A guide to R package management using the pak and cranlogs packages, covering installation, version checking, and analyzing download statistics.

This document provides a comprehensive guide to R package management, focusing on the pak and cranlogs packages. It demonstrates how to use pak for installing, updating, and managing packages from various sources, including CRAN, GitHub, and local files. The guide also covers how to use cranlogs to analyze package download statistics and retrieve information about packages from GitHub. Additionally, it briefly mentions other useful tools for building R packages.

pak installs R packages from CRAN, Bioconductor, GitHub, URLs, git repositories, local files and directories. It is an alternative to install.packages() and devtools::install_github(). pak is fast, safe and convenient.

R packages download and managment tool

install pak

Code

install.packages("pak")

load pak

Code

library(pak)

check pak version

Code

pak_sitrep()

install pacakge from cran

Code

pkg_install("tibble")

install pacakge from github

Code

pkg_install("tidyverse/tibble")

install pacakge file tar.gz from website

Code

pkg_install(
  "url::https://cran.r-project.org/src/contrib/Archive/tibble/tibble_3.1.7.tar.gz"
)

uninstall package

Code

pkg_remove("tibble")

check package

Code

pkg_deps_tree("tibble")

show all Dependencies

Code

pkg_deps("tibble")

Explain dependencies

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pkg_deps_explain("tibble", "rlang")

check pacakge history on cran

Code

pkg_history("tibble")

update package

Code

pkg_install("tibble")

Update all dependencies of a package

Code

pkg_install("tibble", upgrade = TRUE)

Check R pacakge info on Cran

Code

library(pak)
pkg_install("cranlogs")

total pacakge download from last week

Code

library(cranlogs)
cran_downloads(when = "last-week")

total pacakge download from 2014

Code

data=cran_downloads(from = "2014-01-01", to = "2024-12-31")
library(plotly)
plot_ly(data, x = ~date, y = ~count, mode = "lines")

top pacakge download from last week

Code

cran_top_downloads("last-week")

one pacakge download from last week

Code

pacakge_name="tibble"
lastweek=cran_downloads(when = "last-week", package = pacakge_name)
lastweek

Code

print(paste(pacakge_name,"last week been downloaded",sum(lastweek$count),"times"))

check pacakge github info

there is another R package for this gh

Code

library(tidyverse)
library(httr)
library(cranlogs)
library(ggrepel)
library(scales)
library(lubridate)
library(knitr)
library(stringr)

Code

# authenticate to github -------------------------------------------------------
# use Hadley's key and secret
myapp <- oauth_app("github",
                   key = "Ov23lizHQuHjLsuQlgXc",
                   secret = "44ee97da2b3fc85c02bf46b236d1f23739945c8e")
github_token <- oauth2.0_token(oauth_endpoints("github"), myapp)
gtoken <- config(token = github_token)


date_without_zeros <- function(x){
  gsub("0(\\d)", "\\1", format(x, "%m/%d/%y"))
}

gh_from_url <- function(x){
  x <- gsub("http://", "https://", tolower(x))
  x <- gsub("www\\.github\\.com", "github.com", x)
  x <- gsub("^github.com", "https://github.com", x)
  x <- gsub("/issues", "", x)
  x <- gsub("\\.git", "", x)
  x <- gsub("For source code, development versions and issue tracker see", "", x, ignore.case=TRUE)
  x <- trimws(x)
  x <- gsub("development versions and issue tracker see ", "", x, ignore.case=TRUE)
  x <- trimws(x)
  x <- gsub("^<(.*)>$", "\\1", x)
  if(grepl(',', x)){
    x <- strsplit(x, ",")[[1]]
    x <- trimws(x[min(which(grepl('http://github.com|https://github.com|http://www.github.com', x)))])
  }
  if(grepl(' ', x)){  
    x <- strsplit(x, " ")[[1]]
    x <- trimws(x[min(which(grepl('http://github.com|https://github.com|http://www.github.com', x)))])    
  }
  x <- gsub("^(.*)/(.*)#\\([a-zA-z]+\\)\\b", "\\1/\\2", x)
  x <- gsub("^(.*)/(.*)[[:space:]]+\\([a-zA-z]+\\)\\b", "\\1/\\2", x)
  x <- gsub("^(.*) http(.*)$", "http\\2", x)
  x <- trimws(x)
  x <- gsub("/$", "", x)
  x <- trimws(x)
  return(x)
}

