Running ‘testthat.R’ [3s/266s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(avidaR)
  Please, change the name of the repository to access the entire avidaDB database.
  By default, avidaR points to a small subset for testing (avidaDB_test).
  In order to do it, you should run the following:
  
  triplestore$set_access_options(
    url = "https://graphdb.fortunalab.org",
    user = "public_avida",
    password = "public_avida",
    repository = "avidaDB"
  )
  > 
  > test_check("avidaR")
  [ FAIL 26 | WARN 0 | SKIP 0 | PASS 12 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error (test_get_db_summary.R:3:3): get_db_summary ───────────────────────────
  Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached: [graphdb.fortunalab.org] Connection timeout after 10000 ms
  Backtrace:
      ▆
   1. └─avidaR::get_db_summary() at test_get_db_summary.R:3:2
   2.   └─triplestore$submit_query("PREFIX terms: <http://purl.org/dc/terms/>\n                                        PREFIX ONTOAVIDA: <http://purl.obolibrary.org/obo/ONTOAVIDA_>\n                                        select ?abstract where { \n                                          ONTOAVIDA:11111111 terms:abstract ?abstract .\n                                        }")
   3.     └─httr::POST(...)
   4.       └─httr:::request_perform(req, hu$handle$handle)
   5.         ├─httr:::request_fetch(req$output, req$url, handle)
   6.         └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   7.           └─curl::curl_fetch_memory(url, handle = handle)
  ── Error (test_get_genome_id_from_genome_seq.R:6:3): get_genome_id_from_genome_seq ──
  Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached: [graphdb.fortunalab.org] Connection timeout after 10000 ms
  Backtrace:
      ▆
   1. └─avidaR::get_genome_id_from_genome_seq(genome_seq = sequence1) at test_get_genome_id_from_genome_seq.R:6:2
   2.   └─triplestore$submit_query(query = query)
   3.     └─httr::POST(...)
   4.       └─httr:::request_perform(req, hu$handle$handle)
   5.         ├─httr:::request_fetch(req$output, req$url, handle)
   6.         └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   7.           └─curl::curl_fetch_memory(url, handle = handle)
  ── Error (test_get_genome_id_from_logic_operation.R:3:3): get_genome_id_from_logic_operation ──
  Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached: [graphdb.fortunalab.org] Connection timeout after 10001 ms
  Backtrace:
      ▆
   1. └─avidaR::get_genome_id_from_logic_operation(...) at test_get_genome_id_from_logic_operation.R:3:2
   2.   └─avidaR::get_genome_id_from_phenotype_id(...)
   3.     └─triplestore$submit_query(query = query)
   4.       └─httr::POST(...)
   5.         └─httr:::request_perform(req, hu$handle$handle)
   6.           ├─httr:::request_fetch(req$output, req$url, handle)
   7.           └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   8.             └─curl::curl_fetch_memory(url, handle = handle)
  ── Error (test_get_genome_id_from_phenotype_id.R:3:3): get_genome_id_from_phenotype_id ──
  Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached: [graphdb.fortunalab.org] Connection timeout after 10001 ms
  Backtrace:
      ▆
   1. └─avidaR::get_genome_id_from_phenotype_id(phenotype_id = 0, seed_id = 1) at test_get_genome_id_from_phenotype_id.R:3:2
   2.   └─triplestore$submit_query(query = query)
   3.     └─httr::POST(...)
   4.       └─httr:::request_perform(req, hu$handle$handle)
   5.         ├─httr:::request_fetch(req$output, req$url, handle)
   6.         └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   7.           └─curl::curl_fetch_memory(url, handle = handle)
  ── Error (test_get_genome_id_from_transcriptome_id.R:3:3): get_genome_id_from_transcriptome_id ──
  Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached: [graphdb.fortunalab.org] Connection timeout after 10001 ms
  Backtrace:
      ▆
   1. └─avidaR::get_genome_id_from_transcriptome_id(transcriptome_id = 53674) at test_get_genome_id_from_transcriptome_id.R:3:2
   2.   └─triplestore$submit_query(query = query)
   3.     └─httr::POST(...)
