Last updated on 2026-11-09 01:52:24 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 5.1.0 | 19.54 | 658.63 | 678.17 | OK | |
| r-devel-linux-x86_64-debian-gcc | 5.1.0 | 12.38 | 274.16 | 286.54 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 5.1.0 | 15.00 | 494.15 | 509.15 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 5.1.0 | 14.00 | 461.22 | 475.22 | OK | |
| r-devel-windows-x86_64 | 5.1.0 | 21.00 | 410.00 | 431.00 | OK | |
| r-patched-linux-x86_64 | 5.1.0 | OK | ||||
| r-release-linux-x86_64 | 5.1.0 | 19.10 | 624.19 | 643.29 | OK | |
| r-release-macos-arm64 | 5.1.0 | 4.00 | 106.00 | 110.00 | OK | |
| r-release-macos-x86_64 | 5.1.0 | 13.00 | 463.00 | 476.00 | OK | |
| r-release-windows-x86_64 | 5.1.0 | 23.00 | 411.00 | 434.00 | OK | |
| r-oldrel-macos-arm64 | 5.1.0 | 4.00 | 114.00 | 118.00 | OK | |
| r-oldrel-macos-x86_64 | 5.1.0 | 14.00 | 504.00 | 518.00 | OK | |
| r-oldrel-windows-x86_64 | 5.1.0 | 32.00 | 523.00 | 555.00 | OK |
Version: 5.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [177s/121s]
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_pathway_enrichment-3.R
Saving _problems/test-olink_pathway_enrichment-3.R
Saving _problems/test-olink_normalization-4565.R
Saving _problems/test-olink_normalization-4565.R
Saving _problems/test-olink_normalization-4689.R
Saving _problems/test-olink_normalization-4833.R
Saving _problems/test-olink_normalization-4833.R
Saving _problems/test-olink_ordinal_regression-16.R
Saving _problems/test-olink_ordinal_regression-16.R
Saving _problems/test-pca_plot-199.R
Saving _problems/test-pca_plot-199.R
Saving _problems/test-olink_normalization_utils-16.R
Saving _problems/test-olink_normalization_utils-16.R
Saving _problems/test-olink_normalization_utils-1743.R
Saving _problems/test-olink_normalization_utils-1743.R
Saving _problems/test-olink_normalization_utils-2030.R
Saving _problems/test-olink_normalization_utils-2030.R
Saving _problems/test-olink_normalization_utils-2319.R
Saving _problems/test-olink_normalization_utils-2319.R
Saving _problems/test-olink_normalization_utils-2568.R
Saving _problems/test-olink_normalization_utils-4268.R
Saving _problems/test-olink_normalization_utils-4268.R
Saving _problems/test-olink_normalization_utils-4328.R
Saving _problems/test-olink_normalization_utils-4328.R
Saving _problems/test-olink_normalization_utils-4362.R
Saving _problems/test-olink_normalization_utils-4362.R
Saving _problems/test-olink_normalization_utils-4396.R
Saving _problems/test-olink_normalization_utils-4396.R
Saving _problems/test-olink_normalization_utils-4430.R
Saving _problems/test-olink_normalization_utils-4430.R
Saving _problems/test-olink_normalization_utils-4562.R
Saving _problems/test-olink_normalization_utils-4562.R
Saving _problems/test-olink_normalization_utils-6558.R
Saving _problems/test-olink_normalization_utils-6872.R
Saving _problems/test-olink_normalization_utils-6975.R
Saving _problems/test-olink_normalization_utils-7051.R
Saving _problems/test-olink_normalization_utils-7279.R
Saving _problems/test-clean_npx-92.R
Saving _problems/test-clean_npx-92.R
Saving _problems/test-plot_heatmap-73.R
Saving _problems/test-plot_heatmap-73.R
Saving _problems/test-plot_heatmap-238.R
Saving _problems/test-plot_heatmap-238.R
Saving _problems/test-Olink_one_non_parametric-462.R
Saving _problems/test-Olink_one_non_parametric-462.R
Saving _problems/test-Olink_one_non_parametric-490.R
Saving _problems/test-Olink_one_non_parametric-490.R
Saving _problems/test-check_columns-82.R
Saving _problems/test-check_columns-82.R
Saving _problems/test-check_columns-303.R
Saving _problems/test-check_columns-303.R
Saving _problems/test-check_columns-324.R
Saving _problems/test-check_columns-324.R
Saving _problems/test-check_df-178.R
Saving _problems/test-check_df-219.R
Saving _problems/test-check_df-520.R
Saving _problems/test-check_df-757.R
Saving _problems/test-check_df-757.R
Saving _problems/test-check_df-990.R
Saving _problems/test-check_df-993.R
Saving _problems/test-check_df-999.R
Saving _problems/test-check_df-1084.R
Saving _problems/test-check_df-1277.R
Saving _problems/test-check_df-1277.R
Saving _problems/test-check_npx-75.R
Saving _problems/test-check_npx-75.R
Saving _problems/test-check_npx-150.R
Saving _problems/test-check_npx-150.R
Saving _problems/test-check_npx-214.R
Saving _problems/test-check_npx-214.R
Saving _problems/test-check_npx-291.R
Saving _problems/test-check_npx-291.R
Saving _problems/test-check_npx-368.R
Saving _problems/test-check_npx-368.R
Saving _problems/test-check_npx-392.R
Saving _problems/test-check_npx-392.R
Saving _problems/test-check_npx-422.R
Saving _problems/test-check_npx-422.R
Saving _problems/test-check_npx-453.R
Saving _problems/test-check_npx-453.R
Saving _problems/test-check_npx-480.R
Saving _problems/test-check_npx-480.R
Saving _problems/test-check_npx-515.R
Saving _problems/test-check_npx-515.R
Saving _problems/test-check_npx-643.R
Saving _problems/test-check_npx-643.R
Saving _problems/test-check_npx-667.R
Saving _problems/test-check_npx-667.R
Saving _problems/test-check_npx-719.R
Saving _problems/test-check_npx-719.R
Saving _problems/test-check_npx-1321.R
Saving _problems/test-check_npx-1421.R
Saving _problems/test-check_npx-1421.R
Saving _problems/test-check_npx-1447.R
Saving _problems/test-check_npx-1447.R
Saving _problems/test-check_npx-1478.R
Saving _problems/test-check_npx-1478.R
Saving _problems/test-check_npx-1501.R
Saving _problems/test-check_npx-1501.R
Saving _problems/test-check_npx-1603.R
Saving _problems/test-check_npx-1603.R
Saving _problems/test-check_npx-1629.R
Saving _problems/test-check_npx-1629.R
Saving _problems/test-check_npx-1664.R
Saving _problems/test-check_npx-1664.R
Saving _problems/test-check_npx-1687.R
Saving _problems/test-check_npx-1687.R
Saving _problems/test-check_npx-1809.R
Saving _problems/test-check_npx-1864.R
Saving _problems/test-npxProcessing-205.R
Saving _problems/test-npxProcessing-205.R
Saving _problems/test-olink_anova-16.R
Saving _problems/test-olink_anova-16.R
Saving _problems/test-olink_bridge_selector-6.R
Saving _problems/test-olink_bridge_selector-6.R
Saving _problems/test-olink_bridge_selector-282.R
Saving _problems/test-olink_bridge_selector-608.R
Saving _problems/test-olink_bridge_selector-651.R
Saving _problems/test-olink_bridge_selector-651.R
Saving _problems/test-olink_bridge_selector-790.R
Saving _problems/test-olink_bridge_selector-790.R
Saving _problems/test-olink_class-7.R
Saving _problems/test-olink_class-7.R
Saving _problems/test-plot_umap-27.R
Saving _problems/test-plot_umap-80.R
Saving _problems/test-plot_umap-189.R
Saving _problems/test-plot_umap-189.R
Saving _problems/test-plot_umap-251.R
Saving _problems/test-plot_umap-251.R
Saving _problems/test-read_npx_delim-630.R
Saving _problems/test-read_npx_delim-1035.R
Saving _problems/test-read_npx_excel-203.R
Saving _problems/test-read_npx_parquet-80.R
Saving _problems/test-read_npx_parquet-171.R
Saving _problems/test-read_npx_parquet-218.R
Saving _problems/test-read_npx_parquet-269.R
Saving _problems/test-read_npx_parquet-471.R
Saving _problems/test-read_npx_parquet-594.R
Saving _problems/test-read_npx_parquet-656.R
Saving _problems/test-read_npx_utils-102.R
Saving _problems/test-read_npx_zip-172.R
Saving _problems/test-read_npx_zip-256.R
Saving _problems/test-read_npx_zip-356.R
Saving _problems/test-read_npx_zip-462.R
Saving _problems/test-read_npx_zip-564.R
Saving _problems/test-read_npx_zip-665.R
Saving _problems/test-read_npx_zip-667.R
Saving _problems/test-read_npx_zip-669.R
Saving _problems/test-read_npx_zip-777.R
Saving _problems/test-read_npx_zip-874.R
Saving _problems/test-read_npx_zip-876.R
Saving _problems/test-read_npx_zip-878.R
Saving _problems/test-read_npx_zip-987.R
Saving _problems/test-utils-153.R
Saving _problems/test-utils-387.R
Saving _problems/test-utils-394.R
Saving _problems/test-utils-396.R
Saving _problems/test-utils-444.R
Saving _problems/test-utils-451.R
Saving _problems/test-utils-453.R
Saving _problems/test-utils-494.R
Saving _problems/test-utils-550.R
Saving _problems/test-utils-665.R
Saving _problems/test-utils-706.R
Saving _problems/test-utils-711.R
[ FAIL 165 | WARN 0 | SKIP 266 | PASS 974 ]
