# if(dirname(tempdir()) != .TMP){
#   if(!dir.exists(.TMP)) dir.create(.TMP)
#   cat(paste0("TMPDIR = ", .TMP), file="~/.Renviron", sep = "\n")
# }
# message("Using temp directory: ", .TMP)

#---------------------------------------------------
# pacman is optional, you can delete following code
# If you wanna use pacman, please read:
#   <https://www.jianshu.com/p/cb16ded75672>
# Basically,
# #1, you can use 'p_load' to load multiple package into R
#       like p_load(data.table, dplyr)
# #2, you can use 'p_get' just to install package
# #3, you can use 'p_update' to update all packages
#---------------------------------------------------
if(!require(pacman)){
  install.packages("pacman", dependencies = TRUE)
}
library(pacman)
# https://github.com/mikldk/roxytest
library(roxytest)

source(file.path(if (.Platform$OS.type == "windows") file.path(Sys.getenv("HOMEDRIVE"), Sys.getenv("HOMEPATH")) else Sys.getenv("HOME"), ".vscode-R", "init.R"))

# 使用清华镜像源
options(BioC_mirror="https://mirrors.tuna.tsinghua.edu.cn/bioconductor")

.loopInstall = function(pkg) {
  Sys.sleep(1)
  tryCatch(
    {
      message("=> Try installing ", pkg)
      remotes::install_github(pkg)
    },
    error = function(e) {
      .loopInstall(pkg)
    }
  )
}

.browseOnce <- function() {
  old <- getOption("error")
  function() {
    options(error = old)
    browser()
  }
}

options(error = .browseOnce)

[ShixiangWang]

来自 y 叔 https://github.com/GuangchuangYu/rvcheck/blob/master/R/utilities.R

##' load function from package
##'
##'
##' @title get_fun_from_pkg
##' @param pkg package
##' @param fun function
##' @return function
##' @export
##' @author guangchuang yu
get_fun_from_pkg <- function(pkg, fun) {
    ## requireNamespace(pkg)
    ## eval(parse(text=paste0(pkg, "::", fun)))
    require(pkg, character.only = TRUE)
    eval(parse(text = fun))
}

##' check whether packages were installed
##'
##' check whether selected packages were installed 
##' @title is.installed
##' @param packages selected packagtes
##' @return logical vector
##' @export
##' @author Guangchuang Yu
is.installed <- function(packages) {
    vapply(packages, function(pkg) {
        system.file(package = pkg) != ""
        }, logical(1))
}

is.rserver <- function(){
    RStudio.Version = tryCatch(get("RStudio.Version"), error = function(e) NULL)
    if(is.null(RStudio.Version)) return(FALSE)
    if(!is.function(RStudio.Version)) return(FALSE)
    RStudio.Version()$mode == 'server'
}

`%||%` <- function(a, b) ifelse(is.null(a), b, a)

##' open working directory
##'
##'
##' @title o
##' @param file to be open; open workding directory by default
##' @return NULL
##' @author Guangchuang Yu
##' @export
o <- function(file=".") {
    os <- Sys.info()[1]
    if (is.rserver()) {
        if (dir.exists(file)) {
            stop("open directory in RStudio Server is not supported.")
        }
        rserver_ip <- getOption("rserver_ip")
        if (!is.null(rserver_ip)) {
            rserver_port <- getOption("rserver_port") %||% '8787' 
            if (!startsWith(rserver_ip, "http")) {
                rserver_ip = paste0("http://", rserver_ip)
            }
            utils::browseURL(
                       paste0(
                           paste(rserver_ip, rserver_port, sep=":"),
                           "/file_show?path=",
                           file
                       ))
        } else {
            file.edit <- get("file.edit")
            file.edit(file)   
        }
    } else if (os == "Darwin") {
        cmd <- paste("open", file)
        system(cmd)
    } else if (os == "Linux") {
        cmd <- paste("xdg-open", file, "&")
        system(cmd)
    } else if (os == "Windows") {
        ## wd <- sub("/", "\\", getwd())
        ## cmd <- paste("explorer", wd)
        ## suppressWarnings(shell(cmd))
        cmd <- paste("start", file)
        shell(cmd)
    }
}