Running ‘testthat.R’ [17s/108s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(otargen)
  > 
  > test_check("otargen")
  \ Connecting to the Open Targets Genetics GrpahQL API...
  v Connecting to the Open Targets Genetics GrpahQL API... [152ms]
  
  \ Downloading data for ENSG00000169174 ...
  v Downloading data for ENSG00000169174 ... [2.1s]
  
  \ Connecting to the Open Targets Genetics GrpahQL API...
  v Connecting to the Open Targets Genetics GrpahQL API... [54ms]
  
  \ Downloading data for ENSG00000163946 ...
  | Downloading data for ENSG00000163946 ...
  v Downloading data for ENSG00000163946 ... [1.2s]
  
  \ Downloading data for ENSG00000169174 ...
  v Downloading data for ENSG00000169174 ... [407ms]
  
  \ Downloading data for ENSG00000143001 ...
  v Downloading data for ENSG00000143001 ... [627ms]
  
  \ Connecting to the Open Targets Genetics GrpahQL API...
  x Connecting to the Open Targets Genetics GrpahQL API... [9.3s]
  
  \ Connecting to the Open Targets Genetics GrpahQL API...
  v Connecting to the Open Targets Genetics GrpahQL API... [82ms]
  
  \ Downloading data...
  v Downloading data... [324ms]
  
  \ Connecting to the Open Targets Genetics GrpahQL API...
  v Connecting to the Open Targets Genetics GrpahQL API... [4.7s]
  
  \ Downloading data...
  v Downloading data... [426ms]
  
  \ Connecting to the Open Targets Genetics GrpahQL API...
  x Connecting to the Open Targets Genetics GrpahQL API... [223ms]
  
  \ Connecting to the Open Targets Genetics GraphQL API...
  v Connecting to the Open Targets Genetics GraphQL API... [90ms]
  
  \ Downloading data for 1_154453788_C_T ...
  v Downloading data for 1_154453788_C_T ... [1.3s]
  
  \ Connecting to the Open Targets Genetics GraphQL API...
  v Connecting to the Open Targets Genetics GraphQL API... [187ms]
  
  \ Downloading data for rs55808324 ...
  v Downloading data for rs55808324 ... [680ms]
  
  \ Connecting to the Open Targets Genetics GrpahQL API...
  v Connecting to the Open Targets Genetics GrpahQL API... [50ms]
  
  \ Downloading data...
  v Downloading data... [213ms]
  
  \ Connecting to the Open Targets Genetics GrpahQL API...
  v Connecting to the Open Targets Genetics GrpahQL API... [69ms]
  
  \ Downloading data...
  x Downloading data... [291ms]
  
  \ Connecting to the Open Targets Genetics GrpahQL API...
  v Connecting to the Open Targets Genetics GrpahQL API... [57ms]
  
  \ Downloading data...
  v Downloading data... [4.8s]
  
  \ Connecting to the Open Targets Genetics GrpahQL API...
  v Connecting to the Open Targets Genetics GrpahQL API... [98ms]
  
  \ Downloading the data...
  v Downloading the data... [276ms]
  
  \ Connecting to the Open Targets Genetics GrpahQL API...
  v Connecting to the Open Targets Genetics GrpahQL API... [74ms]
  
  \ Downloading the data...
  v Downloading the data... [4.1s]
  
  \ Connecting to the Open Targets Genetics GrpahQL API...
  v Connecting to the Open Targets Genetics GrpahQL API... [51ms]
  
  \ Downloading data...
  v Downloading data... [558ms]
  
  \ Connecting to the Open Targets Genetics GrpahQL API...
  v Connecting to the Open Targets Genetics GrpahQL API... [70ms]
  
  \ Downloading data...
  v Downloading data... [2.8s]
  
  \ Connecting to the Open Targets Genetics GrpahQL API...
  v Connecting to the Open Targets Genetics GrpahQL API... [63ms]
  
  \ Downloading data...
  v Downloading data... [765ms]
  
