Running ‘testthat.R’ [8s/22s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(seeker)
  > 
  > test_check('seeker')
  qs 0.26.3
  reading in files with read_tsv
  1 2 
  transcripts missing from tx2gene: 116471
  summarizing abundance
  summarizing counts
  summarizing length
  [ FAIL 1 | WARN 0 | SKIP 15 | PASS 30 ]
  
  ══ Skipped tests (15) ══════════════════════════════════════════════════════════
  • On CRAN (15): 'test-array-utils.R:33:3', 'test-array-utils.R:154:3',
    'test-array-utils.R:166:3', 'test-array-utils.R:175:3', 'test-array.R:39:3',
    'test-array.R:77:3', 'test-fetch.R:35:3', 'test-qc.R:2:3', 'test-qc.R:21:3',
    'test-qc.R:40:3', 'test-salmon.R:2:3', 'test-seeker.R:2:3',
    'test-seeker.R:22:3', 'test-seeker.R:43:3', 'test-seeker.R:51:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-tximport.R:10:3'): getTx2gene ──────────────────────────────────
  <httr2_failure/httr2_error/rlang_error/error/condition>
  Error in `req_perform(html_request)`: Failed to perform HTTP request.
  Caused by error in `curl::curl_fetch_memory()`:
  ! Timeout was reached: [www.ensembl.org] Operation timed out after 10001 milliseconds with 0 bytes received
  Backtrace:
       ▆
    1. ├─base::do.call(getTx2gene, c(list(outputDir = outputDir), paramsNow$tx2gene)) at test-tximport.R:10:3
    2. └─seeker (local) `<fn>`(outputDir = "data/staging/GSE143524", checkArgsOnly = TRUE)
    3.   ├─data.table::setDT(biomaRt::listEnsemblArchives())
    4.   │ └─data.table::is.data.table(x)
    5.   └─biomaRt::listEnsemblArchives()
    6.     └─biomaRt:::.listEnsemblArchives(https = https, http_config = list())
    7.       └─biomaRt:::.checkArchiveList(https, http_config)
    8.         └─biomaRt:::.getArchiveList(https = https, http_config = http_config)
    9.           └─httr2::req_perform(html_request)
   10.             └─base::tryCatch(...)
   11.               └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   12.                 └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   13.                   └─value[[3L]](cond)
  
  [ FAIL 1 | WARN 0 | SKIP 15 | PASS 30 ]
  Error: Test failures
  Execution halted