══ Skipped tests (266) ═════════════════════════════════════════════════════════
• On CRAN (84): 'test-olink_lmer.R:9:5', 'test-olink_lmer.R:129:5',
'test-olink_lmer.R:165:5', 'test-olink_lmer.R:209:5',
'test-olink_lmer.R:240:5', 'test-olink_lmer.R:332:5',
'test-olink_lmer.R:492:5', 'test-olink_lmer.R:529:5',
'test-olink_lmer.R:565:5', 'test-pca_plot.R:269:5', 'test-pca_plot.R:434:5',
'test-pca_plot.R:821:5', 'test-pca_plot.R:907:5', 'test-pca_plot.R:1067:5',
'test-pca_plot.R:1127:5', 'test-olink_normalization_utils.R:2794:5',
'test-olink_normalization_utils.R:2810:5',
'test-olink_normalization_utils.R:2829:5',
'test-olink_normalization_utils.R:2845:5',
'test-olink_normalization_utils.R:2864:5',
'test-olink_normalization_utils.R:2899:5',
'test-olink_normalization_utils.R:2916:5',
'test-olink_normalization_utils.R:2936:5',
'test-olink_normalization_utils.R:2952:5',
'test-olink_normalization_utils.R:2971:5',
'test-olink_normalization_utils.R:2987:5',
'test-olink_normalization_utils.R:3006:5',
'test-olink_normalization_utils.R:3023:5',
'test-olink_normalization_utils.R:3043:5',
'test-olink_normalization_utils.R:3060:5',
'test-olink_normalization_utils.R:3082:5',
'test-olink_normalization_utils.R:3100:5',
'test-olink_normalization_utils.R:3121:5',
'test-olink_normalization_utils.R:3139:5',
'test-olink_normalization_utils.R:3160:5',
'test-olink_normalization_utils.R:3179:5',
'test-olink_normalization_utils.R:3209:5',
'test-olink_normalization_utils.R:3228:5',
'test-olink_normalization_utils.R:3259:5',
'test-olink_normalization_utils.R:3277:5',
'test-olink_normalization_utils.R:3298:5',
'test-olink_normalization_utils.R:3316:5',
'test-olink_normalization_utils.R:3337:5',
'test-olink_normalization_utils.R:3362:5',
'test-olink_normalization_utils.R:3391:5',
'test-olink_normalization_utils.R:3416:5',
'test-olink_normalization_utils.R:3448:5',
'test-olink_normalization_utils.R:3464:5',
'test-olink_normalization_utils.R:3484:5',
'test-olink_normalization_utils.R:3509:5',
'test-olink_normalization_utils.R:3536:5',
'test-olink_normalization_utils.R:3574:5',
'test-olink_normalization_utils.R:3664:5',
'test-olink_normalization_utils.R:3737:5',
'test-olink_normalization_utils.R:3819:5',
'test-olink_normalization_utils.R:4016:5',
'test-olink_normalization_utils.R:4154:5', 'test-plot_is_bridgeable.R:6:5',
'test-plot_is_bridgeable.R:124:5', 'test-plot_is_bridgeable.R:246:5',
'test-plot_is_bridgeable.R:453:5', 'test-plot_is_bridgeable.R:565:5',
'test-plot_is_bridgeable.R:658:5', 'test-plot_is_bridgeable.R:752:5',
'test-plot_is_bridgeable.R:845:5', 'test-plot_is_bridgeable.R:942:5',
'test-plot_is_bridgeable.R:1060:5', 'test-dist_plot.R:62:5',
'test-dist_plot.R:129:5', 'test-olink_boxplot.R:4:5',
'test-olink_boxplot.R:41:5', 'test-olink_boxplot.R:321:5',
'test-olink_boxplot.R:420:5', 'test-olink_plate_randomizer.R:47:5',
'test-olink_qc_plot.R:220:5', 'test-olink_qc_plot.R:256:5',
'test-olink_ttest.R:154:5', 'test-olink_ttest.R:181:5',
'test-olink_wilcox.R:194:5', 'test-olink_wilcox.R:221:5',
'test-plot_point_range.R:6:5', 'test-plot_point_range.R:105:5',
'test-plot_point_range.R:207:5', 'test-plot_point_range.R:254:5'
• Skipping (159): '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_normalization.R:20:5', 'test-olink_normalization.R:334:5',
'test-olink_normalization.R:869:5', 'test-olink_normalization.R:1170:5',
'test-olink_normalization.R:1470:5', 'test-olink_normalization.R:1996:5',
'test-olink_normalization.R:2220:5', 'test-olink_normalization.R:2648:5',
'test-olink_normalization.R:3111:5', 'test-olink_normalization.R:3573:5',
'test-olink_normalization.R:4059:5', 'test-olink_normalization.R:4880:5',
'test-olink_normalization.R:4991:5', 'test-olink_normalization.R:5072:5',
'test-read_npx_wide.R:21:5', 'test-read_npx_wide.R:306:5',
'test-read_npx_wide.R:775:5', 'test-read_npx_wide.R:925:5',
'test-read_npx_wide.R:1053:5', 'test-read_npx_wide.R:1354:5',
'test-read_npx_wide.R:1464:5', 'test-read_npx_wide.R:1616:5',
'test-read_npx_wide.R:1777:5', 'test-read_npx_wide.R:1936:5',
'test-read_npx_wide.R:2617:5', 'test-read_npx_wide.R:3297:5',
'test-read_npx_wide.R:3713:5', 'test-read_npx_wide.R:4129:5',
'test-read_npx_wide.R:4809:5', 'test-read_npx_wide.R:5490:5',
'test-read_npx_wide.R:6171:5', 'test-read_npx_wide.R:6850:5',
'test-read_npx_wide.R:6949:5', 'test-read_npx_wide.R:7048:5',
'test-read_npx_wide.R:7126:5', 'test-read_npx_wide.R:7186:5',
'test-read_npx_wide.R:7964:5', 'test-read_npx_wide.R:8740:5',
'test-read_npx_wide.R:8928:5', 'test-read_npx_wide.R:9039:5',
'test-read_npx_wide.R:9155:5', 'test-read_npx_wide.R:9888:5',
'test-read_npx_wide.R:10622:5', 'test-read_npx_wide.R:10727:5',
'test-read_npx_wide.R:11292:5', 'test-read_npx_wide.R:11858:5',
'test-read_npx_wide.R:12425:5', 'test-read_npx_wide.R:12988:5',
'test-read_npx_wide.R:13095:5', 'test-read_npx_wide.R:13204:5',
'test-read_npx_wide.R:13303:5', 'test-read_npx_wide.R:13594:5',
'test-read_npx_wide.R:13683:5', 'test-read_npx_wide.R:14632:5',
'test-read_npx_wide.R:15581:5', 'test-read_npx_wide.R:16530:5',
'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:1036:5',
'test-olink_normalization_n.R:1357:5',
'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-pca_plot.R:9:5',
'test-read_npx_format.R:11:5', 'test-read_npx_format.R:712:5',
'test-read_npx_format.R:1455:5', 'test-read_npx_format.R:1559:5',
'test-read_npx_format.R:1879:5', 'test-read_npx_format.R:1921:5',
'test-read_npx_format.R:2005:5', 'test-read_npx_format.R:2092:5',
'test-read_npx_format.R:2193:5', 'test-read_npx_format.R:2311:5',
'test-read_npx_format.R:2461:5', 'test-read_npx_format.R:2559:5',
'test-read_npx_format.R:2666:5', 'test-read_npx_format.R:2951:5',
'test-read_npx_format.R:3006:5', 'test-read_npx_format.R:3061:5',
'test-plot_heatmap.R:9:5', 'test-Olink_one_non_parametric.R:5:5',
'test-Olink_one_non_parametric.R:207:5', 'test-dist_plot.R:8:5',
'test-npxProcessing.R:5:5', 'test-npxProcessing.R:55:5',
'test-olink_bridge_selector.R:94:5', 'test-olink_lod.R:10:5',
'test-olink_lod.R:165:5', 'test-olink_lod.R:320:5',
'test-olink_normalization_product.R:154:5',
'test-olink_normalization_product.R:281:5',
'test-olink_normalization_product.R:400:5',
'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:617:5',
'test-olink_qc_plot.R:6:5', 'test-olink_qc_plot.R:172:5',
'test-olink_ttest.R:6:5', 'test-olink_ttest.R:82:5',
'test-olink_wilcox.R:6:5', 'test-olink_wilcox.R:102:5',
'test-osi_dist_plot.R:4:5', 'test-osi_dist_plot.R:76:5',
'test-osi_dist_plot.R:104:5', 'test-plot_heatmap_helper.R:1:1',
'test-plot_umap.R:297:5', 'test-plot_umap.R:392:5',
'test-plot_volcano.R:5:5', 'test-plot_volcano.R:54:5', 'test-read_npx.R:5:5',
'test-read_npx.R:106:5', 'test-read_npx.R:206:5', 'test-read_npx.R:314:5',
'test-read_npx.R:435:5', 'test-read_npx.R:571:5', 'test-read_npx.R:715:5',
'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-reference_data.R:11:5', 'test-utils.R:905:5', 'test-utils.R:971:5',
'test-utils.R:1048:5'
• 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:1005:5'
• file.exists(test_path("data", "example_3k_data.rds")) is not TRUE (16):
'test-olink_normalization_utils.R:502:5',
'test-olink_normalization_utils.R:802:5',
'test-olink_normalization_utils.R:4618:5',
'test-olink_normalization_utils.R:4749:5',
'test-olink_normalization_utils.R:5041:5',
'test-olink_normalization_utils.R:5113:5',
'test-olink_normalization_utils.R:5162:5',
'test-olink_normalization_utils.R:5246:5',
'test-olink_normalization_utils.R:5406:5',
'test-olink_normalization_utils.R:6630:5',
'test-olink_normalization_utils.R:8083:5',
'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'
• file.exists(test_path("data", "example_HT_data.rds")) is not TRUE (2):
'test-olink_normalization_utils.R:1141:5',
'test-olink_normalization_product.R:1125:5'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-olink_pathway_enrichment.R:1:1'): (code run outside of `test_that()`) ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! This build of the arrow package does not support Datasets
── Error ('test-olink_pathway_enrichment.R:1:1'): (code run outside of `test_that()`) ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! Invalid Error: std::exception
i Context: rapi_execute
