Running 'testthat.R' [6s]
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... [42ms]
  
  \ Downloading data for ENSG00000169174 ...
  x Downloading data for ENSG00000169174 ... [346ms]
  
  \ Connecting to the Open Targets Genetics GrpahQL API...
  v Connecting to the Open Targets Genetics GrpahQL API... [7ms]
  
  \ Downloading data...
  x Downloading data... [78ms]
  
  \ Connecting to the Open Targets Genetics GraphQL API...
  v Connecting to the Open Targets Genetics GraphQL API... [12ms]
  
  \ Downloading data for 1_154453788_C_T ...
  x Downloading data for 1_154453788_C_T ... [62ms]
  
  \ Connecting to the Open Targets Genetics GrpahQL API...
  v Connecting to the Open Targets Genetics GrpahQL API... [12ms]
  
  \ Downloading data...
  x Downloading data... [63ms]
  
  \ Connecting to the Open Targets Genetics GrpahQL API...
  v Connecting to the Open Targets Genetics GrpahQL API... [11ms]
  
  \ Downloading data...
  x Downloading data... [57ms]
  
  \ Connecting to the Open Targets Genetics GrpahQL API...
  v Connecting to the Open Targets Genetics GrpahQL API... [11ms]
  
  \ Downloading the data...
  x Downloading the data... [58ms]
  
  \ Connecting to the Open Targets Genetics GrpahQL API...
  v Connecting to the Open Targets Genetics GrpahQL API... [11ms]
  
  \ Downloading the data...
  x Downloading the data... [57ms]
  
  \ Connecting to the Open Targets Genetics GrpahQL API...
  v Connecting to the Open Targets Genetics GrpahQL API... [10ms]
  
  \ Downloading data...
  x Downloading data... [59ms]
  
  \ Connecting to the Open Targets Genetics GrpahQL API...
  v Connecting to the Open Targets Genetics GrpahQL API... [11ms]
  
  \ Downloading data...
  x Downloading data... [56ms]
  
  \ Connecting to the Open Targets Genetics GrpahQL API...
  v Connecting to the Open Targets Genetics GrpahQL API... [14ms]
  
  \ Downloading data...
  x Downloading data... [67ms]
  
  \ Connecting to the Open Targets Genetics GrpahQL API...
  v Connecting to the Open Targets Genetics GrpahQL API... [11ms]
  
  \ Downloading data...
  x Downloading data... [57ms]
  
  \ Connecting to the Open Targets Genetics GrpahQL API...
  v Connecting to the Open Targets Genetics GrpahQL API... [12ms]
  
  \ Downloading data for variant 1_55063514_G_A ...
  x Downloading data for variant 1_55063514_G_A ... [60ms]
  
  \ Connecting to the Open Targets Genetics GrpahQL API...
  v Connecting to the Open Targets Genetics GrpahQL API... [12ms]
  
  \ Downloading data for ENSG00000169174 ...
  x Downloading data for ENSG00000169174 ... [62ms]
  
  \ Connecting to the Open Targets Genetics GrpahQL API...
  v Connecting to the Open Targets Genetics GrpahQL API... [10ms]
  
  \ Downloading data for ENSG00000167207 ...
  x Downloading data for ENSG00000167207 ... [44ms]
  
  Error in test plot_l2g: Bad Gateway (HTTP 502)
  \ Connecting to the Open Targets Genetics GrpahQL API...
  v Connecting to the Open Targets Genetics GrpahQL API... [10ms]
  
  \ Downloading data...
  x Downloading data... [54ms]
  
  \ Connecting to the Open Targets Genetics GrpahQL API...
  v Connecting to the Open Targets Genetics GrpahQL API... [10ms]
  
  \ Downloading data for variant 14_87978408_G_A ...
  x Downloading data for variant 14_87978408_G_A ... [42ms]
  
  \ Connecting to the Open Targets Genetics GrpahQL API...
  v Connecting to the Open Targets Genetics GrpahQL API... [9ms]
  