aut_maintainer_from_details <- function(x){
  x <- gsub("'|\"", "", x)
  if(grepl(',', x)){
    x <- strsplit(x, "\\],")[[1]]
    aut_cre_ind <- grepl(pattern='\\[aut, cre|\\[cre, aut|\\[cre', x, ignore.case=TRUE)
    if(any(aut_cre_ind)){
      x <- x[min(which(aut_cre_ind))]
      x <- gsub("\\[aut, cre|\\[cre, aut|\\[cre", "", x)
    }
    x <- strsplit(x, ",")[[1]][1]
    x <- trimws(gsub("\\]", "", x))
    x <- trimws(gsub(" \\[aut", "", x))
  }
  x <- trimws(gsub(" \\(.*\\)$", "", x))
  x <- trimws(gsub(" <.*>$", "", x))
  return(x)
}

gh_star_count <- function(url){
  Sys.sleep(0.5)
  stars  <- tryCatch({
    this_url <- gsub("https://github.com/", "https://api.github.com/repos/", url)
    req <- GET(this_url, gtoken)
    stop_for_status(req)
    cont <- content(req)
    cont$stargazers_count  
  }, error = function(e){
    return(NA_integer_)
  })
  return(stars)
}

gh_forks_count <- function(url){
  Sys.sleep(0.5)
  stars  <- tryCatch({
    this_url <- gsub("https://github.com/", "https://api.github.com/repos/", url)
    req <- GET(this_url, gtoken)
    stop_for_status(req)
    cont <- content(req)
    cont$forks  
  }, error = function(e){
    return(NA_integer_)
  })
  return(stars)
}




gh_last_commit_date <- function(url){
  last_commit <- tryCatch({
    this_url <- gsub("https://github.com/", "https://api.github.com/repos/", url)
    req <- GET(paste0(this_url, "/commits?page=1&per_page=1"), gtoken)
    stop_for_status(req)
    cont <- content(req)
    cont[[1]]$commit$committer$date
  }, error = function(e){
    return(NA_character_)
  })
  return(last_commit)
}

Code

github_url="https://github.com/r-lib/styler"

Code

gh_star_count(github_url)

Code

gh_last_commit_date(github_url)

Code

gh_last_commit_date(github_url)

Code

gh_watches_count(github_url)

Tool for build a R pacakge

devtools/roxygen2/usethis/testthat/pkgdown

reference:

https://github.com/r-lib/pak

--- title: "R pacakge download and managment tool" author: "Tony D" execute: warning: false error: false eval: false date: "2025-03-14" categories: - Tool - R image: "my screenshots.png" --- A guide to R package management using the `pak` and `cranlogs` packages, covering installation, version checking, and analyzing download statistics. This document provides a comprehensive guide to R package management, focusing on the `pak` and `cranlogs` packages. It demonstrates how to use `pak` for installing, updating, and managing packages from various sources, including CRAN, GitHub, and local files. The guide also covers how to use `cranlogs` to analyze package download statistics and retrieve information about packages from GitHub. Additionally, it briefly mentions other useful tools for building R packages. pak installs R packages from CRAN, Bioconductor, GitHub, URLs, git repositories, local files and directories. It is an alternative to install.packages() and devtools::install_github(). pak is fast, safe and convenient. # R packages download and managment tool ## install pak ```{r} install.packages("pak") ``` ## load pak ```{r} library(pak) ``` ## check pak version ```{r} pak_sitrep() ``` ## install pacakge from cran ```{r} pkg_install("tibble") ``` # install pacakge from github ```{r} pkg_install("tidyverse/tibble") ``` ## install pacakge file tar.gz from website ```{r} pkg_install( "url::https://cran.r-project.org/src/contrib/Archive/tibble/tibble_3.1.7.tar.gz" ) ``` ## uninstall package ```{r} pkg_remove("tibble") ``` ## check package ```{r} pkg_deps_tree("tibble") ``` ## show all Dependencies ```{r} pkg_deps("tibble") ``` ## Explain dependencies ```{r} pkg_deps_explain("tibble", "rlang") ``` ## check pacakge history on cran ```{r} pkg_history("tibble") ``` ## update package ```{r} pkg_install("tibble") ``` Update all dependencies of a package ```{r} pkg_install("tibble", upgrade = TRUE) ``` # Check R pacakge info on Cran ```{r} library(pak) pkg_install("cranlogs") ``` ## total pacakge download from last week ```{r} library(cranlogs) cran_downloads(when = "last-week") ``` ## total pacakge download from 2014 ```{r} data=cran_downloads(from = "2014-01-01", to = "2024-12-31") library(plotly) plot_ly(data, x = ~date, y = ~count, mode = "lines") ``` ## top pacakge download from last week ```{r} cran_top_downloads("last-week") ``` ## one pacakge download from last week ```{r} pacakge_name="tibble" lastweek=cran_downloads(when = "last-week", package = pacakge_name) lastweek ``` ```{r} print(paste(pacakge_name,"last week been downloaded",sum(lastweek$count),"times")) ``` # check pacakge github info there is another R package for this `gh` ```{r} library(tidyverse) library(httr) library(cranlogs) library(ggrepel) library(scales) library(lubridate) library(knitr) library(stringr) ``` ```{r} # authenticate to github ------------------------------------------------------- # use Hadley's key and secret myapp <- oauth_app("github", key = "Ov23lizHQuHjLsuQlgXc", secret = "44ee97da2b3fc85c02bf46b236d1f23739945c8e") github_token <- oauth2.0_token(oauth_endpoints("github"), myapp) gtoken <- config(token = github_token) date_without_zeros <- function(x){ gsub("0(\\d)", "\\1", format(x, "%m/%d/%y")) } gh_from_url <- function(x){ x <- gsub("http://", "https://", tolower(x)) x <- gsub("www\\.github\\.com", "github.com", x) x <- gsub("^github.com", "https://github.com", x) x <- gsub("/issues", "", x) x <- gsub("\\.git", "", x) x <- gsub("For source code, development versions and issue tracker see", "", x, ignore.case=TRUE) x <- trimws(x) x <- gsub("development versions and issue tracker see ", "", x, ignore.case=TRUE) x <- trimws(x) x <- gsub("^<(.*)>$", "\\1", x) if(grepl(',', x)){ x <- strsplit(x, ",")[[1]] x <- trimws(x[min(which(grepl('http://github.com|https://github.com|http://www.github.com', x)))]) } if(grepl(' ', x)){ x <- strsplit(x, " ")[[1]] x <- trimws(x[min(which(grepl('http://github.com|https://github.com|http://www.github.com', x)))]) } x <- gsub("^(.*)/(.*)#\$[a-zA-z]+\$\\b", "\\1/\\2", x) x <- gsub("^(.*)/(.*)[[:space:]]+\$[a-zA-z]+\$\\b", "\\1/\\2", x) x <- gsub("^(.*) http(.*)$", "http\\2", x) x <- trimws(x) x <- gsub("/$", "", x) x <- trimws(x) return(x) } aut_maintainer_from_details <- function(x){ x <- gsub("'|\"", "", x) if(grepl(',', x)){ x <- strsplit(x, "\\],")[[1]] aut_cre_ind <- grepl(pattern='\\[aut, cre|\\[cre, aut|\\[cre', x, ignore.case=TRUE) if(any(aut_cre_ind)){ x <- x[min(which(aut_cre_ind))] x <- gsub("\\[aut, cre|\\[cre, aut|\\[cre", "", x) } x <- strsplit(x, ",")[[1]][1] x <- trimws(gsub("\\]", "", x)) x <- trimws(gsub(" \\[aut", "", x)) } x <- trimws(gsub(" \$.*\$$", "", x)) x <- trimws(gsub(" <.*>$", "", x)) return(x) } gh_star_count <- function(url){ Sys.sleep(0.5) stars <- tryCatch({ this_url <- gsub("https://github.com/", "https://api.github.com/repos/", url) req <- GET(this_url, gtoken) stop_for_status(req) cont <- content(req) cont$stargazers_count }, error = function(e){ return(NA_integer_) }) return(stars) } gh_forks_count <- function(url){ Sys.sleep(0.5) stars <- tryCatch({ this_url <- gsub("https://github.com/", "https://api.github.com/repos/", url) req <- GET(this_url, gtoken) stop_for_status(req) cont <- content(req) cont$forks }, error = function(e){ return(NA_integer_) }) return(stars) } gh_last_commit_date <- function(url){ last_commit <- tryCatch({ this_url <- gsub("https://github.com/", "https://api.github.com/repos/", url) req <- GET(paste0(this_url, "/commits?page=1&per_page=1"), gtoken) stop_for_status(req) cont <- content(req) cont[[1]]$commit$committer$date }, error = function(e){ return(NA_character_) }) return(last_commit) } ``` ```{r} github_url="https://github.com/r-lib/styler" ``` ```{r} gh_star_count(github_url) ``` ```{r} gh_last_commit_date(github_url) ``` ```{r} gh_last_commit_date(github_url) ``` ```{r} gh_watches_count(github_url) ``` # Tool for build a R pacakge devtools/roxygen2/usethis/testthat/pkgdown # reference: https://github.com/r-lib/pak