   4.       └─httr:::request_perform(req, hu$handle$handle)
   5.         ├─httr:::request_fetch(req$output, req$url, handle)
   6.         └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   7.           └─curl::curl_fetch_memory(url, handle = handle)
  ── Error (test_get_genome_id_of_wild_type_organisms.R:3:3): get_genome_id_of_wild_type_organisms ──
  Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached: [graphdb.fortunalab.org] Connection timeout after 10000 ms
  Backtrace:
      ▆
   1. └─avidaR::get_genome_id_of_wild_type_organisms() at test_get_genome_id_of_wild_type_organisms.R:3:2
   2.   └─triplestore$submit_query(query = query)
   3.     └─httr::POST(...)
   4.       └─httr:::request_perform(req, hu$handle$handle)
   5.         ├─httr:::request_fetch(req$output, req$url, handle)
   6.         └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   7.           └─curl::curl_fetch_memory(url, handle = handle)
  ── Error (test_get_genome_seq_from_genome_id.R:3:3): get_genome_seq_from_genome_id ──
  Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached: [graphdb.fortunalab.org] Connection timeout after 10001 ms
  Backtrace:
      ▆
   1. └─avidaR::get_genome_seq_from_genome_id(genome_id = 1) at test_get_genome_seq_from_genome_id.R:3:2
   2.   └─triplestore$submit_query(query = query)
   3.     └─httr::POST(...)
   4.       └─httr:::request_perform(req, hu$handle$handle)
   5.         ├─httr:::request_fetch(req$output, req$url, handle)
   6.         └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   7.           └─curl::curl_fetch_memory(url, handle = handle)
  ── Error (test_get_logic_operation_from_phenotype_id.R:3:3): get_logic_operation_from_phenotype ──
  Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached: [graphdb.fortunalab.org] Connection timeout after 10001 ms
  Backtrace:
      ▆
   1. └─avidaR::get_logic_operation_from_phenotype_id(phenotype_id = 511) at test_get_logic_operation_from_phenotype_id.R:3:2
   2.   └─triplestore$submit_query(query = query)
   3.     └─httr::POST(...)
   4.       └─httr:::request_perform(req, hu$handle$handle)
   5.         ├─httr:::request_fetch(req$output, req$url, handle)
   6.         └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   7.           └─curl::curl_fetch_memory(url, handle = handle)
  ── Error (test_get_mutant_at_pos.R:3:3): get_mutant_at_pos ─────────────────────
  Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached: [graphdb.fortunalab.org] Connection timeout after 10000 ms
  Backtrace:
      ▆
   1. └─avidaR::get_mutant_at_pos(...) at test_get_mutant_at_pos.R:3:2
   2.   └─avidaR::get_genome_seq_from_genome_id(genome_id)
   3.     └─triplestore$submit_query(query = query)
   4.       └─httr::POST(...)
   5.         └─httr:::request_perform(req, hu$handle$handle)
   6.           ├─httr:::request_fetch(req$output, req$url, handle)
   7.           └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   8.             └─curl::curl_fetch_memory(url, handle = handle)
  ── Error (test_get_phenotype_id_from_genome_id.R:3:3): get_phenotype_id_from_genome_id ──
  Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached: [graphdb.fortunalab.org] Connection timeout after 10001 ms
  Backtrace:
      ▆
   1. └─avidaR::get_phenotype_id_from_genome_id(genome_id = 1) at test_get_phenotype_id_from_genome_id.R:3:2
   2.   └─triplestore$submit_query(query = query)
   3.     └─httr::POST(...)
   4.       └─httr:::request_perform(req, hu$handle$handle)
   5.         ├─httr:::request_fetch(req$output, req$url, handle)
   6.         └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   7.           └─curl::curl_fetch_memory(url, handle = handle)
  ── Error (test_get_phenotype_id_from_genome_seq.R:6:3): get_phenotype_id_from_genome_seq ──
  Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached: [graphdb.fortunalab.org] Connection timeout after 10001 ms
  Backtrace:
      ▆
   1. └─avidaR::get_phenotype_id_from_genome_seq(genome_seq = sequence1) at test_get_phenotype_id_from_genome_seq.R:6:2
   2.   └─triplestore$submit_query(query = query)
   3.     └─httr::POST(...)