  \ Downloading data...
  x Downloading data... [48ms]
  
  \ Connecting the database...
  v Connecting the database... [9ms]
  
  \ Downloading data...
  x Downloading data... [56ms]
  
  \ Connecting to the Open Targets Genetics GrpahQL API...
  v Connecting to the Open Targets Genetics GrpahQL API... [9ms]
  
  \ Downloading data for ENSG00000169174 ...
  x Downloading data for ENSG00000169174 ... [51ms]
  
  \ Connecting to the Open Targets Genetics GrpahQL API...
  v Connecting to the Open Targets Genetics GrpahQL API... [7ms]
  
  \ Downloading data...
  x Downloading data... [54ms]
  
  \ Connecting to the Open Targets Genetics GraphQL API...
  v Connecting to the Open Targets Genetics GraphQL API... [9ms]
  
  \ Downloading data for  GCST003044 , 14_88009660_C_T ...
  x Downloading data for  GCST003044 , 14_88009660_C_T ... [53ms]
  
  \ Connecting to the Open Targets Genetics GrpahQL API...
  v Connecting to the Open Targets Genetics GrpahQL API... [9ms]
  
  \ Downloading data...
  x Downloading data... [51ms]
  
  \ Connecting the database...
  v Connecting the database... [11ms]
  
  \ Downloading data...
  x Downloading data... [52ms]
  
  \ Connecting to the Open Targets Genetics GrpahQL API...
  v Connecting to the Open Targets Genetics GrpahQL API... [10ms]
  
  \ Downloading data...
  x Downloading data... [53ms]
  
  \ Connecting to the Open Targets Genetics GraphQL API...
  v Connecting to the Open Targets Genetics GraphQL API... [10ms]
  
  \ Downloading data...
  x Downloading data... [72ms]
  
