Running ‘testthat.R’ [278s/165s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(OlinkAnalyze)
  > 
  > test_check("OlinkAnalyze")
  Starting 2 test processes.
  Saving _problems/test-olink_normalization_utils-4575.R
  Saving _problems/test-olink_normalization_utils-5369.R
  Saving _problems/test-olink_normalization_utils-5445.R
  [ FAIL 3 | WARN 341 | SKIP 284 | PASS 1409 ]
  
  ══ Skipped tests (284) ═════════════════════════════════════════════════════════
  • On CRAN (81): 'test-dist_plot.R:62:5', 'test-olink_boxplot.R:4:5',
    'test-olink_boxplot.R:41:5', 'test-olink_lmer.R:9:5',
    'test-olink_lmer.R:70:5', 'test-olink_lmer.R:106:5',
    'test-olink_lmer.R:150:5', 'test-olink_lmer.R:181:5',
    'test-olink_lmer.R:273:5', 'test-olink_lmer.R:354:5',
    'test-olink_lmer.R:391:5', 'test-olink_lmer.R:427:5',
    'test-olink_pathway_enrichment.R:10:5',
    'test-olink_pathway_enrichment.R:1132:5',
    'test-olink_plate_randomizer.R:47:5', 'test-olink_qc_plot.R:220:5',
    'test-olink_ttest.R:83:5', 'test-olink_ttest.R:110:5',
    'test-olink_wilcox.R:103:5', 'test-olink_wilcox.R:130:5',
    'test-pca_plot.R:269:5', 'test-pca_plot.R:435:5', 'test-pca_plot.R:521:5',
    'test-pca_plot.R:681:5', 'test-pca_plot.R:741:5',
    'test-plot_is_bridgeable.R:6:5', 'test-plot_is_bridgeable.R:102:5',
    'test-plot_is_bridgeable.R:206:5', 'test-plot_is_bridgeable.R:391:5',
    'test-plot_is_bridgeable.R:485:5', 'test-plot_is_bridgeable.R:557:5',
    'test-plot_is_bridgeable.R:630:5', 'test-plot_is_bridgeable.R:702:5',
    'test-plot_is_bridgeable.R:778:5', 'test-plot_is_bridgeable.R:874:5',
    'test-plot_point_range.R:6:5', 'test-plot_point_range.R:60:5',
    'test-plot_point_range.R:116:5', 'test-plot_point_range.R:163:5',
    'test-olink_normalization_utils.R:1215:5',
    'test-olink_normalization_utils.R:1231:5',
    'test-olink_normalization_utils.R:1250:5',
    'test-olink_normalization_utils.R:1266:5',
    'test-olink_normalization_utils.R:1285:5',
    'test-olink_normalization_utils.R:1320:5',
    'test-olink_normalization_utils.R:1337:5',
    'test-olink_normalization_utils.R:1357:5',
    'test-olink_normalization_utils.R:1373:5',
    'test-olink_normalization_utils.R:1392:5',
    'test-olink_normalization_utils.R:1408:5',
    'test-olink_normalization_utils.R:1427:5',
    'test-olink_normalization_utils.R:1444:5',
    'test-olink_normalization_utils.R:1464:5',
    'test-olink_normalization_utils.R:1481:5',
    'test-olink_normalization_utils.R:1503:5',
    'test-olink_normalization_utils.R:1521:5',
    'test-olink_normalization_utils.R:1542:5',
    'test-olink_normalization_utils.R:1560:5',
    'test-olink_normalization_utils.R:1581:5',
    'test-olink_normalization_utils.R:1600:5',
    'test-olink_normalization_utils.R:1630:5',
    'test-olink_normalization_utils.R:1649:5',
    'test-olink_normalization_utils.R:1680:5',
    'test-olink_normalization_utils.R:1698:5',
    'test-olink_normalization_utils.R:1719:5',
    'test-olink_normalization_utils.R:1737:5',
    'test-olink_normalization_utils.R:1758:5',
    'test-olink_normalization_utils.R:1783:5',
    'test-olink_normalization_utils.R:1812:5',
    'test-olink_normalization_utils.R:1837:5',
    'test-olink_normalization_utils.R:1869:5',
