Running ‘testthat.R’ [15s/34s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(biomartr)
  > 
  > test_check("biomartr")
  trying URL 'ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/archaea/assembly_summary.txt'
  ── 1. Error: The getAssemblyStats() throws error when undefined 'organism' is se
  The FTP site 'ftp://ftp.ncbi.nlm.nih.gov/' cannot be reached. 
                  Are you connected to the internet? Is the the FTP site 'ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/archaea/assembly_summary.txt' currently available?
  1: expect_message(getAssemblyStats(db = "refseq", organism = "somethingelse", type = "download")) at testthat/test-getAssemblyStats.R:85
  2: quasi_capture(enquo(object), capture_messages, label = label)
  3: capture(act$val <- eval_bare(get_expr(quo), get_env(quo)))
  4: withCallingHandlers(code, message = function(condition) {
         out$push(condition)
         invokeRestart("muffleMessage")
     })
  5: eval_bare(get_expr(quo), get_env(quo))
  6: getAssemblyStats(db = "refseq", organism = "somethingelse", type = "download")
  7: getKingdomAssemblySummary(db = db)
  8: getSummaryFile(db = db, kingdom = kgdoms[i])
  9: tryCatch({
         suppressMessages(downloader::download(paste0("ftp://ftp.ncbi.nlm.nih.gov/genomes/", 
             db, "/", kingdom, "/assembly_summary.txt"), destfile = file.path(tempdir(), 
             paste0("assembly_summary_", kingdom, "_", db, ".txt")), mode = "wb"))
     }, error = function(e) stop("The FTP site 'ftp://ftp.ncbi.nlm.nih.gov/' cannot be reached. \n                Are you connected to the internet? Is the the FTP site '", 
         paste0("ftp://ftp.ncbi.nlm.nih.gov/genomes/", db, "/", kingdom, "/assembly_summary.txt"), 
         "' currently available?", call. = FALSE))
  10: tryCatchList(expr, classes, parentenv, handlers)
  11: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  12: value[[3L]](cond)
  13: stop("The FTP site 'ftp://ftp.ncbi.nlm.nih.gov/' cannot be reached. \n                Are you connected to the internet? Is the the FTP site '", 
         paste0("ftp://ftp.ncbi.nlm.nih.gov/genomes/", db, "/", kingdom, "/assembly_summary.txt"), 
         "' currently available?", call. = FALSE)
  
  trying URL 'ftp://ftp.ncbi.nlm.nih.gov/genomes/GENOME_REPORTS/overview.txt'
  Content type 'unknown' length 3047324 bytes (2.9 MB)
  ==================================================
  trying URL 'ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/metagenomes/assembly_summary.txt'
  Content type 'unknown' length 595587 bytes (581 KB)
  ==================================================
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 6 SKIPPED: 60 FAILED: 1
  1. Error: The getAssemblyStats() throws error when undefined 'organism' is selected
            .. (@test-getAssemblyStats.R#85) 
  
  Error: testthat unit tests failed
  Execution halted