   4.       └─httr:::request_perform(req, hu$handle$handle)
   5.         ├─httr:::request_fetch(req$output, req$url, handle)
   6.         └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   7.           └─curl::curl_fetch_memory(url, handle = handle)
  ── Error (test_get_phenotype_id_from_logic_operation.R:3:3): get_phenotype_id_from_logic_operation ──
  Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached: [graphdb.fortunalab.org] Connection timeout after 10000 ms
  Backtrace:
      ▆
   1. └─avidaR::get_phenotype_id_from_logic_operation(logic_operation = "") at test_get_phenotype_id_from_logic_operation.R:3:2
   2.   └─triplestore$submit_query(query = query)
   3.     └─httr::POST(...)
   4.       └─httr:::request_perform(req, hu$handle$handle)
   5.         ├─httr:::request_fetch(req$output, req$url, handle)
   6.         └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   7.           └─curl::curl_fetch_memory(url, handle = handle)
  ── Error (test_get_phenotype_id_from_transcriptome_id.R:3:3): get_phenotype_id_from_transcriptome_id ──
  Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached: [graphdb.fortunalab.org] Connection timeout after 10001 ms
  Backtrace:
      ▆
   1. └─avidaR::get_phenotype_id_from_transcriptome_id(transcriptome_id = 53674) at test_get_phenotype_id_from_transcriptome_id.R:3:2
   2.   └─triplestore$submit_query(query = query)
   3.     └─httr::POST(...)
   4.       └─httr:::request_perform(req, hu$handle$handle)
   5.         ├─httr:::request_fetch(req$output, req$url, handle)
   6.         └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   7.           └─curl::curl_fetch_memory(url, handle = handle)
  ── Error (test_get_tandem_id_from_genome_id.R:3:3): get_tandem_id_from_genome_id ──
  Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached: [graphdb.fortunalab.org] Connection timeout after 10001 ms
  Backtrace:
      ▆
   1. └─avidaR::get_tandem_id_from_genome_id(genome_id = 1) at test_get_tandem_id_from_genome_id.R:3:2
   2.   └─triplestore$submit_query(query = query)
   3.     └─httr::POST(...)
   4.       └─httr:::request_perform(req, hu$handle$handle)
   5.         ├─httr:::request_fetch(req$output, req$url, handle)
   6.         └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   7.           └─curl::curl_fetch_memory(url, handle = handle)
  ── Error (test_get_tandem_id_from_genome_seq.R:6:3): get_tandem_id_from_genome_seq ──
  Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached: [graphdb.fortunalab.org] Connection timeout after 10001 ms
  Backtrace:
       ▆
    1. └─avidaR::get_tandem_id_from_genome_seq(genome_seq = sequence1) at test_get_tandem_id_from_genome_seq.R:6:2
    2.   ├─base::gsub("genome_", "", get_genome_id_from_genome_seq(genome_seq)$genome_id)
    3.   │ └─base::is.factor(x)
    4.   └─avidaR::get_genome_id_from_genome_seq(genome_seq)
    5.     └─triplestore$submit_query(query = query)
    6.       └─httr::POST(...)
    7.         └─httr:::request_perform(req, hu$handle$handle)
    8.           ├─httr:::request_fetch(req$output, req$url, handle)
    9.           └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   10.             └─curl::curl_fetch_memory(url, handle = handle)
  ── Error (test_get_tandem_id_from_logic_operation.R:3:3): get_tandem_id_from_logic_operation ──
  Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached: [graphdb.fortunalab.org] Connection timeout after 10000 ms
  Backtrace:
      ▆
   1. └─avidaR::get_tandem_id_from_logic_operation(...) at test_get_tandem_id_from_logic_operation.R:3:2
   2.   └─avidaR::get_tandem_id_from_phenotype_id(...)
   3.     └─triplestore$submit_query(query = query)
   4.       └─httr::POST(...)
