using 加载R包
using函数是我写在$HOME/.Rprofile中的函数，因此每次打开R就能使用。
using的功能是一次加载多个包，并且使用了suppressPackageStartupMessages函数，因此不会显示加载包过程中的信息。
$HOME/.Rprofile文件
Sys.setenv(LANGUAGE = "en")
options(
bitmapType = "cairo",
warnPartialMatchArgs = TRUE,
warnPartialMatchAttr = TRUE,
warnPartialMatchDollar = TRUE,
timeout = 999999,
R_MAX_VSIZE = 2^30
)
# library
using <- function(...) {
packages <- as.character(match.call(expand.dots = FALSE)[[2]])
if (length(packages) == 0) {
return(invisible())
}
# Attempt to load packages making note of which don't load
loaded <- sapply(packages, function(x) {
# Try to load package
if (suppressPackageStartupMessages(require(x, character.only = TRUE, quietly = TRUE))) {
return(TRUE)
}
# Couldn't load
return(FALSE)
})
# Give a warning if some packags couldn't be loaded
if (!all(loaded)) {
failed <- packages[!loaded]
warning("n Failed to load: ", paste(failed, collapse = ", "))
}
return(invisible(loaded))
}
# pre-library packages
using(pak, data.table, stringr, tibble, dplyr, tidyr, purrr, magrittr)
# mirrors
pak::repo_add(
CRAN = "https://mirrors.tuna.tsinghua.edu.cn/CRAN",
BioCsoft = "https://mirrors.tuna.tsinghua.edu.cn/bioconductor/packages/3.16/bioc",
BioCann = "https://mirrors.tuna.tsinghua.edu.cn/bioconductor/packages/3.16/data/annotation",
BioCexp = "https://mirrors.tuna.tsinghua.edu.cn/bioconductor/packages/3.16/data/experiment",
BioCworkflows = "https://mirrors.tuna.tsinghua.edu.cn/bioconductor/packages/3.16/workflows"
)pak添加镜像
写在$HOME/.Rprofile文件中
pak::repo_add(
CRAN = "https://mirrors.tuna.tsinghua.edu.cn/CRAN",
BioCsoft = "https://mirrors.tuna.tsinghua.edu.cn/bioconductor/packages/3.16/bioc",
BioCann = "https://mirrors.tuna.tsinghua.edu.cn/bioconductor/packages/3.16/data/annotation",
BioCexp = "https://mirrors.tuna.tsinghua.edu.cn/bioconductor/packages/3.16/data/experiment",
BioCworkflows = "https://mirrors.tuna.tsinghua.edu.cn/bioconductor/packages/3.16/workflows"
)pak安装R包
使用pak管理R包，可以从Bioconductor、CRAN、Github、本地、URL安装R包，解决了R包安装需要多个不同R包去安装的问题。
除了本地安装使用local_install函数，其他几种安装方式都是用pkg_install函数
install.packages("pak")
using(pak)- CRAN
pak::pkg_install("dplyr")- Bioconductor
pak::pkg_install("ComplexHeatmap")- GitHub
pak::pkg_install("sqjin/CellChat")- URL
pak::pkg_install("url::https://cytotrace.stanford.edu/CytoTRACE_0.3.3.tar.gz")- local
# shell
wget https://cytotrace.stanford.edu/CytoTRACE_0.3.3.tar.gz
tar -xf CytoTRACE_0.3.3.tar.gz # 解压后为CytoTRACE
# R
pak::local_install("CytoTRACE")- 一次安装多个R包
pak::pkg_install(c("BiocNeighbors", "ComplexHeatmap", "circlize", "NMF"))pak删除R包
代码语言：shell复制pkg_remove("CytoTRACE")pak查寻依赖包
只能查CRAN 或 Bioconductor的包的依赖
代码语言：shell复制pak::pkg_deps("tibble")✔ Updated metadata database: 7.30 MB in 9 files.
