Running ‘testthat.R’ [4s/77s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(biolink)
  > 
  > test_check("biolink")
  ── 1. Error: PubMed tag substitution (@test-tags-pubmed.r#26)  ─────────────────
  HTTP failure: 400
  LB grop of viewer for database: pubmed - has no active hosts
  1: link_pubmed(id, "<journal>", format = "html") at testthat/test-tags-pubmed.r:26
  2: sub_var(text, id, "pubmed")
  3: withVisible(`_f`(x = x, id = id, db = db))
  4: `_f`(x = x, id = id, db = db)
  5: query_pubmed(id, field)
  6: query_ncbi(check_id(id, "pubmed"), "pubmed")
  7: xml2::read_xml(rentrez::entrez_fetch(db, id, rettype = "xml"))
  8: rentrez::entrez_fetch(db, id, rettype = "xml")
  9: do.call(make_entrez_query, args)
  10: (function (util, config, interface = ".fcgi?", by_id = FALSE, debug_mode = FALSE, 
         ...) 
     {
         uri <- paste0("https://eutils.ncbi.nlm.nih.gov/entrez/eutils/", util, interface)
         args <- list(..., email = entrez_email(), tool = entrez_tool())
         if (!("api_key" %in% names(args))) {
             if (is_entrez_key_set()) {
                 args$api_key <- Sys.getenv("ENTREZ_KEY")
             }
         }
         if ("id" %in% names(args)) {
             if (by_id) {
                 ids_string <- paste0("id=", args$id, collapse = "&")
                 args$id <- NULL
                 uri <- paste0(uri, ids_string)
             }
             else {
                 args$id <- paste(args$id, collapse = ",")
             }
         }
         if (debug_mode) {
             return(list(uri = uri, args = args))
         }
         if (length(args$id) > 200) {
             response <- httr::POST(uri, body = args, config = config)
         }
         else {
             response <- httr::GET(uri, query = args, config = config)
         }
         entrez_check(response)
         Sys.sleep(sleep_time(args))
         httr::content(response, as = "text", encoding = "UTF-8")
     })("efetch", db = "pubmed", rettype = "xml", config = NULL, retmode = "", id = "22066989")
  11: entrez_check(response)
  12: stop("HTTP failure: ", req$status_code, "\n", message, call. = FALSE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 118 SKIPPED: 1 FAILED: 1
  1. Error: PubMed tag substitution (@test-tags-pubmed.r#26) 
  
  Error: testthat unit tests failed
  Execution halted