  \ Connecting to the Open Targets Genetics GrpahQL API...
  v Connecting to the Open Targets Genetics GrpahQL API... [18ms]
  
  \ Downloading data...
  v Downloading data... [2.4s]
  
  \ Connecting to the Open Targets Genetics GrpahQL API...
  v Connecting to the Open Targets Genetics GrpahQL API... [73ms]
  
  \ Downloading data for variant 1_55063514_G_A ...
  v Downloading data for variant 1_55063514_G_A ... [408ms]
  
  \ Connecting to the Open Targets Genetics GrpahQL API...
  v Connecting to the Open Targets Genetics GrpahQL API... [204ms]
  
  \ Downloading data for variant rs72698179 ...
  v Downloading data for variant rs72698179 ... [605ms]
  
  \ Connecting to the Open Targets Genetics GrpahQL API...
  v Connecting to the Open Targets Genetics GrpahQL API... [17ms]
  
  \ Downloading data for ENSG00000169174 ...
  | Downloading data for ENSG00000169174 ...
  v Downloading data for ENSG00000169174 ... [1.6s]
  
  Selecting by Trait_reported_trimmed
  \ Connecting to the Open Targets Genetics GrpahQL API...
  v Connecting to the Open Targets Genetics GrpahQL API... [69ms]
  
  \ Downloading data for ENSG00000167207 ...
  v Downloading data for ENSG00000167207 ... [541ms]
  
  \ Downloading data for ENSG00000096968 ...
  v Downloading data for ENSG00000096968 ... [835ms]
  
  \ Downloading data for ENSG00000138821 ...
  | Downloading data for ENSG00000138821 ...
  v Downloading data for ENSG00000138821 ... [730ms]
  
  \ Downloading data for ENSG00000125255 ...
  v Downloading data for ENSG00000125255 ... [494ms]
  
  Selecting by Trait_reported_trimmed
  \ Connecting to the Open Targets Genetics GrpahQL API...
  v Connecting to the Open Targets Genetics GrpahQL API... [140ms]
  
  \ Downloading data for ENSG00000141510 ...
  v Downloading data for ENSG00000141510 ... [1s]
  
  Selecting by Trait_reported_trimmed
  \ Connecting to the Open Targets Genetics GrpahQL API...
  v Connecting to the Open Targets Genetics GrpahQL API... [231ms]
  
  \ Downloading data for ENSG00000169174 ...
  v Downloading data for ENSG00000169174 ... [298ms]
  
  \ Downloading data for ENSG00000163946 ...
  v Downloading data for ENSG00000163946 ... [626ms]
  
  \ Downloading data for ENSG00000141510 ...
  v Downloading data for ENSG00000141510 ... [785ms]
  
  Selecting by Trait_reported_trimmed
  \ Connecting to the Open Targets Genetics GrpahQL API...
  v Connecting to the Open Targets Genetics GrpahQL API... [19ms]
  
  \ Downloading data for ENSG00000167207 ...
  v Downloading data for ENSG00000167207 ... [6s]
  
  \ Downloading data for ENSG00000096968 ...
  v Downloading data for ENSG00000096968 ... [5.7s]
  
  \ Connecting to the Open Targets Genetics GrpahQL API...
  v Connecting to the Open Targets Genetics GrpahQL API... [39ms]
  
  \ Downloading data for ENSG00000167207 ...
  v Downloading data for ENSG00000167207 ... [5.7s]
  
  \ Downloading data for ENSG00000096968 ...
  v Downloading data for ENSG00000096968 ... [5.5s]
  
  \ Connecting to the Open Targets Genetics GrpahQL API...
  v Connecting to the Open Targets Genetics GrpahQL API... [47ms]
  
  \ Downloading data...
  v Downloading data... [2.4s]
  
  \ Connecting to the Open Targets Genetics GrpahQL API...
  v Connecting to the Open Targets Genetics GrpahQL API... [19ms]
  