i Error type: INVALID
── Error ('test-olink_normalization.R:4563:5'): norm_internal_preferred_names - works ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! This build of the arrow package does not support Datasets
── Error ('test-olink_normalization.R:4563:5'): norm_internal_preferred_names - works ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! Invalid Error: std::exception
i Context: rapi_execute
i Error type: INVALID
── Error ('test-olink_normalization.R:4687:5'): norm_internal_preferred_names - works - no error when AssayQC is missing ──
Error in `compute.arrow_dplyr_query(x)`: Key error: No function registered with name: match_substring_regex
Backtrace:
▆
1. ├─base::suppressWarnings(suppressMessages(check_npx(df = ref_df))) at test-olink_normalization.R:4687:5
2. │ └─base::withCallingHandlers(...)
3. ├─base::suppressMessages(check_npx(df = ref_df))
4. │ └─base::withCallingHandlers(...)
5. └─OlinkAnalyze::check_npx(df = ref_df)
6. └─OlinkAnalyze:::check_npx_olinkid(df = df, col_names = check_npx_out_lst[["col_names"]])
7. ├─dplyr::pull(...)
8. ├─dplyr::collect(...)
9. └─arrow:::collect.arrow_dplyr_query(...)
10. └─arrow:::compute.arrow_dplyr_query(x)
11. └─base::tryCatch(...)
12. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
13. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
14. └─value[[3L]](cond)
15. └─arrow:::augment_io_error_msg(e, call, schema = schema())
16. └─rlang::abort(msg, call = call)
── Error ('test-olink_normalization.R:4831:5'): norm_internal_update_df_names - renames data and check log ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! This build of the arrow package does not support Datasets
── Error ('test-olink_normalization.R:4831:5'): norm_internal_update_df_names - renames data and check log ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! Invalid Error: std::exception
i Context: rapi_execute
i Error type: INVALID
── Error ('test-olink_ordinal_regression.R:16:1'): (code run outside of `test_that()`) ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! This build of the arrow package does not support Datasets
── Error ('test-olink_ordinal_regression.R:16:1'): (code run outside of `test_that()`) ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! Invalid Error: std::exception
i Context: rapi_execute
i Error type: INVALID
── Error ('test-pca_plot.R:197:5'): olink_pca_plot - works ─────────────────────
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! This build of the arrow package does not support Datasets
── Error ('test-pca_plot.R:197:5'): olink_pca_plot - works ─────────────────────
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! Invalid Error: std::exception
i Context: rapi_execute
i Error type: INVALID
── Error ('test-olink_normalization_utils.R:14:5'): olink_norm_input_check - works - bridge normalization ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! This build of the arrow package does not support Datasets
── Error ('test-olink_normalization_utils.R:14:5'): olink_norm_input_check - works - bridge normalization ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! Invalid Error: std::exception
i Context: rapi_execute
i Error type: INVALID
── Error ('test-olink_normalization_utils.R:1741:5'): olink_norm_input_check - works - intensity (subset all samples) norm ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! This build of the arrow package does not support Datasets
── Error ('test-olink_normalization_utils.R:1741:5'): olink_norm_input_check - works - intensity (subset all samples) norm ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! Invalid Error: std::exception
i Context: rapi_execute
i Error type: INVALID
── Error ('test-olink_normalization_utils.R:2028:5'): olink_norm_input_check - works - subset normalization ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! This build of the arrow package does not support Datasets
── Error ('test-olink_normalization_utils.R:2028:5'): olink_norm_input_check - works - subset normalization ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! Invalid Error: std::exception
i Context: rapi_execute
i Error type: INVALID
── Error ('test-olink_normalization_utils.R:2317:5'): olink_norm_input_check - works - reference median normalization ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! This build of the arrow package does not support Datasets
── Error ('test-olink_normalization_utils.R:2317:5'): olink_norm_input_check - works - reference median normalization ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! Invalid Error: std::exception
i Context: rapi_execute
i Error type: INVALID
── Error ('test-olink_normalization_utils.R:2560:5'): olink_norm_input_check - works - bridge normalization - mixed inputs ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! Invalid Error: std::exception
i Context: rapi_execute
i Error type: INVALID
── Error ('test-olink_normalization_utils.R:4268:12'): olink_norm_input_check_df_cols - message - non-required columns ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! This build of the arrow package does not support Datasets
── Error ('test-olink_normalization_utils.R:4268:12'): olink_norm_input_check_df_cols - message - non-required columns ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! Invalid Error: std::exception
i Context: rapi_execute
i Error type: INVALID
── Error ('test-olink_normalization_utils.R:4328:12'): olink_norm_input_check_df_cols - error - different quant methods ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! This build of the arrow package does not support Datasets
── Error ('test-olink_normalization_utils.R:4328:12'): olink_norm_input_check_df_cols - error - different quant methods ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! Invalid Error: std::exception
i Context: rapi_execute
i Error type: INVALID
── Error ('test-olink_normalization_utils.R:4362:12'): olink_norm_input_check_df_cols - error - different olink_id cols ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! This build of the arrow package does not support Datasets
── Error ('test-olink_normalization_utils.R:4362:12'): olink_norm_input_check_df_cols - error - different olink_id cols ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! Invalid Error: std::exception
i Context: rapi_execute
i Error type: INVALID
── Error ('test-olink_normalization_utils.R:4396:12'): olink_norm_input_check_df_cols - error - different sample_id cols ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! This build of the arrow package does not support Datasets
── Error ('test-olink_normalization_utils.R:4396:12'): olink_norm_input_check_df_cols - error - different sample_id cols ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! Invalid Error: std::exception
i Context: rapi_execute
i Error type: INVALID
── Error ('test-olink_normalization_utils.R:4430:12'): olink_norm_input_check_df_cols - message - missing non-required cols ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! This build of the arrow package does not support Datasets
── Error ('test-olink_normalization_utils.R:4430:12'): olink_norm_input_check_df_cols - message - missing non-required cols ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! Invalid Error: std::exception
i Context: rapi_execute
i Error type: INVALID
── Error ('test-olink_normalization_utils.R:4562:12'): olink_norm_input_check_df_cols - error - non-matching col classes ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! This build of the arrow package does not support Datasets
── Error ('test-olink_normalization_utils.R:4562:12'): olink_norm_input_check_df_cols - error - non-matching col classes ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! Invalid Error: std::exception
i Context: rapi_execute
i Error type: INVALID
── Error ('test-olink_normalization_utils.R:6546:5'): olink_norm_input_clean_assays - works - invalid OID in df* ──
Error in `dplyr::compute(.data)`: Key error: No function registered with name: match_substring_regex
Backtrace:
▆
1. ├─testthat::expect_message(...) at test-olink_normalization_utils.R:6546:5
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. └─OlinkAnalyze:::olink_norm_input_clean_assays(...)