  [ FAIL 25 | WARN 0 | SKIP 0 | PASS 0 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-colocalisationsForGene.R:2:3'): test colocalisationsForGene works ──
  Error: Bad Gateway (HTTP 502)
  Backtrace:
      ▆
   1. └─otargen::colocalisationsForGene(genes = "ENSG00000169174") at test-colocalisationsForGene.R:2:3
   2.   └─con$exec(qry$queries$getgenColocal, variables)
   3.     ├─ghql:::cont(gh_POST(self$url, body, self$headers, ...), encoding = encoding)
   4.     └─ghql:::gh_POST(self$url, body, self$headers, ...)
   5.       └─res$raise_for_status()
  ── Error ('test-geneInfo.R:2:3'): test geneInfo works ──────────────────────────
  Error: Bad Gateway (HTTP 502)
  Backtrace:
      ▆
   1. └─otargen::geneInfo(gene = "ENSG00000004864") at test-geneInfo.R:2:3
   2.   ├─jsonlite::fromJSON(...)
   3.   └─otg_cli$exec(otg_qry$queries$geneInfoQuery, variables)
   4.     ├─ghql:::cont(gh_POST(self$url, body, self$headers, ...), encoding = encoding)
   5.     └─ghql:::gh_POST(self$url, body, self$headers, ...)
   6.       └─res$raise_for_status()
  ── Error ('test-genesForVariant.R:2:5'): test genesForVariant works ────────────
  Error: Bad Gateway (HTTP 502)
  Backtrace:
      ▆
   1. └─otargen::genesForVariant(variant_id = "1_154453788_C_T") at test-genesForVariant.R:2:5
   2.   └─base::tryCatch(...)
   3.     └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   4.       └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   5.         └─value[[3L]](cond)
  ── Error ('test-getLociGenes.R:2:3'): test get_genes works ─────────────────────
  Error: Bad Gateway (HTTP 502)
  Backtrace:
      ▆
   1. └─otargen::get_genes(chromosome = "2", start = 239634984, end = 241634984) at test-getLociGenes.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)
  ── Error ('test-gwasColocalisation.R:2:3'): test the gwasColocalisation works ──
  Error: Bad Gateway (HTTP 502)
  Backtrace:
      ▆
   1. └─otargen::gwasColocalisation(study_id = "GCST90002357", variant_id = "1_154119580_C_A") at test-gwasColocalisation.R:2:3
   2.   ├─jsonlite::fromJSON(...)
   3.   └─otg_cli$exec(otg_qry$queries$gwascol_query, variables)
   4.     ├─ghql:::cont(gh_POST(self$url, body, self$headers, ...), encoding = encoding)
   5.     └─ghql:::gh_POST(self$url, body, self$headers, ...)
   6.       └─res$raise_for_status()
  ── Error ('test-gwasColocalisationForRegion.R:2:2'): test gwasColocalizationForRegion works ──
  Error: Bad Gateway (HTTP 502)
  Backtrace:
      ▆
   1. └─otargen::gwasColocalisationForRegion(...) at test-gwasColocalisationForRegion.R:2:2
   2.   └─base::tryCatch(...)
   3.     └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   4.       └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   5.         └─value[[3L]](cond)
  ── Error ('test-gwasCredibleSet.R:2:3'): test gwasCredibleSet works ────────────
  Error: Bad Gateway (HTTP 502)
  Backtrace:
      ▆
   1. └─otargen::gwasCredibleSet(study_id = "GCST006614_3", variant_id = "1_55058182_G_A") at test-gwasCredibleSet.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)
  ── Error ('test-gwasRegional.R:2:3'): test gwasRegional works ──────────────────
  Error: Bad Gateway (HTTP 502)
  Backtrace:
      ▆
   1. └─otargen::gwasRegional(...) at test-gwasRegional.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)
  ── Error ('test-indexVariantsAndStudiesForTagVariant.R:2:3'): test indexVariantsAndStudiesForTagVariant works ──
  Error: Bad Gateway (HTTP 502)
  Backtrace:
      ▆
   1. └─otargen::indexVariantsAndStudiesForTagVariant(...) at test-indexVariantsAndStudiesForTagVariant.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)
  ── Error ('test-manhattan.R:2:3'): test manhattan  works ───────────────────────
  Error: Bad Gateway (HTTP 502)
  Backtrace:
      ▆
   1. └─otargen::manhattan(...) at test-manhattan.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)
  ── Error ('test-overlapinfoForStudy.R:2:3'): test overlapinfoForStudy works ────
  Error: Bad Gateway (HTTP 502)
  Backtrace:
      ▆
   1. └─otargen::overlapInfoForStudy(...) at test-overlapinfoForStudy.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)
  ── Error ('test-pheWAS.R:2:3'): test phewas works ──────────────────────────────
  Error: Bad Gateway (HTTP 502)
  Backtrace:
      ▆
   1. └─otargen::pheWAS(variant_id = "1_55063514_G_A") at test-pheWAS.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)
  ── Error ('test-plot_coloc.R:2:3'): test plot_coloc works ──────────────────────
  Error: Bad Gateway (HTTP 502)
