lintr: A 'Linter' for R Code

#!/usr/bin/env Rscript
library(withr)
library(pkgload)
library(data.table)
library(glue)

if (!file.exists("revdep-repos")) {
  stop("Please run .dev/revdep_get_repos.R first before running this")
}
withr::local_options(width = 180)
repo_data <- rbind(
  data.table::fread("revdep-repos"),
  # land after the initial lines of comments on the header line
  data.table::fread("revdep-extra-repos", skip = "package,repo"),
  data.table::fread("revdep-no-repos")
)
setkey(repo_data, repo)

new_packages <- setdiff(repo_data$package, rownames(installed.packages()))
install.packages(new_packages, repos = "https://cran.rstudio.com")
failed_install <- setdiff(new_packages, rownames(installed.packages()))
if (length(failed_install) > 0L) {
  stop("Failed to install some dependencies; please install these packages manually: ", toString(failed_install))
}

dev_dir <- getwd()
dev_branch <- system2("git", c("rev-parse", "--abbrev-ref", "HEAD"), stdout = TRUE)
old_release <- "v3.0.2"
main <- "main"

all_repos <- repo_data$repo

lint_timings <- new.env()
lint_timings$repo_timing <- vector("list", length(all_repos))
names(lint_timings$repo_timing) <- all_repos

# ---- Shims of deleted linters ----
# these help unearth issues in packages which are using the deleted functions,
#   by ensuring lint_package() at least gets past parsing .lintr (with warning)
absolute_paths_linter <-
camel_case_linter <-
multiple_dots_linter <-
snake_case_linter <-
trailing_semicolons_linter <- function(...) {
  # .call=TRUE means the linter name will be displayed in the warning
  warning("Using deleted linter")
  Linter(function(...) list())
}


# ---- Helpers ----
get_hash <- function() system2("git", c("rev-parse", "HEAD"), stdout = TRUE)

result_path <- function(...) file.path(dev_dir, "revdep_comparison", ...)

setup <- function(version) {
  message("Checking out & loading ", version)
  system2("git", c("checkout", "--quiet", version))
  pkgload::load_all(quiet = TRUE)
  out_dir <- result_path(version)
  dir.create(out_dir, recursive = TRUE, showWarnings = FALSE)
  message("Cloning repos and running lint_package()...")
  out_dir
}

cleanup <- function(version) {
  repo_data[, paste0("elapsed_", version) := elapsed]
  repo_data[, elapsed := NULL]

  setwd(dev_dir)
  system2("git", c("checkout", "--quiet", dev_branch))
}

find_r_package_below <- function(top_dir) {
  withr::local_dir(top_dir)
  # most common case: we land in the package directory
  if (file.exists("DESCRIPTION")) {
    return(top_dir)
  }
  # could also do well with breadth-first search, but this code is simpler
  desc_file <- list.files(top_dir, full.names = TRUE, recursive = TRUE, pattern = "^DESCRIPTION$")
  if (length(desc_file) == 0L) {
    stop("Could not find any DESCRIPTION below ", top_dir)
  } else if (length(desc_file) > 1L) {
    stop("Could not uniquely identify an R package in ", top_dir, ". Found these: ", toString(desc_file))
  }
  dirname(desc_file)
}

clone_and_lint <- function(repo_url) {
  message("  * ", repo_url)
  repo_dir <- withr::local_tempdir(basename(repo_url))
  # gert::git_clone() doesn't support shallow clones -- gert#101
  system2(
    "git",
    c("clone", "--depth=1", "--quiet", repo_url, repo_dir)
  )
  withr::local_dir(find_r_package_below(repo_dir))
  repo_data[.(repo_url), git_hash := get_hash()]
  package <- read.dcf("DESCRIPTION", "Package")

  start_time <- proc.time()
  on.exit(repo_data[.(repo_url), elapsed := (proc.time() - start_time)["elapsed"]])
  warnings <- character()
  withCallingHandlers(
    tryCatch(
      {
        lints <- lintr::lint_package()
        utils::write.csv(
          as.data.frame(lints),
          file.path(out_dir, paste0(package, ".csv")),
          row.names = FALSE
        )
      },
      error = function(cond) {
        writeLines(conditionMessage(cond), file.path(out_dir, paste0(package, ".failure")))
      }
    ),
    warning = function(cond) {
      warnings <<- c(warnings, conditionMessage(cond))
      invokeRestart("muffleWarning")
    }
  )
  if (length(warnings) > 0L) {
    writeLines(warnings, file.path(out_dir, paste0(package, ".warnings")))
  }
}