8. └─base::lapply(...)
9. └─OlinkAnalyze (local) FUN(X[[i]], ...)
10. └─OlinkAnalyze:::pull_col(...)
11. ├─dplyr::pull(.data, .data[[col]], as_vector = TRUE)
12. └─arrow:::pull.arrow_dplyr_query(.data, .data[[col]], as_vector = TRUE)
13. ├─dplyr::compute(.data)
14. └─arrow:::compute.arrow_dplyr_query(.data)
15. └─base::tryCatch(...)
16. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
17. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
18. └─value[[3L]](cond)
19. └─arrow:::augment_io_error_msg(e, call, schema = schema())
20. └─rlang::abort(msg, call = call)
── Error ('test-olink_normalization_utils.R:6859:5'): olink_norm_input_clean_assays - works - invalid OID in reference_medians ──
Error: Key error: No function registered with name: match_substring_regex
Backtrace:
▆
1. ├─testthat::expect_message(...) at test-olink_normalization_utils.R:6859:5
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. └─OlinkAnalyze:::olink_norm_input_clean_assays(...)
8. └─base::nrow(lst_out$reference_medians)
9. ├─base::dim(x)
10. └─arrow:::dim.arrow_dplyr_query(x)
11. ├─base::nrow(as_arrow_table(x))
12. ├─arrow::as_arrow_table(x)
13. └─arrow:::as_arrow_table.arrow_dplyr_query(x)
14. ├─arrow::as_record_batch_reader(x)
15. └─arrow:::as_record_batch_reader.arrow_dplyr_query(x)
16. └─plan$Build(x)
17. └─node$Filter(.data$filtered_rows)
18. ├─self$preserve_extras(ExecNode_Filter(self, expr))
19. └─arrow:::ExecNode_Filter(self, expr)
── Failure ('test-olink_normalization_utils.R:6961:5'): olink_norm_input_clean_assays - works - no excluded assays ──
Expected `expect_no_warning(...)` not to throw any errors.
Actually got a <rlang_error> with message:
Key error: No function registered with name: match_substring_regex
── Failure ('test-olink_normalization_utils.R:7035:5'): olink_norm_input_clean_assays - works - no excluded assays ──
Expected `expect_no_warning(...)` not to throw any errors.
Actually got a <rlang_error> with message:
Key error: No function registered with name: match_substring_regex
── Error ('test-olink_normalization_utils.R:7261:5'): olink_norm_input_clean_assays - works - excluded assays in df* ──
Error in `dplyr::compute(.data)`: Key error: No function registered with name: match_substring_regex
Backtrace:
▆
1. ├─testthat::expect_message(...) at test-olink_normalization_utils.R:7261:5
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. └─OlinkAnalyze:::olink_norm_input_clean_assays(...)
8. └─base::lapply(...)
9. └─OlinkAnalyze (local) FUN(X[[i]], ...)
10. └─OlinkAnalyze:::pull_col(...)
11. ├─dplyr::pull(.data, .data[[col]], as_vector = TRUE)
12. └─arrow:::pull.arrow_dplyr_query(.data, .data[[col]], as_vector = TRUE)
13. ├─dplyr::compute(.data)
14. └─arrow:::compute.arrow_dplyr_query(.data)
15. └─base::tryCatch(...)
16. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
17. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
18. └─value[[3L]](cond)
19. └─arrow:::augment_io_error_msg(e, call, schema = schema())
20. └─rlang::abort(msg, call = call)
── Error ('test-clean_npx.R:90:1'): (code run outside of `test_that()`) ────────
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! This build of the arrow package does not support Datasets
── Error ('test-clean_npx.R:90:1'): (code run outside of `test_that()`) ────────
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! Invalid Error: std::exception
i Context: rapi_execute
i Error type: INVALID
── Error ('test-plot_heatmap.R:69:5'): olink_heatmap_plot - works - snapshots ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! This build of the arrow package does not support Datasets
── Error ('test-plot_heatmap.R:69:5'): olink_heatmap_plot - works - snapshots ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! Invalid Error: std::exception
i Context: rapi_execute
i Error type: INVALID
── Error ('test-plot_heatmap.R:234:5'): olink_heatmap_plot - works - olink_class and arrow ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! This build of the arrow package does not support Datasets
── Error ('test-plot_heatmap.R:234:5'): olink_heatmap_plot - works - olink_class and arrow ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! Invalid Error: std::exception
i Context: rapi_execute
i Error type: INVALID
── Error ('test-Olink_one_non_parametric.R:460:5'): olink_one_non_parametric - error - missing input ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! This build of the arrow package does not support Datasets
── Error ('test-Olink_one_non_parametric.R:460:5'): olink_one_non_parametric - error - missing input ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! Invalid Error: std::exception
i Context: rapi_execute
i Error type: INVALID
── Error ('test-Olink_one_non_parametric.R:488:5'): olink_one_non_parametric - warn - assays with only NA in one level ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! This build of the arrow package does not support Datasets
── Error ('test-Olink_one_non_parametric.R:488:5'): olink_one_non_parametric - warn - assays with only NA in one level ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! Invalid Error: std::exception
i Context: rapi_execute
i Error type: INVALID
── Error ('test-check_columns.R:80:5'): check_columns - works - olink_class ────
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! This build of the arrow package does not support Datasets
── Error ('test-check_columns.R:80:5'): check_columns - works - olink_class ────
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! Invalid Error: std::exception
i Context: rapi_execute
i Error type: INVALID
── Error ('test-check_columns.R:301:5'): check_log_colname - works ─────────────
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! This build of the arrow package does not support Datasets
── Error ('test-check_columns.R:301:5'): check_log_colname - works ─────────────
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! Invalid Error: std::exception
i Context: rapi_execute
i Error type: INVALID
── Error ('test-check_columns.R:322:5'): check_log_colname - error - missing column ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! This build of the arrow package does not support Datasets
── Error ('test-check_columns.R:322:5'): check_log_colname - error - missing column ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! Invalid Error: std::exception
i Context: rapi_execute
i Error type: INVALID
── Error ('test-check_df.R:172:9'): check is arrow object - csv - TRUE ─────────
Error: This build of the arrow package does not support Datasets
Backtrace:
▆
1. └─withr::with_tempfile(...) at test-check_df.R:143:5
2. └─base::eval(substitute(code), envir = env)
3. └─base::eval(substitute(code), envir = env)
4. └─arrow::open_delim_dataset(...) at test-check_df.R:172:9
5. └─arrow::open_dataset(...)
6. └─arrow:::stop_if_no_datasets()
── Error ('test-check_df.R:209:9'): check is arrow object - parquet - TRUE ─────
Error in `parquet___WriterProperties___Builder__create()`: Cannot call parquet___WriterProperties___Builder__create(). See https://arrow.apache.org/docs/r/articles/install.html for help installing Arrow C++ libraries.
Backtrace:
▆
1. └─withr::with_tempfile(...) at test-check_df.R:203:5
2. └─base::eval(substitute(code), envir = env)
3. └─base::eval(substitute(code), envir = env)
4. └─arrow::write_parquet(...) at test-check_df.R:209:9
5. ├─ParquetFileWriter$create(...)
6. │ └─arrow:::parquet___arrow___ParquetFileWriter__Open(...)
7. └─ParquetWriterProperties$create(...)
8. └─arrow:::parquet___WriterProperties___Builder__create()
── Error ('test-check_df.R:510:9'): check is tibble - parquet - TRUE ───────────
Error in `parquet___WriterProperties___Builder__create()`: Cannot call parquet___WriterProperties___Builder__create(). See https://arrow.apache.org/docs/r/articles/install.html for help installing Arrow C++ libraries.
Backtrace:
▆
1. └─withr::with_tempfile(...) at test-check_df.R:504:5
2. └─base::eval(substitute(code), envir = env)
3. └─base::eval(substitute(code), envir = env)
4. └─arrow::write_parquet(...) at test-check_df.R:510:9
5. ├─ParquetFileWriter$create(...)
6. │ └─arrow:::parquet___arrow___ParquetFileWriter__Open(...)
7. └─ParquetWriterProperties$create(...)
8. └─arrow:::parquet___WriterProperties___Builder__create()
── Error ('test-check_df.R:755:5'): check is olink class - TRUE ────────────────
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! This build of the arrow package does not support Datasets
── Error ('test-check_df.R:755:5'): check is olink class - TRUE ────────────────
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! Invalid Error: std::exception
i Context: rapi_execute
i Error type: INVALID
── Failure ('test-check_df.R:982:9'): check_is_dataset - works - csv to tibble or arrow ──
Expected `... <- NULL` not to throw any conditions.