  Backtrace:
      ▆
   1. ├─... %>% otargen::plot_coloc(biobank = TRUE) at test-plot_coloc.R:2:3
   2. ├─otargen::plot_coloc(., biobank = TRUE)
   3. └─otargen::colocalisationsForGene(gene = "ENSG00000169174")
   4.   └─con$exec(qry$queries$getgenColocal, variables)
   5.     ├─ghql:::cont(gh_POST(self$url, body, self$headers, ...), encoding = encoding)
   6.     └─ghql:::gh_POST(self$url, body, self$headers, ...)
   7.       └─res$raise_for_status()
  ── Failure ('test-plot_l2g.R:23:5'): test plot_l2g works ───────────────────────
  FALSE is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  An error occurred in plotting.
  Backtrace:
      ▆
   1. └─base::tryCatch(...) at test-plot_l2g.R:3:3
   2.   └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   3.     └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   4.       └─value[[3L]](cond)
   5.         └─testthat::expect_true(FALSE, "An error occurred in plotting.") at test-plot_l2g.R:23:5
  ── Error ('test-plot_manhattan.R:2:3'): test plot_manhattan works ──────────────
  Error: Bad Gateway (HTTP 502)
  Backtrace:
       ▆
    1. ├─otargen::manhattan(study_id = "GCST003044") %>% otargen::plot_manhattan() at test-plot_manhattan.R:2:3
    2. ├─otargen::plot_manhattan(.)
    3. │ └─... %>% ...
    4. ├─dplyr::rename(...)
    5. ├─base::unique(.)
    6. ├─dplyr::select(...)
    7. └─otargen::manhattan(study_id = "GCST003044")
    8.   └─base::tryCatch(...)
    9.     └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   10.       └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   11.         └─value[[3L]](cond)
  ── Error ('test-plot_phewas.R:2:3'): test plot_phewas works ────────────────────
  Error: Bad Gateway (HTTP 502)
  Backtrace:
      ▆
   1. ├─otargen::pheWAS(variant_id = "14_87978408_G_A") %>% ... at test-plot_phewas.R:2:3
   2. ├─otargen::plot_phewas(., disease = TRUE)
   3. └─otargen::pheWAS(variant_id = "14_87978408_G_A")
   4.   └─base::tryCatch(...)
   5.     └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   6.       └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   7.         └─value[[3L]](cond)
  ── Error ('test-qtlColocalisationVariantQuery.R:2:3'): test qtlColocalisationVariantQuery works ──
  Error: Bad Gateway (HTTP 502)
  Backtrace:
      ▆
   1. └─otargen::qtlColocalisationVariantQuery(...) at test-qtlColocalisationVariantQuery.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)
  ── Error ('test-qtlCredibleSet.R:2:3'): test qtlCredibleSet works ──────────────
  Error: Bad Gateway (HTTP 502)
  Backtrace:
      ▆
   1. └─otargen::qtlCredibleSet(...) at test-qtlCredibleSet.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)
  ── 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)
  ── Error ('test-studyInfo.R:2:3'): test studyInfo works ────────────────────────
  Error: Bad Gateway (HTTP 502)
  Backtrace:
      ▆
   1. └─otargen::studyInfo(study_id = "GCST90002357") at test-studyInfo.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)
  ── Error ('test-studyLocus2GeneTable.R:2:3'): test studyLocus2GeneTable works ──
  Error: Bad Gateway (HTTP 502)
  Backtrace:
      ▆
   1. └─otargen::studyLocus2GeneTable(study_id = "GCST003044", variant_id = "14_88009660_C_T") at test-studyLocus2GeneTable.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)
  ── Error ('test-studyVariants.R:2:3'): test studyVariants works ────────────────
  Error: Bad Gateway (HTTP 502)
  Backtrace:
      ▆
   1. └─otargen::studyVariants(study_id = "GCST003155") at test-studyVariants.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)
  ── Error ('test-tagVariantsAndStudiesForIndexVariant.R:2:3'): test tagVariantsAndStudiesForIndexVariant works ──
  Error: Bad Gateway (HTTP 502)
  Backtrace:
      ▆
   1. └─otargen::tagVariantsAndStudiesForIndexVariant(...) at test-tagVariantsAndStudiesForIndexVariant.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)
  ── Error ('test-topOverlappedStudies.R:2:3'): test the topOverlappedStudies  works ──
  Error: Bad Gateway (HTTP 502)
  Backtrace:
      ▆
   1. └─otargen::manhattan(...) at test-topOverlappedStudies.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)
  ── Error ('test-variantInfo.R:2:3'): test variantInfo works ────────────────────
  Error: Bad Gateway (HTTP 502)
  Backtrace:
      ▆
   1. └─otargen::variantInfo(variant_id = "1_55039974_G_T") at test-variantInfo.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 25 | WARN 0 | SKIP 0 | PASS 0 ]
  Error: Test failures
  Execution halted