load_lints <- function(version, filter_errors = TRUE) {
  csv_files <- list.files(result_path(version), pattern = "\\.csv$", full.names = TRUE)
  names(csv_files) <- gsub("\\.csv$", "", basename(csv_files))
  # fread mangles quotes: data.table#1109
  lints <- data.table::rbindlist(lapply(csv_files, utils::read.csv), idcol = "repo")
  if (filter_errors) lints <- lints[, if (!any(type == "error")) .SD, by = .(repo, filename)]
  lints
}

as.data.table.proc_time <- function(x) {
  data.table(user = x[[1L]], system = x[[2L]], elapsed = x[[3L]])
}

match_and_strip <- function(x, pattern) gsub(pattern, "", grep(pattern, x, value = TRUE))

summarize_failures <- function(version, failures) {
  files <- result_path(version, failures)
  packages <- gsub("\\.failures$", "", failures)

  package_failures <- sapply(files, function(x) paste(unique(readLines(x)), collapse = " ||| "))

  paste(sprintf("  %s: %s", packages, package_failures), collapse = "\n")
}

summarize_lint_delta <- function(new, old) {
  new_version <- new$version[1L]
  old_version <- old$version[1L]

  new_error_files <- new[type == "error", .(. = TRUE), by = .(package, filename)]
  old_error_files <- new[type == "error", .(. = TRUE), by = .(package, filename)]

  all_error_files <- merge(
    new_error_files, old_error_files,
    by = c("package", "filename"), suffixes = c("new", "old"),
    all = TRUE
  )
  if (anyNA(all_error_files)) {
    if (anyNA(all_error_files$.new)) {
      all_error_files[
        is.na(.new),
        message("Linting failed ", old_version, " but not ", new_version, ": ", toString(filename))
      ]
    }
    if (anyNA(all_error_files$.old)) {
      all_error_files[
        is.na(.old),
        message("Linting failed ", new_version, " but not ", old_version, ": ", toString(filename))
      ]
    }
  }
  new <- new[!all_error_files, on = c("package", "filename")]
  old <- old[!all_error_files, on = c("package", "filename")]

  new_only <- new[!old, on = c("package", "filename", "line_number")]
  new_only[, version := NULL]

  old_only <- old[!new, on = c("package", "filename", "line_number")]
  old_only[, version := NULL]

  withr::local_options(datatable.print.nrows = Inf)

  message("Count of lints found on ", new_version, " but not on ", old_version, ": ", nrow(new_only))
  message("Count of these by linter:")
  print(new_only[, .N, by = linter][order(-N)])
  message("Sample of <=10 hits from each linter:")
  new_only[
    sample(.N),
    head(.SD, 10L),
    by = linter
  ][, .(line = sprintf("%s [%s]", line, linter), location = paste0(package, ":", filename))
  ][, print(.SD)]

  message("Count of lints found on ", old_version, " but not on ", new_version, ": ", nrow(old_only))
  message("Count of these by linter:")
  print(old_only[, .N, by = linter][order(-N)])
  message("Sample of <=10 hits from each linter:")
  old_only[
    sample(.N),
    head(.SD, 10L),
    by = linter
  ][, .(line = sprintf("%s [%s]", line, linter), location = paste0(package, ":", filename))
  ][, print(.SD)]

  invisible()
}

# ---- Main linting execution ----
out_dir <- setup(main)
main_hash <- get_hash()
for (repo in all_repos) clone_and_lint(repo)
cleanup(main)

out_dir <- setup(old_release)
for (repo in all_repos) clone_and_lint(repo)
cleanup(old_release)

# ---- Success comparison ----
main_results <- list.files(result_path(main), full.names = TRUE)
old_results <- list.files(result_path(old_release), full.names = TRUE)

main_only <- setdiff(basename(main_results), basename(old_results))
old_only <- setdiff(basename(old_results), basename(main_results))
shared <- intersect(basename(main_results), basename(old_results))

summarize_warned <- function(warned, label) {
  message("The following packages warned on ", label, ":")
  if (length(warned) > 0) {
    message("  ", toString(match_and_strip(warned, "\\.warnings$")), "\n")
  } else {
    message("  None! 🎉")
  }
}
summarize_warned(main_only, "main only")
summarize_warned(old_only, paste(old_release, "only"))
summarize_warned(shared, "both branches")

main_only <- grep("warnings$", main_only, invert = TRUE, value = TRUE)
old_only <- grep("warnings$", old_only, invert = TRUE, value = TRUE)
shared <- grep("warnings$", shared, invert = TRUE, value = TRUE)

message("The following packages failed on ", main, " only: ")
message(summarize_failures(main, grep("\\.failure", main_only, value = TRUE)))
message("The following packages failed on ", old_release, " only: ")
message(summarize_failures(old_release, grep("\\.failure", old_only, value = TRUE)))
message("The following packages failed on both branches:\n  ", toString(match_and_strip(shared, "\\.failure")), "\n")

shared <- grep("csv$", shared, value = TRUE)