Actually got a <simpleError> with message:
This build of the arrow package does not support Datasets
Backtrace:
▆
1. └─withr::with_tempfile(...) at test-check_df.R:948:5
2. └─base::eval(substitute(code), envir = env)
3. └─base::eval(substitute(code), envir = env)
4. └─testthat::expect_no_condition(...) at test-check_df.R:982:9
── Failure ('test-check_df.R:993:9'): check_is_dataset - works - csv to tibble or arrow ──
Expected `exists("df_read")` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
Backtrace:
▆
1. └─withr::with_tempfile(...) at test-check_df.R:948:5
2. └─base::eval(substitute(code), envir = env)
3. └─base::eval(substitute(code), envir = env)
4. └─testthat::expect_true(object = exists("df_read")) at test-check_df.R:993:9
── Error ('test-check_df.R:996:9'): check_is_dataset - works - csv to tibble or arrow ──
<objectNotFoundError/error/condition>
Error in `eval(substitute(code), envir = env)`: object 'df_read' not found
Backtrace:
▆
1. └─withr::with_tempfile(...) at test-check_df.R:948:5
2. └─base::eval(substitute(code), envir = env)
3. └─base::eval(substitute(code), envir = env)
4. ├─testthat::expect_true(...) at test-check_df.R:996:9
5. │ └─testthat::quasi_label(enquo(object), label)
6. │ └─rlang::eval_bare(expr, quo_get_env(quo))
7. └─OlinkAnalyze:::check_is_dataset(x = df_read, error = TRUE)
8. └─OlinkAnalyze:::check_is_arrow_object(x = x, error = FALSE)
── Error ('test-check_df.R:1074:9'): check_is_dataset - works - parquet to arrow or tibble ──
Error in `parquet___WriterProperties___Builder__create()`: Cannot call parquet___WriterProperties___Builder__create(). See https://arrow.apache.org/docs/r/articles/install.html for help installing Arrow C++ libraries.
Backtrace:
▆
1. └─withr::with_tempfile(...) at test-check_df.R:1068:5
2. └─base::eval(substitute(code), envir = env)
3. └─base::eval(substitute(code), envir = env)
4. └─arrow::write_parquet(...) at test-check_df.R:1074:9
5. ├─ParquetFileWriter$create(...)
6. │ └─arrow:::parquet___arrow___ParquetFileWriter__Open(...)
7. └─ParquetWriterProperties$create(...)
8. └─arrow:::parquet___WriterProperties___Builder__create()
── Error ('test-check_df.R:1275:5'): check_is_dataset - works - olink_class ────
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! This build of the arrow package does not support Datasets
── Error ('test-check_df.R:1275:5'): check_is_dataset - works - olink_class ────
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! Invalid Error: std::exception
i Context: rapi_execute
i Error type: INVALID
── Error ('test-check_npx.R:71:5'): check_npx - works - minimum set of columns, results as expected ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! This build of the arrow package does not support Datasets
── Error ('test-check_npx.R:71:5'): check_npx - works - minimum set of columns, results as expected ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! Invalid Error: std::exception
i Context: rapi_execute
i Error type: INVALID
── Error ('test-check_npx.R:143:5'): check_npx - works - full set of columns, results as expected ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! This build of the arrow package does not support Datasets
── Error ('test-check_npx.R:143:5'): check_npx - works - full set of columns, results as expected ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! Invalid Error: std::exception
i Context: rapi_execute
i Error type: INVALID
── Error ('test-check_npx.R:201:5'): check_npx - warnings - invalid OlinkID, duplicate SampleID and NPX non-num ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! This build of the arrow package does not support Datasets
── Error ('test-check_npx.R:201:5'): check_npx - warnings - invalid OlinkID, duplicate SampleID and NPX non-num ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! Invalid Error: std::exception
i Context: rapi_execute
i Error type: INVALID
── Error ('test-check_npx.R:282:5'): check_npx - warnings - OlinkIDs mapped with >1 Uniprots ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! This build of the arrow package does not support Datasets
── Error ('test-check_npx.R:282:5'): check_npx - warnings - OlinkIDs mapped with >1 Uniprots ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! Invalid Error: std::exception
i Context: rapi_execute
i Error type: INVALID
── Error ('test-check_npx.R:359:5'): check_npx - warnings - outdated DARID and PanelDataArchiveVersion ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! This build of the arrow package does not support Datasets
── Error ('test-check_npx.R:359:5'): check_npx - warnings - outdated DARID and PanelDataArchiveVersion ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! Invalid Error: std::exception
i Context: rapi_execute
i Error type: INVALID
── Error ('test-check_npx.R:390:5'): get_check_npx - works - extracts check_log from olink_class ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! This build of the arrow package does not support Datasets
── Error ('test-check_npx.R:390:5'): get_check_npx - works - extracts check_log from olink_class ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! Invalid Error: std::exception
i Context: rapi_execute
i Error type: INVALID
── Error ('test-check_npx.R:420:5'): get_check_npx - works - extracts check_log from ArrowObject ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! This build of the arrow package does not support Datasets
── Error ('test-check_npx.R:420:5'): get_check_npx - works - extracts check_log from ArrowObject ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! Invalid Error: std::exception
i Context: rapi_execute
i Error type: INVALID
── Error ('test-check_npx.R:451:5'): get_check_npx - works - uses provided check_log when df has none ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! This build of the arrow package does not support Datasets
── Error ('test-check_npx.R:451:5'): get_check_npx - works - uses provided check_log when df has none ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! Invalid Error: std::exception
i Context: rapi_execute
i Error type: INVALID
── Error ('test-check_npx.R:478:5'): get_check_npx - works - uses provided check_log when ArrowObject has none ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! This build of the arrow package does not support Datasets
── Error ('test-check_npx.R:478:5'): get_check_npx - works - uses provided check_log when ArrowObject has none ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! Invalid Error: std::exception
i Context: rapi_execute
i Error type: INVALID
── Error ('test-check_npx.R:515:9'): get_check_npx - works - runs check_npx when no check_log provided ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! This build of the arrow package does not support Datasets
── Error ('test-check_npx.R:515:9'): get_check_npx - works - runs check_npx when no check_log provided ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! Invalid Error: std::exception
i Context: rapi_execute
i Error type: INVALID
── Error ('test-check_npx.R:641:5'): get_check_npx - prefers embedded check_log over provided check_log argument ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! This build of the arrow package does not support Datasets
── Error ('test-check_npx.R:641:5'): get_check_npx - prefers embedded check_log over provided check_log argument ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! Invalid Error: std::exception
i Context: rapi_execute
i Error type: INVALID
── Error ('test-check_npx.R:665:5'): get_preferred_names - works - check_log match ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! This build of the arrow package does not support Datasets
── Error ('test-check_npx.R:665:5'): get_preferred_names - works - check_log match ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! Invalid Error: std::exception
i Context: rapi_execute
i Error type: INVALID
── Error ('test-check_npx.R:714:5'): get_preferred_names - works - check_log match ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! This build of the arrow package does not support Datasets
── Error ('test-check_npx.R:714:5'): get_preferred_names - works - check_log match ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! Invalid Error: std::exception
i Context: rapi_execute
i Error type: INVALID
── Error ('test-check_npx.R:1317:5'): check_npx_olinkid - works - all OlinkID are valid ──
Error in `compute.arrow_dplyr_query(x)`: Key error: No function registered with name: match_substring_regex
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-check_npx.R:1317:5
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─OlinkAnalyze:::check_npx_olinkid(df = df, col_names = col_names)
5. ├─dplyr::pull(...)
6. ├─dplyr::collect(...)
7. └─arrow:::collect.arrow_dplyr_query(...)
8. └─arrow:::compute.arrow_dplyr_query(x)
9. └─base::tryCatch(...)
10. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
11. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
12. └─value[[3L]](cond)
13. └─arrow:::augment_io_error_msg(e, call, schema = schema())
14. └─rlang::abort(msg, call = call)
── Error ('test-check_npx.R:1412:5'): check_npx_all_na_assays - warning - all-NA assay captured ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! This build of the arrow package does not support Datasets
── Error ('test-check_npx.R:1412:5'): check_npx_all_na_assays - warning - all-NA assay captured ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! Invalid Error: std::exception
i Context: rapi_execute
i Error type: INVALID
── Error ('test-check_npx.R:1443:5'): check_npx_all_na_assays - works - no assay has all NAs ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! This build of the arrow package does not support Datasets
── Error ('test-check_npx.R:1443:5'): check_npx_all_na_assays - works - no assay has all NAs ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! Invalid Error: std::exception
i Context: rapi_execute
i Error type: INVALID
── Error ('test-check_npx.R:1469:5'): check_npx_all_na_assays - warning - arrow - all-NA assay captured ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! This build of the arrow package does not support Datasets
── Error ('test-check_npx.R:1469:5'): check_npx_all_na_assays - warning - arrow - all-NA assay captured ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! Invalid Error: std::exception
i Context: rapi_execute
i Error type: INVALID
── Error ('test-check_npx.R:1497:5'): check_npx_all_na_assays - works - arrow - no assay has all NAs ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! This build of the arrow package does not support Datasets
── Error ('test-check_npx.R:1497:5'): check_npx_all_na_assays - works - arrow - no assay has all NAs ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! Invalid Error: std::exception
i Context: rapi_execute
i Error type: INVALID
── Error ('test-check_npx.R:1594:5'): check_npx_all_na_sample - warning - all-NA assays captured ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["sample_id"]], col_names[["quant"]]))), .data[[col_names[["sample_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! This build of the arrow package does not support Datasets
── Error ('test-check_npx.R:1594:5'): check_npx_all_na_sample - warning - all-NA assays captured ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["sample_id"]], col_names[["quant"]]))), .data[[col_names[["sample_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! Invalid Error: std::exception
i Context: rapi_execute
i Error type: INVALID
── Error ('test-check_npx.R:1625:5'): check_npx_all_na_sample - works - no sample has all NAs ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["sample_id"]], col_names[["quant"]]))), .data[[col_names[["sample_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! This build of the arrow package does not support Datasets
── Error ('test-check_npx.R:1625:5'): check_npx_all_na_sample - works - no sample has all NAs ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["sample_id"]], col_names[["quant"]]))), .data[[col_names[["sample_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! Invalid Error: std::exception
i Context: rapi_execute
i Error type: INVALID
── Error ('test-check_npx.R:1655:5'): check_npx_all_na_sample - warning - arrow - all-NA assay captured ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["sample_id"]], col_names[["quant"]]))), .data[[col_names[["sample_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! This build of the arrow package does not support Datasets
── Error ('test-check_npx.R:1655:5'): check_npx_all_na_sample - warning - arrow - all-NA assay captured ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["sample_id"]], col_names[["quant"]]))), .data[[col_names[["sample_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! Invalid Error: std::exception
i Context: rapi_execute
i Error type: INVALID
── Error ('test-check_npx.R:1683:5'): check_npx_all_na_sample - works - arrow - no assay has all NAs ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["sample_id"]], col_names[["quant"]]))), .data[[col_names[["sample_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! This build of the arrow package does not support Datasets
── Error ('test-check_npx.R:1683:5'): check_npx_all_na_sample - works - arrow - no assay has all NAs ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["sample_id"]], col_names[["quant"]]))), .data[[col_names[["sample_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! Invalid Error: std::exception
i Context: rapi_execute
i Error type: INVALID
── Error ('test-check_npx.R:1805:5'): check_npx_qcwarn_assays - works - no assay with warning ──
Error in `compute.arrow_dplyr_query(x)`: Key error: No function registered with name: match_substring_regex
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-check_npx.R:1805:5
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─OlinkAnalyze:::check_npx_qcwarn_assays(df = df, col_names = col_names)
5. ├─base::sort(...)
6. ├─base::unique(...)
7. ├─dplyr::pull(...)
8. ├─dplyr::collect(...)
9. └─arrow:::collect.arrow_dplyr_query(...)
10. └─arrow:::compute.arrow_dplyr_query(x)
11. └─base::tryCatch(...)
12. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
13. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
14. └─value[[3L]](cond)
15. └─arrow:::augment_io_error_msg(e, call, schema = schema())
16. └─rlang::abort(msg, call = call)
── Error ('test-check_npx.R:1857:5'): check_npx_qcwarn_assays - works - assays with warnings ──
Error in `compute.arrow_dplyr_query(x)`: Key error: No function registered with name: match_substring_regex
Backtrace:
▆
1. ├─testthat::expect_message(...) at test-check_npx.R:1857:5
2. │ └─testthat:::expect_condition_matching_(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─testthat::expect_equal(...)
8. │ └─testthat::quasi_label(enquo(object), label)
9. │ └─rlang::eval_bare(expr, quo_get_env(quo))
10. └─OlinkAnalyze:::check_npx_qcwarn_assays(df = df, col_names = col_names)
11. ├─base::sort(...)
12. ├─base::unique(...)
13. ├─dplyr::pull(...)
14. ├─dplyr::collect(...)
15. └─arrow:::collect.arrow_dplyr_query(...)
16. └─arrow:::compute.arrow_dplyr_query(x)
17. └─base::tryCatch(...)
18. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
19. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
20. └─value[[3L]](cond)
21. └─arrow:::augment_io_error_msg(e, call, schema = schema())
22. └─rlang::abort(msg, call = call)
── Error ('test-npxProcessing.R:203:5'): npxProcessing_forDimRed - works - olink_class and arrow ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! This build of the arrow package does not support Datasets
── Error ('test-npxProcessing.R:203:5'): npxProcessing_forDimRed - works - olink_class and arrow ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! Invalid Error: std::exception
i Context: rapi_execute
i Error type: INVALID
── Error ('test-olink_anova.R:16:1'): (code run outside of `test_that()`) ──────
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! This build of the arrow package does not support Datasets
── Error ('test-olink_anova.R:16:1'): (code run outside of `test_that()`) ──────
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! Invalid Error: std::exception
i Context: rapi_execute
i Error type: INVALID
── Error ('test-olink_bridge_selector.R:4:5'): olink_bridgeselector - works ────
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! This build of the arrow package does not support Datasets
── Error ('test-olink_bridge_selector.R:4:5'): olink_bridgeselector - works ────
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! Invalid Error: std::exception
i Context: rapi_execute
i Error type: INVALID
── Error ('test-olink_bridge_selector.R:259:5'): olink_bridgeselector - works - alternative column names ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! Invalid Error: std::exception
i Context: rapi_execute
i Error type: INVALID
── Error ('test-olink_bridge_selector.R:585:5'): olink_bridgeselector - works - alternative argument names ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! Invalid Error: std::exception
i Context: rapi_execute
i Error type: INVALID
── Error ('test-olink_bridge_selector.R:649:5'): olink_bridgeselector - errors ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! This build of the arrow package does not support Datasets
── Error ('test-olink_bridge_selector.R:649:5'): olink_bridgeselector - errors ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! Invalid Error: std::exception
i Context: rapi_execute
i Error type: INVALID
── Error ('test-olink_bridge_selector.R:788:5'): olink_bridgeselector - warning for additional arguments ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! This build of the arrow package does not support Datasets
── Error ('test-olink_bridge_selector.R:788:5'): olink_bridgeselector - warning for additional arguments ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! Invalid Error: std::exception
i Context: rapi_execute
i Error type: INVALID
── Error ('test-olink_class.R:5:1'): (code run outside of `test_that()`) ───────
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! This build of the arrow package does not support Datasets
── Error ('test-olink_class.R:5:1'): (code run outside of `test_that()`) ───────
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! Invalid Error: std::exception
i Context: rapi_execute
i Error type: INVALID
── Error ('test-plot_umap.R:21:5'): olink_umap_plot - works - snapshot ─────────
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! Invalid Error: std::exception
i Context: rapi_execute
i Error type: INVALID
── Error ('test-plot_umap.R:74:5'): olink_umap_plot - works - snapshot ─────────
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! Invalid Error: std::exception
i Context: rapi_execute
i Error type: INVALID
── Error ('test-plot_umap.R:187:5'): olink_umap_plot - works - clusters are there and outlier group is detected ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! This build of the arrow package does not support Datasets
── Error ('test-plot_umap.R:187:5'): olink_umap_plot - works - clusters are there and outlier group is detected ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! Invalid Error: std::exception
i Context: rapi_execute
i Error type: INVALID
── Error ('test-plot_umap.R:234:5'): olink_umap_plot - warnings ────────────────
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! This build of the arrow package does not support Datasets
── Error ('test-plot_umap.R:234:5'): olink_umap_plot - warnings ────────────────
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! Invalid Error: std::exception
i Context: rapi_execute
i Error type: INVALID
── Error ('test-read_npx_delim.R:620:9'): read_npx_delim - error - long format - file not delimited ──
Error in `parquet___WriterProperties___Builder__create()`: Cannot call parquet___WriterProperties___Builder__create(). See https://arrow.apache.org/docs/r/articles/install.html for help installing Arrow C++ libraries.
Backtrace:
▆
1. └─withr::with_tempfile(...) at test-read_npx_delim.R:614:5
2. └─base::eval(substitute(code), envir = env)
3. └─base::eval(substitute(code), envir = env)
4. └─arrow::write_parquet(...) at test-read_npx_delim.R:620:9
5. ├─ParquetFileWriter$create(...)
6. │ └─arrow:::parquet___arrow___ParquetFileWriter__Open(...)
7. └─ParquetWriterProperties$create(...)
8. └─arrow:::parquet___WriterProperties___Builder__create()
── Error ('test-read_npx_delim.R:1025:9'): get_field_separator - error - unable to read the file ──
Error in `parquet___WriterProperties___Builder__create()`: Cannot call parquet___WriterProperties___Builder__create(). See https://arrow.apache.org/docs/r/articles/install.html for help installing Arrow C++ libraries.