    'test-olink_normalization_utils.R:1884:5',
    'test-olink_normalization_utils.R:1903:5',
    'test-olink_normalization_utils.R:1928:5',
    'test-olink_normalization_utils.R:1955:5',
    'test-olink_normalization_utils.R:1993:5',
    'test-olink_normalization_utils.R:2083:5',
    'test-olink_normalization_utils.R:2154:5',
    'test-olink_normalization_utils.R:2236:5',
    'test-olink_normalization_utils.R:2433:5',
    'test-olink_normalization_utils.R:2571:5'
  • Skipping (178): 'test-read_npx_legacy.R:12:5',
    'test-read_npx_legacy.R:567:5', 'test-read_npx_legacy.R:617:5',
    'test-read_npx_legacy.R:670:5', 'test-read_npx_legacy.R:735:5',
    'test-read_npx_legacy.R:1499:5', 'test-read_npx_legacy.R:2263:5',
    'test-read_npx_legacy.R:3024:5', 'test-read_npx_legacy.R:3777:5',
    'test-read_npx_legacy.R:3871:5', 'test-read_npx_legacy.R:3923:5',
    'test-Olink_one_non_parametric.R:5:5',
    'test-Olink_one_non_parametric.R:114:5', 'test-read_npx_wide.R:21:5',
    'test-read_npx_wide.R:226:5', 'test-read_npx_wide.R:695:5',
    'test-read_npx_wide.R:787:5', 'test-read_npx_wide.R:915:5',
    'test-read_npx_wide.R:1216:5', 'test-read_npx_wide.R:1326:5',
    'test-read_npx_wide.R:1478:5', 'test-read_npx_wide.R:1639:5',
    'test-read_npx_wide.R:1798:5', 'test-read_npx_wide.R:2479:5',
    'test-read_npx_wide.R:3159:5', 'test-read_npx_wide.R:3575:5',
    'test-read_npx_wide.R:3991:5', 'test-read_npx_wide.R:4671:5',
    'test-read_npx_wide.R:5352:5', 'test-read_npx_wide.R:6033:5',
    'test-read_npx_wide.R:6712:5', 'test-read_npx_wide.R:6811:5',
    'test-read_npx_wide.R:6910:5', 'test-read_npx_wide.R:6988:5',
    'test-read_npx_wide.R:7048:5', 'test-read_npx_wide.R:7826:5',
    'test-read_npx_wide.R:8602:5', 'test-read_npx_wide.R:8790:5',
    'test-read_npx_wide.R:8901:5', 'test-read_npx_wide.R:9017:5',
    'test-read_npx_wide.R:9750:5', 'test-read_npx_wide.R:10484:5',
    'test-read_npx_wide.R:10589:5', 'test-read_npx_wide.R:11154:5',
    'test-read_npx_wide.R:11720:5', 'test-read_npx_wide.R:12287:5',
    'test-read_npx_wide.R:12850:5', 'test-read_npx_wide.R:12957:5',
    'test-read_npx_wide.R:13066:5', 'test-read_npx_wide.R:13165:5',
    'test-read_npx_wide.R:13456:5', 'test-read_npx_wide.R:13545:5',
    'test-read_npx_wide.R:14494:5', 'test-read_npx_wide.R:15443:5',
    'test-read_npx_wide.R:16392:5', 'test-dist_plot.R:8:5',
    'test-npxProcessing.R:5:5', 'test-npxProcessing.R:55:5',
    'test-olink_anova.R:20:1', 'test-olink_normalization.R:17:5',
    'test-olink_normalization.R:168:5', 'test-olink_normalization.R:543:5',
    'test-olink_normalization.R:685:5', 'test-olink_normalization.R:827:5',
    'test-olink_normalization.R:1198:5', 'test-olink_normalization.R:1314:5',
    'test-olink_normalization.R:1637:5', 'test-olink_normalization.R:1759:5',
    'test-olink_normalization.R:1880:5', 'test-olink_normalization.R:2001:5',
    'test-olink_normalization.R:2438:5', 'test-olink_normalization.R:2531:5',
    'test-olink_normalization.R:2612:5',
    'test-olink_normalization_format.R:10:5',
    'test-olink_normalization_format.R:263:5',
    'test-olink_normalization_format.R:516:5',
    'test-olink_normalization_format.R:729:5',
    'test-olink_normalization_format.R:1118:5',