# ---- Lint output comparison ----
main_lints <- rbindlist(lapply(setNames(result_path(main, shared), shared), utils::read.csv), idcol = "package")
main_lints[, version := main]
main_lints[, package := gsub("\\.csv$", "", package)]
old_lints <- rbindlist(lapply(setNames(result_path(old_release, shared), shared), utils::read.csv), idcol = "package")
old_lints[, version := old_release]
old_lints[, package := gsub("\\.csv$", "", package)]

summarize_lint_delta(main_lints, old_lints)

# ---- Timing comparison ----
elapsed_main <- repo_data[[paste0("elapsed_", main)]]
elapsed_old <- repo_data[[paste0("elapsed_", old_release)]]

message("Comparison of total time to run lint_packages() across all repos:")
message(sprintf(
  "  %.0fm to run on %s, %.0fm to run on %s",
  sum(elapsed_main), main, sum(elapsed_old), old_release
))

repo_data[, delta := elapsed_main - elapsed_old]
repo_data[, delta_pct := 100 * delta / elapsed_old]
message("Comparison of time to run lint_package() on each repo (new - old; negative -> faster)")
repo_data[
  order(delta),
  { print(.SD, nrows = Inf); quantile(delta, 0:10/10) },
  .SDcols = patterns("^elapsed|package|^delta")
]

# ---- Prepare e-mails for maintainers ----
email_dir <- file.path(dev_dir, "revdep_emails")
dir.create(email_dir, showWarnings = FALSE)
email_template <- readChar("revdep-email-template", file.size("revdep-email-template"))
for (ii in seq_len(nrow(repo_data))) {
  package <- repo_data$package[ii]
  repo_url <- repo_data$repo[ii]
  git_hash <- repo_data$git_hash[ii]

  maintainer_email <- utils::maintainer(package)
  maintainer <- sub(" <.*$", "", maintainer_email)
  email <- gsub("^[^<]*<|>$", "", maintainer_email)

  main_duration <- round(elapsed_main[ii])
  old_duration <- round(elapsed_old[ii])

  dir.create(file.path(email_dir, package), showWarnings = FALSE)
  writeLines(glue::glue(email_template), file.path(email_dir, package, "email-body"))

  attachments_dir <- file.path(email_dir, package, "attachments")
  dir.create(attachments_dir, showWarnings = FALSE)
  failure_file <- result_path(main, paste0(package, ".failure"))
  if (failure_file %in% main_results) {
    if (paste0(package, ".failure") %in% basename(old_results)) next

    file.copy(failure_file, file.path(attachments_dir, basename(failure_file)))
  }

  warning_file <- result_path(main, paste0(package, ".warnings"))
  if (warning_file %in% main_results) {
    old_warning_file <- result_path(old_release, paste0(package, ".warnings"))
    if (old_warning_file %in% old_results) {
      new_warnings <- setdiff(readLines(warning_file), readLines(old_warning_file))
      writeLines(new_warnings, file.path(attachments_dir, basename(warning_file)))
    } else {
      file.copy(warning_file, file.path(attachments_dir, basename(warning_file)))
    }
  }

  PKG = package
  main_only_lints <- main_lints[package == PKG][!old_lints, on = c("package", "filename", "line_number")]
  if (nrow(main_only_lints) > 0L) {
    utils::write.csv(
      main_only_lints[, c("filename", "line_number", "column_number", "type", "message", "line", "linter")],
      file.path(attachments_dir, "lints_in_devel_not_cran.csv"),
      row.names = FALSE
    )
  }

  old_only_lints <- old_lints[package == PKG][!main_lints, on = c("package", "filename", "line_number")]
  if (nrow(old_only_lints) > 0L) {
    utils::write.csv(
      old_only_lints[, c("filename", "line_number", "column_number", "type", "message", "line", "linter")],
      file.path(attachments_dir, "lints_in_cran_not_devel.csv"),
      row.names = FALSE
    )
  }
}