Backtrace:
▆
1. └─withr::with_tempfile(...) at test-read_npx_delim.R:1019:5
2. └─base::eval(substitute(code), envir = env)
3. └─base::eval(substitute(code), envir = env)
4. └─arrow::write_parquet(...) at test-read_npx_delim.R:1025:9
5. ├─ParquetFileWriter$create(...)
6. │ └─arrow:::parquet___arrow___ParquetFileWriter__Open(...)
7. └─ParquetWriterProperties$create(...)
8. └─arrow:::parquet___WriterProperties___Builder__create()
── Error ('test-read_npx_excel.R:193:9'): read_npx_excel - error - file not excel ──
Error in `parquet___WriterProperties___Builder__create()`: Cannot call parquet___WriterProperties___Builder__create(). See https://arrow.apache.org/docs/r/articles/install.html for help installing Arrow C++ libraries.
Backtrace:
▆
1. └─withr::with_tempfile(...) at test-read_npx_excel.R:186:5
2. └─base::eval(substitute(code), envir = env)
3. └─base::eval(substitute(code), envir = env)
4. └─arrow::write_parquet(...) at test-read_npx_excel.R:193:9
5. ├─ParquetFileWriter$create(...)
6. │ └─arrow:::parquet___arrow___ParquetFileWriter__Open(...)
7. └─ParquetWriterProperties$create(...)
8. └─arrow:::parquet___WriterProperties___Builder__create()
── Error ('test-read_npx_parquet.R:76:9'): read_npx_parquet - error - required metadata fields are missing ──
Error in `parquet___WriterProperties___Builder__create()`: Cannot call parquet___WriterProperties___Builder__create(). See https://arrow.apache.org/docs/r/articles/install.html for help installing Arrow C++ libraries.
Backtrace:
▆
1. └─withr::with_tempfile(...) at test-read_npx_parquet.R:60:5
2. └─base::eval(substitute(code), envir = env)
3. └─base::eval(substitute(code), envir = env)
4. └─arrow::write_parquet(x = df, sink = pfile_metadata, compression = "gzip") at test-read_npx_parquet.R:76:9
5. ├─ParquetFileWriter$create(...)
6. │ └─arrow:::parquet___arrow___ParquetFileWriter__Open(...)
7. └─ParquetWriterProperties$create(...)
8. └─arrow:::parquet___WriterProperties___Builder__create()
── Error ('test-read_npx_parquet.R:167:9'): read_npx_parquet - error - Product field is incorrect ──
Error in `parquet___WriterProperties___Builder__create()`: Cannot call parquet___WriterProperties___Builder__create(). See https://arrow.apache.org/docs/r/articles/install.html for help installing Arrow C++ libraries.
Backtrace:
▆
1. └─withr::with_tempfile(...) at test-read_npx_parquet.R:142:5
2. └─base::eval(substitute(code), envir = env)
3. └─base::eval(substitute(code), envir = env)
4. └─arrow::write_parquet(x = df, sink = pfile_product, compression = "gzip") at test-read_npx_parquet.R:167:9
5. ├─ParquetFileWriter$create(...)
6. │ └─arrow:::parquet___arrow___ParquetFileWriter__Open(...)
7. └─ParquetWriterProperties$create(...)
8. └─arrow:::parquet___WriterProperties___Builder__create()
── Error ('test-read_npx_parquet.R:214:9'): read_npx_parquet - error - DataFileType field is incorrect ──
Error in `parquet___WriterProperties___Builder__create()`: Cannot call parquet___WriterProperties___Builder__create(). See https://arrow.apache.org/docs/r/articles/install.html for help installing Arrow C++ libraries.
Backtrace:
▆
1. └─withr::with_tempfile(...) at test-read_npx_parquet.R:191:5
2. └─base::eval(substitute(code), envir = env)
3. └─base::eval(substitute(code), envir = env)
4. └─arrow::write_parquet(x = df, sink = pfile_datafiletype, compression = "gzip") at test-read_npx_parquet.R:214:9
5. ├─ParquetFileWriter$create(...)
6. │ └─arrow:::parquet___arrow___ParquetFileWriter__Open(...)
7. └─ParquetWriterProperties$create(...)
8. └─arrow:::parquet___WriterProperties___Builder__create()
── Error ('test-read_npx_parquet.R:265:9'): read_npx_parquet - works - all DataFileType ──
Error in `parquet___WriterProperties___Builder__create()`: Cannot call parquet___WriterProperties___Builder__create(). See https://arrow.apache.org/docs/r/articles/install.html for help installing Arrow C++ libraries.
Backtrace:
▆
1. └─withr::with_tempfile(...) at test-read_npx_parquet.R:256:5
2. └─base::eval(substitute(code), envir = env)
3. └─base::eval(substitute(code), envir = env)
4. └─arrow::write_parquet(x = df, sink = pfile_test, compression = "gzip") at test-read_npx_parquet.R:265:9
5. ├─ParquetFileWriter$create(...)
6. │ └─arrow:::parquet___arrow___ParquetFileWriter__Open(...)
7. └─ParquetWriterProperties$create(...)
8. └─arrow:::parquet___WriterProperties___Builder__create()
── Error ('test-read_npx_parquet.R:467:9'): read_npx_parquet - works - all Product ──
Error in `parquet___WriterProperties___Builder__create()`: Cannot call parquet___WriterProperties___Builder__create(). See https://arrow.apache.org/docs/r/articles/install.html for help installing Arrow C++ libraries.
Backtrace:
▆
1. └─withr::with_tempfile(...) at test-read_npx_parquet.R:458:5
2. └─base::eval(substitute(code), envir = env)
3. └─base::eval(substitute(code), envir = env)
4. └─arrow::write_parquet(x = df, sink = pfile_test, compression = "gzip") at test-read_npx_parquet.R:467:9
5. ├─ParquetFileWriter$create(...)
6. │ └─arrow:::parquet___arrow___ParquetFileWriter__Open(...)
7. └─ParquetWriterProperties$create(...)
8. └─arrow:::parquet___WriterProperties___Builder__create()
── Error ('test-read_npx_parquet.R:590:9'): read_npx_parquet - works ───────────
Error in `parquet___WriterProperties___Builder__create()`: Cannot call parquet___WriterProperties___Builder__create(). See https://arrow.apache.org/docs/r/articles/install.html for help installing Arrow C++ libraries.
Backtrace:
▆
1. └─withr::with_tempfile(...) at test-read_npx_parquet.R:567:5
2. └─base::eval(substitute(code), envir = env)
3. └─base::eval(substitute(code), envir = env)
4. └─arrow::write_parquet(x = df, sink = pfile_test, compression = "gzip") at test-read_npx_parquet.R:590:9
5. ├─ParquetFileWriter$create(...)
6. │ └─arrow:::parquet___arrow___ParquetFileWriter__Open(...)
7. └─ParquetWriterProperties$create(...)
8. └─arrow:::parquet___WriterProperties___Builder__create()
── Error ('test-read_npx_parquet.R:652:9'): read_npx_parquet - works - RUO file ──
Error in `parquet___WriterProperties___Builder__create()`: Cannot call parquet___WriterProperties___Builder__create(). See https://arrow.apache.org/docs/r/articles/install.html for help installing Arrow C++ libraries.
Backtrace:
▆
1. └─withr::with_tempfile(...) at test-read_npx_parquet.R:625:5
2. └─base::eval(substitute(code), envir = env)
3. └─base::eval(substitute(code), envir = env)
4. └─arrow::write_parquet(x = df, sink = pfile_ruo, compression = "uncompressed") at test-read_npx_parquet.R:652:9
5. ├─ParquetFileWriter$create(...)
6. │ └─arrow:::parquet___arrow___ParquetFileWriter__Open(...)
7. └─ParquetWriterProperties$create(...)
8. └─arrow:::parquet___WriterProperties___Builder__create()
── Error ('test-read_npx_utils.R:96:9'): read_npx_format_colnames - error - long read as wide delim ──
Error: This build of the arrow package does not support Datasets
Backtrace:
▆
1. └─withr::with_tempfile(...) at test-read_npx_utils.R:68:5
2. └─base::eval(substitute(code), envir = env)
3. └─base::eval(substitute(code), envir = env)
4. └─arrow::open_delim_dataset(...) at test-read_npx_utils.R:96:9
5. └─arrow::open_dataset(...)
6. └─arrow:::stop_if_no_datasets()
── Failure ('test-read_npx_zip.R:163:13'): read NPX zip - NPX file only ────────
Expected `expect_no_warning(...)` not to throw any errors.