    'test-olink_normalization_format.R:1237:5',
    'test-olink_normalization_format.R:1357:5',
    'test-olink_normalization_format.R:1501:5',
    'test-olink_normalization_format.R:1562:5',
    'test-olink_normalization_format.R:1752:5',
    'test-olink_normalization_format.R:2152:5',
    'test-olink_normalization_format.R:2286:5',
    'test-olink_normalization_n.R:6:5', 'test-olink_normalization_n.R:153:5',
    'test-olink_normalization_n.R:300:5', 'test-olink_normalization_n.R:449:5',
    'test-olink_normalization_n.R:637:5', 'test-olink_normalization_n.R:867:5',
    'test-olink_normalization_n.R:1021:5', 'test-olink_bridge_selector.R:94:5',
    'test-olink_bridge_selector.R:573:5',
    'test-olink_normalization_product.R:154:5',
    'test-olink_normalization_product.R:281:5',
    'test-olink_normalization_product.R:400:5',
    'test-olink_ordinal_regression.R:20:1',
    'test-olink_pathway_enrichment.R:41:5',
    'test-olink_pathway_enrichment.R:89:5',
    'test-olink_pathway_enrichment.R:182:5',
    'test-olink_pathway_enrichment.R:231:5',
    'test-olink_pathway_enrichment.R:280:5',
    'test-olink_pathway_enrichment.R:332:5',
    'test-olink_pathway_enrichment.R:383:5',
    'test-olink_pathway_enrichment.R:432:5',
    'test-olink_pathway_enrichment.R:481:5',
    'test-olink_pathway_enrichment.R:535:5',
    'test-olink_pathway_enrichment.R:681:5',
    'test-olink_pathway_enrichment.R:704:5',
    'test-olink_pathway_enrichment.R:730:5',
    'test-olink_pathway_enrichment.R:750:5',
    'test-olink_pathway_enrichment.R:770:5',
    'test-olink_pathway_enrichment.R:792:5',
    'test-olink_pathway_enrichment.R:939:5',
    'test-olink_pathway_enrichment.R:993:5',
    'test-olink_pathway_enrichment.R:1029:5',
    'test-olink_pathway_enrichment.R:1046:5',
    'test-olink_pathway_enrichment.R:1095:5',
    'test-olink_pathway_enrichment.R:1509:5', 'test-olink_pathway_heatmap.R:5:5',
    'test-olink_pathway_visualization.R:5:5',
    'test-olink_plate_randomizer.R:25:5', 'test-olink_plate_randomizer.R:97:5',
    'test-olink_plate_randomizer.R:211:5', 'test-olink_plate_randomizer.R:248:5',
    'test-olink_plate_randomizer.R:294:5', 'test-olink_plate_randomizer.R:402:5',
    'test-olink_plate_randomizer.R:473:5', 'test-olink_plate_randomizer.R:620:5',
    'test-olink_qc_plot.R:6:5', 'test-olink_qc_plot.R:172:5',
    'test-olink_ttest.R:6:5', 'test-olink_ttest.R:44:5',
    'test-olink_wilcox.R:6:5', 'test-olink_wilcox.R:54:5',
    'test-osi_dist_plot.R:4:5', 'test-osi_dist_plot.R:76:5',
    'test-pca_plot.R:9:5', 'test-plot_heatmap.R:9:5',
    'test-plot_heatmap_helper.R:1:1', 'test-plot_umap.R:145:5',
    'test-plot_umap.R:188:5', 'test-plot_umap.R:283:5',
    'test-plot_volcano.R:5:5', 'test-plot_volcano.R:54:5', 'test-read_npx.R:5:5',
    'test-read_npx.R:74:5', 'test-read_npx.R:143:5', 'test-read_npx.R:212:5',
    'test-read_npx.R:298:5', 'test-read_npx.R:397:5', 'test-read_npx.R:504:5',
    'test-read_npx_delim.R:139:5', 'test-read_npx_delim.R:420:5',
    'test-read_npx_delim.R:513:5', 'test-read_npx_delim.R:649:5',
    'test-read_npx_delim.R:729:5', 'test-read_npx_delim.R:874:5',
    'test-read_npx_excel.R:8:5', 'test-read_npx_excel.R:98:5',
    'test-read_npx_format.R:11:5', 'test-read_npx_format.R:712:5',
