Running ‘testthat.R’ [44s/47s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > test_check("qtl2")
  Loading required package: qtl2
  Saving _problems/test-find_marker-42.R
  Saving _problems/test-find_peaks-4.R
  [ FAIL 2 | WARN 8 | SKIP 112 | PASS 8581 ]
  
  ══ Skipped tests (112) ═════════════════════════════════════════════════════════
  • On CRAN (47): 'test-est_herit.R:32:5', 'test-est_herit.R:68:5',
    'test-estmap.R:23:5', 'test-estmap.R:43:5', 'test-estmap.R:61:5',
    'test-estmap.R:85:5', 'test-estmap.R:106:5', 'test-estmap.R:126:5',
    'test-estmap.R:147:5', 'test-estmap.R:168:5', 'test-estmap.R:187:5',
    'test-estmap2.R:16:5', 'test-estmap2.R:30:5', 'test-hmmbasic-ailpk.R:180:5',
    'test-hmmbasic-ailpk.R:329:5', 'test-hmmbasic-do.R:164:5',
    'test-hmmbasic-do.R:245:5', 'test-hmmbasic-dopk.R:155:5',
    'test-hmmbasic-dopk.R:224:5', 'test-hmmbasic-genail.R:63:5',
    'test-hmmbasic-genail.R:142:5', 'test-hmmbasic-genril.R:41:5',
    'test-hmmbasic-genril.R:85:5', 'test-rcbind_scan1.R:37:5',
    'test-rcbind_scan1.R:56:5', 'test-rcbind_scan1.R:75:5',
    'test-rcbind_scan1.R:108:5', 'test-rcbind_simgeno.R:25:5',
    'test-rcbind_simgeno.R:65:5', 'test-reduced_rank_covar_scan.R:28:5',
    'test-scan1_binary.R:52:5', 'test-scan1_binary.R:101:5',
    'test-scan1_binary.R:153:5', 'test-scan1_pg.R:344:5',
    'test-scan1blup.R:83:5', 'test-scan1coef.R:168:5', 'test-scan1coef.R:295:5',
    'test-scan1coef.R:416:5', 'test-scan1coef.R:549:5',
    'test-scan1coef_pg.R:143:5', 'test-scan1coef_pg.R:188:5',
    'test-scan1coef_pg.R:212:5', 'test-scan1perm_binary.R:32:5',
    'test-simgeno.R:65:5', 'test-simgeno.R:127:5', 'test-simgeno.R:143:5',
    'test-viterbi.R:76:5'
  • plot tests only run locally (7): 'test-plot_coef.R:5:5',
    'test-plot_genes.R:5:5', 'test-plot_genoprob.R:5:5', 'test-plot_peaks.R:5:5',
    'test-plot_pxg.R:5:5', 'test-plot_scan1.R:5:5', 'test-plot_sdp.R:5:5'
  • this test only run locally (58): 'test-basic_summaries.R:129:5',
    'test-calc_het.R:31:5', 'test-calc_kinship.R:250:5',
    'test-calc_raw_summaries.R:5:5', 'test-calcerrorlod.R:114:5',
    'test-calcgenoprob.R:284:5', 'test-calcgenoprob2.R:239:5',
    'test-check_cross.R:105:5', 'test-compare_founder_geno.R:13:5',
    'test-compare_geno.R:76:5', 'test-create_snpinfo.R:5:5',
    'test-create_snpinfo.R:28:5', 'test-decomp_kinship.R:48:5',
    'test-estmap.R:203:5', 'test-find_ibd_segments.R:5:5', 'test-fit1.R:108:5',
    'test-fit1.R:263:5', 'test-fit1.R:344:5', 'test-fit1.R:517:5',
    'test-fit1.R:546:5', 'test-fit1_binary.R:358:5',
    'test-genoprob_to_alleleprob.R:59:5', 'test-index_snps.R:5:5',
    'test-predict_snpgeno.R:5:5', 'test-predict_snpgeno.R:29:5',
    'test-pseudomarkermap.R:133:5', 'test-recode_snps.R:5:5',
    'test-scan1.R:208:5', 'test-scan1.R:328:5', 'test-scan1.R:375:5',
    'test-scan1.R:462:5', 'test-scan1.R:540:5', 'test-scan1.R:613:5',
    'test-scan1.R:636:5', 'test-scan1_pg.R:64:5', 'test-scan1_pg.R:127:5',
    'test-scan1_pg.R:232:5', 'test-scan1_pg.R:417:5', 'test-scan1_pg.R:493:5',
    'test-scan1_pg.R:521:5', 'test-scan1_pg.R:548:5', 'test-scan1_pg.R:580:5',
    'test-scan1_pg.R:716:5', 'test-scan1blup.R:108:5', 'test-scan1blup.R:133:5',
    'test-scan1max.R:59:5', 'test-scan1perm.R:135:5', 'test-scan1perm.R:252:5',
    'test-scan1snps.R:5:5', 'test-scanhk.R:79:5', 'test-scanhk.R:157:5',
    'test-scanhk.R:216:5', 'test-scanhk.R:278:5', 'test-scanhk.R:343:5',
    'test-simgeno.R:95:5', 'test-snpprobs.R:384:5', 'test-top_snps.R:4:5',
    'test-zip_datafiles.R:5:5'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-find_marker.R:42:5'): find_markerpos works ─────────────────────
  Error in `utils::unzip(file, exdir = dir)`: cannot open file '/tmp/RtmpnZyQHE/qtl2_o4v90ff47j3mutn/iron_geno.csv': No space left on device
  Backtrace:
      ▆
   1. └─qtl2::read_cross2(system.file("extdata", "iron.zip", package = "qtl2")) at test-find_marker.R:42:5
   2.   └─utils::unzip(file, exdir = dir)
  ── Error ('test-find_peaks.R:4:1'): (code run outside of `test_that()`) ────────
  Error in `utils::unzip(file, exdir = dir)`: cannot open file '/tmp/RtmpnZyQHE/qtl2_4817y8uz5c17gkf/iron_gmap.csv': No space left on device
  Backtrace:
      ▆
   1. └─qtl2::read_cross2(system.file("extdata", "iron.zip", package = "qtl2")) at test-find_peaks.R:4:1
   2.   └─utils::unzip(file, exdir = dir)
  
  [ FAIL 2 | WARN 8 | SKIP 112 | PASS 8581 ]
  Deleting unused snapshots: 'plot_coef/plot-coef.svg',
  'plot_genes/plot-genes.svg', 'plot_genoprob/plot-genoprob.svg',
  'plot_peaks/plot-peaks-noci.svg', 'plot_peaks/plot-peaks.svg',
  'plot_pxg/plot-pxg-se.svg', 'plot_pxg/plot-pxg.svg',
  'plot_scan1/plot-scan1-onechr.svg', 'plot_scan1/plot-scan1.svg', and
  'plot_sdp/plot-sdp.svg'
  Error:
  ! Test failures.
  Execution halted