   5.         └─httr:::request_perform(req, hu$handle$handle)
   6.           ├─httr:::request_fetch(req$output, req$url, handle)
   7.           └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   8.             └─curl::curl_fetch_memory(url, handle = handle)
  ── Error (test_get_tandem_id_from_phenotype_id.R:3:3): get_tandem_id_from_phenotype ──
  Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached: [graphdb.fortunalab.org] Connection timeout after 10000 ms
  Backtrace:
      ▆
   1. └─avidaR::get_tandem_id_from_phenotype_id(phenotype_id = 1, seed_id = 1) at test_get_tandem_id_from_phenotype_id.R:3:2
   2.   └─triplestore$submit_query(query = query)
   3.     └─httr::POST(...)
   4.       └─httr:::request_perform(req, hu$handle$handle)
   5.         ├─httr:::request_fetch(req$output, req$url, handle)
   6.         └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   7.           └─curl::curl_fetch_memory(url, handle = handle)
  ── Error (test_get_tandem_seq_from_tandem_id.R:3:5): get_tandem_seq_from_tandem_id ──
  Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached: [graphdb.fortunalab.org] Connection timeout after 10000 ms
  Backtrace:
      ▆
   1. └─avidaR::get_tandem_seq_from_tandem_id(tandem_id = 87873) at test_get_tandem_seq_from_tandem_id.R:3:4
   2.   └─triplestore$submit_query(query = query)
   3.     └─httr::POST(...)
   4.       └─httr:::request_perform(req, hu$handle$handle)
   5.         ├─httr:::request_fetch(req$output, req$url, handle)
   6.         └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   7.           └─curl::curl_fetch_memory(url, handle = handle)
  ── Error (test_get_transcriptome_id_from_genome_id.R:3:3): get_transcriptome_id_from_genome_id ──
  Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached: [graphdb.fortunalab.org] Connection timeout after 10001 ms
  Backtrace:
      ▆
   1. └─avidaR::get_transcriptome_id_from_genome_id(genome_id = 1) at test_get_transcriptome_id_from_genome_id.R:3:2
   2.   └─triplestore$submit_query(query = query)
   3.     └─httr::POST(...)
   4.       └─httr:::request_perform(req, hu$handle$handle)
   5.         ├─httr:::request_fetch(req$output, req$url, handle)
   6.         └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   7.           └─curl::curl_fetch_memory(url, handle = handle)
  ── Error (test_get_transcriptome_id_from_genome_seq.R:6:3): get_transcriptome_id_from_genome_seq ──
  Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached: [graphdb.fortunalab.org] Connection timeout after 10000 ms
  Backtrace:
      ▆
   1. └─avidaR::get_transcriptome_id_from_genome_seq(genome_seq = sequence1) at test_get_transcriptome_id_from_genome_seq.R:6:2
   2.   └─triplestore$submit_query(query = query)
   3.     └─httr::POST(...)
   4.       └─httr:::request_perform(req, hu$handle$handle)
   5.         ├─httr:::request_fetch(req$output, req$url, handle)
   6.         └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   7.           └─curl::curl_fetch_memory(url, handle = handle)
  ── Error (test_get_transcriptome_id_from_logic_operation.R:3:3): get_transcriptome_id_from_logic_operation ──
  Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached: [graphdb.fortunalab.org] Connection timeout after 10000 ms
  Backtrace:
      ▆
   1. └─avidaR::get_transcriptome_id_from_logic_operation(...) at test_get_transcriptome_id_from_logic_operation.R:3:2
   2.   └─avidaR::get_transcriptome_id_from_phenotype_id(...)
   3.     └─triplestore$submit_query(query = query)
   4.       └─httr::POST(...)
   5.         └─httr:::request_perform(req, hu$handle$handle)
   6.           ├─httr:::request_fetch(req$output, req$url, handle)
   7.           └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   8.             └─curl::curl_fetch_memory(url, handle = handle)
  ── Error (test_get_transcriptome_id_from_phenotype_id.R:3:3): get_transcriptome_id_from_phenotype ──
  Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached: [graphdb.fortunalab.org] Connection timeout after 10000 ms
  Backtrace:
      ▆
   1. └─avidaR::get_transcriptome_id_from_phenotype_id(...) at test_get_transcriptome_id_from_phenotype_id.R:3:2
   2.   └─triplestore$submit_query(query = query)
   3.     └─httr::POST(...)