    'test-read_npx_format.R:1453:5', 'test-read_npx_format.R:1773:5',
    'test-read_npx_format.R:1815:5', 'test-read_npx_format.R:1899:5',
    'test-read_npx_format.R:2000:5', 'test-read_npx_format.R:2118:5',
    'test-read_npx_format.R:2267:5', 'test-read_npx_format.R:2364:5',
    'test-read_npx_format.R:2470:5', 'test-read_npx_format.R:2755:5',
    'test-read_npx_format.R:2810:5', 'test-read_npx_format.R:2865:5',
    'test-reference_data.R:11:5', 'test-utils.R:194:5', 'test-utils.R:268:5'
  • dir.exists(test_dir) is not TRUE (2): 'test-plot_heatmap.R:97:5',
    'test-plot_umap.R:44:5'
  • file.exists(file_legacy_v) is not TRUE (3): 'test-reference_data.R:594:5',
    'test-reference_data.R:610:5', 'test-reference_data.R:626:5'
  • file.exists(test_path("_snaps", "npxProcessing.md")) is not TRUE (1):
    'test-npxProcessing.R:146:5'
  • file.exists(test_path("_snaps", "pca_plot.md")) is not TRUE (1):
    'test-pca_plot.R:619:5'
  • file.exists(test_path("data", "example_3k_data.rds")) is not TRUE (16):
    'test-olink_normalization_product.R:7:5',
    'test-olink_normalization_product.R:528:5',
    'test-olink_normalization_product.R:670:5',
    'test-olink_normalization_product.R:810:5',
    'test-olink_normalization_product.R:891:5',
    'test-olink_normalization_utils.R:331:5',
    'test-olink_normalization_utils.R:441:5',
    'test-olink_normalization_utils.R:3035:5',
    'test-olink_normalization_utils.R:3166:5',
    'test-olink_normalization_utils.R:3458:5',
    'test-olink_normalization_utils.R:3530:5',
    'test-olink_normalization_utils.R:3579:5',
    'test-olink_normalization_utils.R:3663:5',
    'test-olink_normalization_utils.R:3823:5',
    'test-olink_normalization_utils.R:5024:5',
    'test-olink_normalization_utils.R:6459:5'
  • file.exists(test_path("data", "example_HT_data.rds")) is not TRUE (2):
    'test-olink_normalization_product.R:1125:5',
    'test-olink_normalization_utils.R:581:5'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-olink_normalization_utils.R:4564:5'): olink_norm_input_ref_medians - check cols ──
  Expected `expect_no_message(...)` not to throw any warnings.
  Actually got a <deprecatedWarning> with message:
    Replacing special names '.Names' is deprecated; use 'names' instead.
  ── Failure ('test-olink_normalization_utils.R:5355:5'): olink_norm_input_clean_assays - works - no excluded assays ──
  Expected `expect_no_warning(...)` not to throw any errors.
  Actually got a <expectation_failure> with message:
    Expected `expect_no_message(...)` not to throw any warnings.
    Actually got a <deprecatedWarning> with message:
      Replacing special names '.Names' is deprecated; use 'names' instead.
  ── Failure ('test-olink_normalization_utils.R:5429:5'): olink_norm_input_clean_assays - works - no excluded assays ──
  Expected `expect_no_warning(...)` not to throw any errors.
  Actually got a <expectation_failure> with message:
    Expected `expect_no_message(...)` not to throw any warnings.
    Actually got a <deprecatedWarning> with message:
      Replacing special names '.Names' is deprecated; use 'names' instead.
  
  [ FAIL 3 | WARN 341 | SKIP 284 | PASS 1409 ]
  Error:
  ! Test failures.
  Execution halted