✔ Updating metadata database ... done
# A data frame: 11 × 32
ref type direct directpkg status package version license needscompilation
<chr> <chr> <lgl> <lgl> <chr> <chr> <chr> <chr> <lgl>
1 cli stan… FALSE FALSE OK cli 3.6.1 MIT … FALSE
2 fansi stan… FALSE FALSE OK fansi 1.0.4 GPL-2 … FALSE
3 glue stan… FALSE FALSE OK glue 1.6.2 MIT … FALSE
4 lifec… stan… FALSE FALSE OK lifecy… 1.0.3 MIT … FALSE
5 magri… stan… FALSE FALSE OK magrit… 2.0.3 MIT … FALSE
6 pillar stan… FALSE FALSE OK pillar 1.9.0 MIT … FALSE
7 pkgco… stan… FALSE FALSE OK pkgcon… 2.0.3 MIT … FALSE
8 rlang stan… FALSE FALSE OK rlang 1.1.0 MIT … FALSE
9 tibble stan… TRUE TRUE OK tibble 3.2.1 MIT … FALSE
10 utf8 stan… FALSE FALSE OK utf8 1.2.3 Apache… FALSE
11 vctrs stan… FALSE FALSE OK vctrs 0.6.1 MIT … FALSE
# ℹ 23 more variables: priority <chr>, md5sum <chr>, sha256 <chr>,
# filesize <int>, built <chr>, platform <chr>, rversion <chr>,
# repotype <chr>, repodir <chr>, target <chr>, deps <list>, mirror <chr>,
# sources <list>, remote <list>, error <list>, metadata <list>,
# dep_types <list>, params <list>, sysreqs <chr>, cache_status <chr>,
# lib_status <chr>, old_version <chr>, new_version <chr>依赖树
代码语言：shell复制pak::pkg_deps_tree("tibble")tibble 3.2.1 ✨ ⬇ (unknown size)
├─fansi 1.0.4 ✨ ⬇ (unknown size)
├─lifecycle 1.0.3 ✨ ⬇ (unknown size)
│ ├─cli 3.6.1 ✨ ⬇ (unknown size)
│ ├─glue 1.6.2 ✨ ⬇ (unknown size)
│ └─rlang 1.1.0 ✨ ⬇ (unknown size)
├─magrittr 2.0.3 ✨ ⬇ (unknown size)
├─pillar 1.9.0 ✨ ⬇ (unknown size)
│ ├─cli
│ ├─fansi
│ ├─glue
│ ├─lifecycle
│ ├─rlang
│ ├─utf8 1.2.3 ✨ ⬇ (unknown size)
│ └─vctrs 0.6.1 ✨ ⬇ (unknown size)
│ ├─cli
│ ├─glue
│ ├─lifecycle
│ └─rlang
├─pkgconfig 2.0.3 ✨ ⬇ (unknown size)
├─rlang
└─vctrs
Key: ✨ new | ⬇ download一个文件夹中的依赖关系
这个tree实在太长了，我只保留前几行和后几行
代码语言：text复制# shell
wget https://cytotrace.stanford.edu/CytoTRACE_0.3.3.tar.gz
tar -xf CytoTRACE_0.3.3.tar.gz # 解压后为CytoTRACE
# R
pak::local_deps_tree("CytoTRACE")✔ Loading metadata database ... done
local::CytoTRACE 0.3.3 ✨?? ⬇ (unknown size)
├─sva 3.46.0 ✨ ⬇ (unknown size)
│ ├─mgcv 1.8-42
│ │ ├─nlme 3.1-162
│ └─magrittr
└─plyr 1.8.8 ✨ ⬇ (unknown size)
└─Rcpp
Key: ✨ new | ✋ outdated | ⬇ download | ?? build安装一个文件夹中的依赖s
代码语言：text复制local_install_deps("CytoTRACE")
# Installs development and optional dependencies as well.
local_install_dev_deps("CytoTRACE")→ Will update 3 packages.
→ Will download 4 packages with unknown size.
DEoptimR 1.0-11 → 1.0-12 ⬇
RCurl 1.98-1.10 → 1.98-1.12 ⬇
RSQLite 2.3.0 → 2.3.1 ⬇
? Do you want to continue (Y/n) pak还有更多功能，比如增加Repositories、Lock file等可以在官网查看
Reference
代码语言：shell复制https://pak.r-lib.org/reference/get-started.html
