Running ‘testthat.R’ [15s/93s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(biomartr)
  > 
  > test_check("biomartr")
  1. Error: The biomart() interface works properly.. (@test-biomart.R#14) --------
  Unexpected format to the list of available marts.
  Please check the following URL manually, and try ?listMarts for advice.
  http://www.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt
  1: expect_true(equal_lists(as.list(biomart(genes = "GUCA2A", mart = as.character(marts$mart[ex_mart]), 
         dataset = "hsapiens_gene_ensembl", attributes = c("start_position", "end_position", 
             "description"), filters = "hgnc_symbol")[1, 1:3]), list(hgnc_symbol = "GUCA2A", 
         start_position = 42162691, end_position = 42164718))) at testthat/test-biomart.R:14
  2: expect(identical(as.vector(object), TRUE), sprintf("%s isn't true.", lab), info = info)
  3: as.expectation(exp, ..., srcref = srcref)
  4: identical(as.vector(object), TRUE)
  5: as.vector(object)
  6: equal_lists(as.list(biomart(genes = "GUCA2A", mart = as.character(marts$mart[ex_mart]), 
         dataset = "hsapiens_gene_ensembl", attributes = c("start_position", "end_position", 
             "description"), filters = "hgnc_symbol")[1, 1:3]), list(hgnc_symbol = "GUCA2A", 
         start_position = 42162691, end_position = 42164718))
  7: isTRUE(all.equal(df1, df2)) at testthat/test-biomart.R:4
  8: all.equal(df1, df2)
  9: as.list(biomart(genes = "GUCA2A", mart = as.character(marts$mart[ex_mart]), dataset = "hsapiens_gene_ensembl", 
         attributes = c("start_position", "end_position", "description"), filters = "hgnc_symbol")[1, 
         1:3])
  10: biomart(genes = "GUCA2A", mart = as.character(marts$mart[ex_mart]), dataset = "hsapiens_gene_ensembl", 
         attributes = c("start_position", "end_position", "description"), filters = "hgnc_symbol")
  11: biomaRt::useMart(mart, host = "www.ensembl.org")
  12: listMarts(host = host, path = path, port = port, includeHosts = TRUE, archive = archive, 
         ssl.verifypeer = ssl.verifypeer, ensemblRedirect = ensemblRedirect)
  13: stop("Unexpected format to the list of available marts.\n", "Please check the following URL manually, ", 
         "and try ?listMarts for advice.\n", request)
  
  trying URL 'ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/archaea/assembly_summary.txt'
  Content type 'unknown' length 195191 bytes (190 KB)
  ==================================================
  trying URL 'ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/assembly_summary.txt'
  Content type 'unknown' length 26547893 bytes (25.3 MB)
  ==================================================
  trying URL 'ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/fungi/assembly_summary.txt'
  Content type 'unknown' length 79196 bytes (77 KB)
  ==================================================
  trying URL 'ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/invertebrate/assembly_summary.txt'
  Content type 'unknown' length 43811 bytes (42 KB)
  ==================================================
  trying URL 'ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/plant/assembly_summary.txt'
  Content type 'unknown' length 27738 bytes (27 KB)
  ==================================================
  trying URL 'ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/protozoa/assembly_summary.txt'
  Content type 'unknown' length 24012 bytes (23 KB)
  ==================================================
  trying URL 'ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/assembly_summary.txt'
  Content type 'unknown' length 33589 bytes (32 KB)
  ==================================================
  trying URL 'ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_other/assembly_summary.txt'
  Content type 'unknown' length 38025 bytes (37 KB)
  ==================================================
  trying URL 'ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/viral/assembly_summary.txt'
  Content type 'unknown' length 1756171 bytes (1.7 MB)
  ==================================================
  trying URL 'ftp://ftp.ncbi.nlm.nih.gov/genomes/GENOME_REPORTS/overview.txt'
  Content type 'unknown' length 2202652 bytes (2.1 MB)
  ==================================================
  trying URL 'ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/metagenomes/assembly_summary.txt'
  Content type 'unknown' length 353537 bytes (345 KB)
  ==================================================
  testthat results ================================================================
  OK: 5 SKIPPED: 48 FAILED: 1
  1. Error: The biomart() interface works properly.. (@test-biomart.R#14) 
  
  Error: testthat unit tests failed
  Execution halted