tools/extra-tests.R

In jackwasey/icd: Comorbidity Calculations and Tools for ICD-9 and ICD-10 Codes

#!/usr/bin/env Rscript

wd_icd <- function() {
  icd_home <- Sys.getenv("ICD_HOME", unset = NA_character_)
  if (is.na(icd_home)) {
    warning(
      "Shell environment variable ICD_HOME is unset. ",
      "Set to top of working set to avoid ambiguity. E.g.:"
    )
    message(
      "Sys.setenv(ICD_HOME = Sys.getenv(\"ICD_HOME\")\""
    )
    message(
      "Sys.setenv(ICD_HOME = Sys.getenv(\"ICD_HOME\")\""
    )
    warning(
      "Setting working directory to top of this package source tree, ",
      "if possible"
    )
    devtools::wd()
  } else {
    message("PWD=", getwd())
    message("ICD_HOME=", icd_home)
    setwd(icd_home)
  }
  invisible(icd_home)
}

release_sanity_checks <- function() {
  message("superficially checking data download before and after attaching")
  icd::download_all_icd_data()
  suppressPackageStartupMessages(
    library(
      "icd",
      quietly = TRUE,
      warn.conflicts = FALSE
    )
  )
  download_all_icd_data()

  wd_icd()

  message("style check")
  # exclude R_user_dir.R so easier to diff with upstream
  styler::style_pkg(
    exclude_dirs = c("icd.Rcheck"),
    exclude_files = c(
      "R/RcppExports.R",
      "R/R_user_dir.R"
    ),
    dry = "fail"
  )

  message("codetools on everything")
  codetools::checkUsagePackage("icd",
                               all = TRUE,
                               suppressLocal = TRUE)

  message("Missing NAMESPACE S3")
  s <- devtools::missing_s3()
  if (length(s)) s


  message("spelling")
  aspell_package_Rd_files(".")
}

check_rhub_no_prebuilt_vign <- function(check_fun = rhub::check_for_cran,
                                        check_fun_args = list()) {
  wd_icd()
  td <- tempfile("icd-no-static-vignettes")
  dir.create(td)
  message("Using temp dir: ", td)
  ih <- Sys.getenv("ICD_HOME")
  if (ih == "") ih <- file.path("~", "icd")
  file.copy(ih, td, recursive = TRUE, overwrite = TRUE)
  icd_tmp_path <- file.path(td, "icd")
  setwd(icd_tmp_path)
  cat("^vignettes\\/.*\\.Rnw$",
    fill = TRUE,
    append = TRUE,
    file = file.path(icd_tmp_path, ".Rbuildignore")
  )
  do.call(check_fun, check_fun_args)
  message("Completed check using tree at: ", td)
}

check_local_gctorture <- function(filter = ".*", args = character()) {
  wd_icd()
  with_split_tests(
    rcmdcheck::rcmdcheck(args = c("--use-gct", args = args))
  )
}

# THIS DOESN'T WORK! Eigen spews out warnings when RcppEigen itself is
# installed, not when icd is installed.
check_rhub_valgrind <- function(fun = rhub::check_with_valgrind,
                                filter = ".*") {
  wd_icd()
  shutup <-
    paste0(
      "CXX11FLAGS=",
      paste0(
        "-Wno-",
        c(
          "unused-parameter",
          "unused-variable",
          "ignored-attributes",
          "cast-function-type",
          "unknown-pragmas",
          "unknown-warning-option",
          "unknown-warning"
        ),
        collapse = " "
      )
    )
  with_split_tests(
    fun(
      check_args = paste(
        "--no-vignettes",
        "--no-build-vignettes",
        "--ignore-vignettes",
        paste0("--install-args='--configure-vars=\"", shutup, "\"'")
      )
    )
  )
}