  \ Downloading data for variant 14_87978408_G_A ...
  v Downloading data for variant 14_87978408_G_A ... [265ms]
  
  \ Connecting to the Open Targets Genetics GrpahQL API...
  v Connecting to the Open Targets Genetics GrpahQL API... [131ms]
  
  \ Downloading data for variant rs55808324 ...
  v Downloading data for variant rs55808324 ... [197ms]
  
  \ Connecting to the Open Targets Genetics GrpahQL API...
  v Connecting to the Open Targets Genetics GrpahQL API... [19ms]
  
  \ Downloading data...
  v Downloading data... [148ms]
  
  \ Connecting the database...
  v Connecting the database... [17ms]
  
  \ Downloading data...
  v Downloading data... [104ms]
  
  \ Connecting the database...
  v Connecting the database... [186ms]
  
  \ Downloading data...
  v Downloading data... [120ms]
  
  \ Connecting to the Open Targets Genetics GrpahQL API...
  v Connecting to the Open Targets Genetics GrpahQL API... [19ms]
  
  \ Downloading data for ENSG00000169174 ...
  x Downloading data for ENSG00000169174 ... [10.1s]
  
  \ Connecting to the Open Targets Genetics GrpahQL API...
  v Connecting to the Open Targets Genetics GrpahQL API... [37ms]
  
  \ Downloading data...
  v Downloading data... [184ms]
  
  \ Connecting to the Open Targets Genetics GraphQL API...
  v Connecting to the Open Targets Genetics GraphQL API... [37ms]
  
  \ Downloading data for  GCST003044 , 14_88009660_C_T ...
  v Downloading data for  GCST003044 , 14_88009660_C_T ... [752ms]
  
  \ Connecting to the Open Targets Genetics GrpahQL API...
  v Connecting to the Open Targets Genetics GrpahQL API... [24ms]
  
  \ Downloading data...
  v Downloading data... [236ms]
  
  \ Connecting the database...
  v Connecting the database... [17ms]
  
  \ Downloading data...
  v Downloading data... [259ms]
  
  \ Connecting to the Open Targets Genetics GrpahQL API...
  v Connecting to the Open Targets Genetics GrpahQL API... [39ms]
  
  \ Downloading data...
  v Downloading data... [160ms]
  
  \ Connecting to the Open Targets Genetics GraphQL API...
  v Connecting to the Open Targets Genetics GraphQL API... [35ms]
  
  \ Downloading data...
  v Downloading data... [151ms]
  
  \ Connecting to the Open Targets Genetics GraphQL API...
  v Connecting to the Open Targets Genetics GraphQL API... [119ms]
  
  \ Downloading data...
  v Downloading data... [221ms]
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 70 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-colocalisationsForGene.R:4:3'): test colocalisationsForGene works ──
  Error: Bad Gateway (HTTP 502)
  Backtrace:
      ▆
   1. └─otargen::colocalisationsForGene(genes = c("TP53", "TASOR", "PCSK9")) at test-colocalisationsForGene.R:4:3
   2.   ├─jsonlite::fromJSON(...)
   3.   └─con$exec(qry$queries$gene2ensembl, variables)
   4.     ├─ghql:::cont(gh_POST(self$url, body, self$headers, ...), encoding = encoding)
   5.     └─ghql:::gh_POST(self$url, body, self$headers, ...)
   6.       └─res$raise_for_status()
  ── Error ('test-studiesAndLeadVariantsForGeneByL2G.R:2:3'): test studiesAndLeadVariantsForGeneByL2G works ──
  Error: Bad Gateway (HTTP 502)
  Backtrace:
      ▆
   1. └─otargen::studiesAndLeadVariantsForGeneByL2G(gene = "ENSG00000169174") at test-studiesAndLeadVariantsForGeneByL2G.R:2:3
   2.   └─base::tryCatch(...)
   3.     └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   4.       └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   5.         └─value[[3L]](cond)
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 70 ]
  Error: Test failures
  Execution halted