   4.       └─httr:::request_perform(req, hu$handle$handle)
   5.         ├─httr:::request_fetch(req$output, req$url, handle)
   6.         └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   7.           └─curl::curl_fetch_memory(url, handle = handle)
  ── Error (test_get_transcriptome_seq_from_transcriptome_id.R:3:3): get_transcriptome_seq_from_transcriptome_id ──
  Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached: [graphdb.fortunalab.org] Connection timeout after 10000 ms
  Backtrace:
      ▆
   1. └─avidaR::get_transcriptome_seq_from_transcriptome_id(transcriptome_id = 53674) at test_get_transcriptome_seq_from_transcriptome_id.R:3:2
   2.   └─triplestore$submit_query(query = query)
   3.     └─httr::POST(...)
   4.       └─httr:::request_perform(req, hu$handle$handle)
   5.         ├─httr:::request_fetch(req$output, req$url, handle)
   6.         └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   7.           └─curl::curl_fetch_memory(url, handle = handle)
  ── Error (test_ontology.R:3:3): ongology ───────────────────────────────────────
  Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached: [graphdb.fortunalab.org] Connection timeout after 10000 ms
  Backtrace:
      ▆
   1. └─triplestore$ontology() at test_ontology.R:3:2
   2.   └─self$submit_query("PREFIX owl: <http://www.w3.org/2002/07/owl#>\n                                     PREFIX dc: <http://purl.org/dc/elements/1.1/>\n                                     PREFIX obo: <http://purl.obolibrary.org/obo/>\n                                     select * where { \n                                       obo:ontoavida.owl dc:title ?title ;\n                                         dc:description ?description ;\n                                         owl:versionIRI ?versionIRI .\n                                     }")
   3.     └─httr::POST(...)
   4.       └─httr:::request_perform(req, hu$handle$handle)
   5.         ├─httr:::request_fetch(req$output, req$url, handle)
   6.         └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   7.           └─curl::curl_fetch_memory(url, handle = handle)
  ── Error (test_plot_transcriptome.R:3:3): plot_transcriptome ───────────────────
  Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached: [graphdb.fortunalab.org] Connection timeout after 10001 ms
  Backtrace:
      ▆
   1. └─avidaR::plot_transcriptome(...) at test_plot_transcriptome.R:3:2
   2.   └─avidaR::get_transcriptome_seq_from_transcriptome_id(...)
   3.     └─triplestore$submit_query(query = query)
   4.       └─httr::POST(...)
   5.         └─httr:::request_perform(req, hu$handle$handle)
   6.           ├─httr:::request_fetch(req$output, req$url, handle)
   7.           └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   8.             └─curl::curl_fetch_memory(url, handle = handle)
  ── Error (test_set_access_options.R:7:3): set_access_options ───────────────────
  Error in `curl::curl_fetch_memory(url, handle = handle)`: Timeout was reached: [graphdb.fortunalab.org] Connection timeout after 10001 ms
  Backtrace:
      ▆
   1. └─triplestore$set_access_options(...) at test_set_access_options.R:7:2
   2.   ├─httr::content(httr::GET(url = protocol_url, config = private$authentication))
   3.   │ ├─base::stopifnot(is.response(x))
   4.   │ └─httr:::is.response(x)
   5.   └─httr::GET(url = protocol_url, config = private$authentication)
   6.     └─httr:::request_perform(req, hu$handle$handle)
   7.       ├─httr:::request_fetch(req$output, req$url, handle)
   8.       └─httr:::request_fetch.write_memory(req$output, req$url, handle)
   9.         └─curl::curl_fetch_memory(url, handle = handle)
  
  [ FAIL 26 | WARN 0 | SKIP 0 | PASS 12 ]
  Error: Test failures
  Execution halted