Script for finding loaded but unused packages in R scripts

analyze_pkg_usage.R

#!/usr/bin/env Rscript

suppressPackageStartupMessages({
    library(globals)
    library(readr)
    library(stringr)
    library(rex)
    library(magrittr)
    library(rlang)
    library(knitr)
    library(assertthat)
    library(withr)
    library(glue)
    library(BiocParallel)
    register(MulticoreParam())
})

match_identical <- function(x, table, nomatch=NA_integer_) {
    assert_that(is_list(table))
    for (i in seq_along(table)) {
        if (identical(x, table[[i]])) {
            return(i)
        }
    }
    return(nomatch)
}

get_Rmd_source <- function(fname) {
    with_tempfile("temp", {
        purl(fname, output=temp, quiet=TRUE)
        read_file(temp)
    })
}

analyze_pkg_usage <- function(fname) {
    if (str_detect(fname, regex(rex(".Rmd", end), ignore_case=TRUE))) {
        ## Rmd file
        file_text <- get_Rmd_source(fname)
    } else {
        # R file
        file_text <- read_file(fname)
    }
    lib_regex <- rex(
        "library",
        zero_or_more(space),
        "(",
        zero_or_more(space),
        capture(one_or_more(any, type="lazy")),
        zero_or_more(space),
        one_of(",", ")"))
    loaded_pkgs <- unique(do.call(rbind, str_match_all(file_text, lib_regex))[,2])
    missing_pkgs <- character(0)
    for (pkg in loaded_pkgs) {
        if (!suppressMessages(suppressWarnings(
            library(package=pkg, character.only=TRUE, logical.return = TRUE)))) {
            missing_pkgs <- c(missing_pkgs, pkg)
        }
    }
    loaded_pkgs %<>% setdiff(missing_pkgs)
    package_envs <- loaded_pkgs %>% set_names %>%
        lapply(. %>% str_c("package:", .) %>% as.environment)
    package_namespaces <- loaded_pkgs %>% set_names %>% lapply(asNamespace)

    file_exprs <- parse(text=file_text)
    expr_globals <- lapply(file_exprs, globalsOf, mustExist=FALSE)
    used_envs <- unique(do.call(c, lapply(expr_globals, attr, "where")))
    used_pkgs <- character(0)
    for (env in used_envs) {
        for (envlist in list(package_envs, package_namespaces)) {
            found <- match_identical(env, envlist)
            if (!is.na(found)) {
                used_pkgs <- c(used_pkgs, names(envlist)[found])
                break()
            }
        }
    }

    pkg_usage <- list(Used = used_pkgs,
                               Unused = setdiff(loaded_pkgs, used_pkgs))
    if (length(missing_pkgs) > 0) {
        pkg_usage$Missing <- missing_pkgs
    }
    pkg_usage
}

fnames <- commandArgs(TRUE)

pkg_usage <- bplapply(set_names(fnames), function(fname) {
    message("Analyzing ", deparse(fname))
    try(analyze_pkg_usage(fname))
})

message("Package usage:")
print(pkg_usage)
saveRDS(pkg_usage, "pkg_usage.RDS")

If you think my script is missing some cases, I'd like to know about it so I can fix it.

My script depends on functions from the packages:

• pacman (function p_load())
• ggspatial (layer_spatial())
• data.table (fread())
• dplyr (group_by())
• ggrepel (geom_text_repel())
• rgdal
• raster (shapefile())
• lubridate (ymd())

It fails if I don't require one of those packages. The analysis script found that sf is unused and this is correct (in fact, the line library(sf) was commented out in the R script, but the analysis script found it). However, it only listed one used package. I can't remember which one now but I am happy to check later when I'm back at that computer.

It is entirely possible that I just didn't use the script correctly or didn't quite understand what it aims to output, I'm sorry if that is the case.