Diagnostic testing

Run a set of diagnostic tests to check for common issues found when setting up R on a DfE system. The function runs each check_*() helper in turn and returns a combined list of detected settings. Problems can optionally be fixed by passing clean = TRUE.

The checks include:

• Proxy settings in the Git configuration and system environment (check_proxy_settings())

• Git SSL-verify setting (check_git_sslverify())

• The location of the global .gitconfig file (check_gitconfig_location())

• The GITHUB_PAT system variable (check_github_pat())

• renv download method in .Renviron (check_renv_download_method())

• The RENV_DOWNLOAD_FILE_METHOD system variable (check_renv_dl_file_method())

• Presence of an RTools/make toolchain (check_rtools())

• The location of .Renviron and .Rprofile (check_renv_rprof_location())

Usage

diagnostic_test(clean = FALSE, full = FALSE)

Arguments

clean

If TRUE, attempt to clean detected issues. Default FALSE.

full

If TRUE, append a session-dump section after the per-check output containing renv::diagnostics(), Sys.getenv() and options(). Useful for sharing a full diagnostic with support. Defaults to FALSE. Environment variables whose names look sensitive (containing e.g. TOKEN, SECRET, KEY, PAT, PASSWORD, CRED) are masked, but the options() and renv::diagnostics() sections are printed as-is, so review the output before sharing it in public channels.

Value

Invisibly, a named list keyed by check (proxy, sslverify, gitconfig, github_pat, renv_download, renv_download_file, rtools, renviron_rprofile). Each entry is the result list returned by the corresponding check_* helper, plus a status field.

Details

Each check returns a list including a status field, one of "pass", "fail", "fixed" or "info", depending on the outcome of the check.

Examples

diagnostic_test()
#> 
#> ── dfeR diagnostics ────────────────────────────────────────────────────────────
#> 
#> ── Proxy settings ──
#> 
#> ✔ No proxy settings found in your Git config or system environment.
#> 
#> ── Git sslverify ──
#> 
#> ✔ sslverify is not explicitly set.
#> 
#> ── Global .gitconfig location ──
#> 
#> ℹ No entries found in your global .gitconfig (Git could not locate one).
#> 
#> ── GITHUB_PAT ──
#> 
#> ✖ GITHUB_PAT is set (length 377, ending ...Ng-Q). This may cause issues with installing packages from GitHub such as dfeR and dfeshiny. The GITHUB_PAT value is sensitive - do not share it.
#> 
#> ── renv download method ──
#> 
#> ✖ RENV_DOWNLOAD_METHOD is not currently set.
#> To manually update your .Renviron file:
#> • Run `usethis::edit_r_environ()` in the R console.
#> • Add the following line to .Renviron: `RENV_DOWNLOAD_METHOD="curl"`
#> Or run `dfeR::check_renv_download_method(clean = TRUE)`.
#> 
#> ── RENV_DOWNLOAD_FILE_METHOD ──
#> 
#> ✔ RENV_DOWNLOAD_FILE_METHOD is not set.
#> 
#> ── RTools / make toolchain ──
#> 
#> ✔ Found 'make' at /usr/bin/make.
#> 
#> ── .Renviron / .Rprofile location ──
#> 
#> .Renviron: not found in any location R reads (working directory or home).
#> 
#> .Rprofile:
#> • /home/runner/.Rprofile [USED]
#> 
#> ── Summary ─────────────────────────────────────────────────────────────────────
#> 
#> ✖ 4 PASS, 2 FAIL (github_pat, renv_download), 2 INFO