Actually got a <rlang_error> with message:
Key error: No function registered with name: match_substring_regex
Backtrace:
▆
1. └─withr::with_tempfile(...) at test-read_npx_zip.R:108:5
2. └─base::eval(substitute(code), envir = env)
3. └─base::eval(substitute(code), envir = env)
4. └─withr::with_tempfile(...) at test-read_npx_zip.R:146:9
5. └─base::eval(substitute(code), envir = env)
6. └─base::eval(substitute(code), envir = env)
7. └─testthat::expect_no_error(...) at test-read_npx_zip.R:163:13
── Failure ('test-read_npx_zip.R:247:13'): read NPX zip - NPX and README files only ──
Expected `expect_no_warning(...)` not to throw any errors.
Actually got a <rlang_error> with message:
Key error: No function registered with name: match_substring_regex
Backtrace:
▆
1. └─withr::with_tempfile(...) at test-read_npx_zip.R:192:5
2. └─base::eval(substitute(code), envir = env)
3. └─base::eval(substitute(code), envir = env)
4. └─withr::with_tempfile(...) at test-read_npx_zip.R:230:9
5. └─base::eval(substitute(code), envir = env)
6. └─base::eval(substitute(code), envir = env)
7. └─testthat::expect_no_error(...) at test-read_npx_zip.R:247:13
── Failure ('test-read_npx_zip.R:347:17'): read NPX zip - NPX, README and random non-npx ──
Expected `expect_no_warning(...)` not to throw any errors.
Actually got a <rlang_error> with message:
Key error: No function registered with name: match_substring_regex
Backtrace:
▆
1. └─withr::with_tempfile(...) at test-read_npx_zip.R:281:5
2. └─base::eval(substitute(code), envir = env)
3. └─base::eval(substitute(code), envir = env)
4. └─withr::with_tempfile(...) at test-read_npx_zip.R:319:9
5. └─base::eval(substitute(code), envir = env)
6. └─base::eval(substitute(code), envir = env)
7. └─withr::with_tempfile(...) at test-read_npx_zip.R:325:13
8. └─base::eval(substitute(code), envir = env)
9. └─base::eval(substitute(code), envir = env)
10. └─testthat::expect_no_error(...) at test-read_npx_zip.R:347:17
── Failure ('test-read_npx_zip.R:448:17'): read NPX zip - NPX, README and random non-npx - .ignore_files works v1 ──
Expected `expect_no_message(...)` not to throw any errors.
Actually got a <rlang_error> with message:
Key error: No function registered with name: match_substring_regex
Backtrace:
▆
1. └─withr::with_tempfile(...) at test-read_npx_zip.R:384:5
2. └─base::eval(substitute(code), envir = env)
3. └─base::eval(substitute(code), envir = env)
4. └─withr::with_tempfile(...) at test-read_npx_zip.R:422:9
5. └─base::eval(substitute(code), envir = env)
6. └─base::eval(substitute(code), envir = env)
7. └─withr::with_tempfile(...) at test-read_npx_zip.R:427:13
8. └─base::eval(substitute(code), envir = env)
9. └─base::eval(substitute(code), envir = env)
10. └─testthat::expect_no_error(...) at test-read_npx_zip.R:448:17
── Failure ('test-read_npx_zip.R:552:17'): read NPX zip - NPX, README and random npx - .ignore_files works v2 ──
Expected `expect_no_warning(...)` not to throw any errors.
Actually got a <rlang_error> with message:
Key error: No function registered with name: match_substring_regex
Backtrace:
▆
1. └─withr::with_tempfile(...) at test-read_npx_zip.R:489:5
2. └─base::eval(substitute(code), envir = env)
3. └─base::eval(substitute(code), envir = env)
4. └─withr::with_tempfile(...) at test-read_npx_zip.R:527:9
5. └─base::eval(substitute(code), envir = env)
6. └─base::eval(substitute(code), envir = env)
7. └─withr::with_tempfile(...) at test-read_npx_zip.R:532:13
8. └─base::eval(substitute(code), envir = env)
9. └─base::eval(substitute(code), envir = env)
10. └─testthat::expect_no_error(...) at test-read_npx_zip.R:552:17
── Failure ('test-read_npx_zip.R:656:13'): read NPX zip - NPX, README and MD5 checksum ──
Expected `expect_no_warning(...)` not to throw any errors.
Actually got a <rlang_error> with message:
Key error: No function registered with name: match_substring_regex
Backtrace:
▆
1. └─withr::with_tempfile(...) at test-read_npx_zip.R:591:5
2. └─base::eval(substitute(code), envir = env)
3. └─base::eval(substitute(code), envir = env)
4. └─withr::with_tempfile(...) at test-read_npx_zip.R:636:9
5. └─base::eval(substitute(code), envir = env)
6. └─base::eval(substitute(code), envir = env)
7. └─testthat::expect_no_error(...) at test-read_npx_zip.R:656:13
── Failure ('test-read_npx_zip.R:667:13'): read NPX zip - NPX, README and MD5 checksum ──
Expected `exists("df_out_arrow")` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
Backtrace:
▆
1. └─withr::with_tempfile(...) at test-read_npx_zip.R:591:5
2. └─base::eval(substitute(code), envir = env)
3. └─base::eval(substitute(code), envir = env)
4. └─withr::with_tempfile(...) at test-read_npx_zip.R:636:9
5. └─base::eval(substitute(code), envir = env)
6. └─base::eval(substitute(code), envir = env)
7. └─testthat::expect_true(exists("df_out_arrow")) at test-read_npx_zip.R:667:13
── Error ('test-read_npx_zip.R:669:13'): read NPX zip - NPX, README and MD5 checksum ──
<objectNotFoundError/error/condition>
Error in `eval(substitute(code), envir = env)`: object 'df_out_arrow' not found
Backtrace:
▆
1. └─withr::with_tempfile(...) at test-read_npx_zip.R:591:5
2. └─base::eval(substitute(code), envir = env)
3. └─base::eval(substitute(code), envir = env)
4. └─withr::with_tempfile(...) at test-read_npx_zip.R:636:9
5. └─base::eval(substitute(code), envir = env)
6. └─base::eval(substitute(code), envir = env)
7. ├─testthat::expect_true(inherits(x = df_out_arrow, what = "ArrowObject")) at test-read_npx_zip.R:669:13
8. │ └─testthat::quasi_label(enquo(object), label)
9. │ └─rlang::eval_bare(expr, quo_get_env(quo))
10. └─base::inherits(x = df_out_arrow, what = "ArrowObject")
── Failure ('test-read_npx_zip.R:768:13'): read NPX zip - NPX and MD5 checksum ──
Expected `expect_no_warning(...)` not to throw any errors.
Actually got a <rlang_error> with message:
Key error: No function registered with name: match_substring_regex
Backtrace:
▆
1. └─withr::with_tempfile(...) at test-read_npx_zip.R:706:5
2. └─base::eval(substitute(code), envir = env)
3. └─base::eval(substitute(code), envir = env)
4. └─withr::with_tempfile(...) at test-read_npx_zip.R:751:9
5. └─base::eval(substitute(code), envir = env)
6. └─base::eval(substitute(code), envir = env)
7. └─testthat::expect_no_error(...) at test-read_npx_zip.R:768:13
── Failure ('test-read_npx_zip.R:865:13'): read NPX zip - NPX, README and SHA256 checksum ──
Expected `expect_no_warning(...)` not to throw any errors.
Actually got a <rlang_error> with message:
Key error: No function registered with name: match_substring_regex
Backtrace:
▆
1. └─withr::with_tempfile(...) at test-read_npx_zip.R:802:5
2. └─base::eval(substitute(code), envir = env)
3. └─base::eval(substitute(code), envir = env)
4. └─withr::with_tempfile(...) at test-read_npx_zip.R:847:9
5. └─base::eval(substitute(code), envir = env)
6. └─base::eval(substitute(code), envir = env)
7. └─testthat::expect_no_error(...) at test-read_npx_zip.R:865:13
── Failure ('test-read_npx_zip.R:876:13'): read NPX zip - NPX, README and SHA256 checksum ──
Expected `exists("df_out_arrow")` to be TRUE.
Differences:
`actual`: FALSE
`expected`: TRUE
Backtrace:
▆
1. └─withr::with_tempfile(...) at test-read_npx_zip.R:802:5
2. └─base::eval(substitute(code), envir = env)
3. └─base::eval(substitute(code), envir = env)
4. └─withr::with_tempfile(...) at test-read_npx_zip.R:847:9
5. └─base::eval(substitute(code), envir = env)
6. └─base::eval(substitute(code), envir = env)
7. └─testthat::expect_true(exists("df_out_arrow")) at test-read_npx_zip.R:876:13
── Error ('test-read_npx_zip.R:878:13'): read NPX zip - NPX, README and SHA256 checksum ──
<objectNotFoundError/error/condition>
Error in `eval(substitute(code), envir = env)`: object 'df_out_arrow' not found
Backtrace:
▆
1. └─withr::with_tempfile(...) at test-read_npx_zip.R:802:5
2. └─base::eval(substitute(code), envir = env)
3. └─base::eval(substitute(code), envir = env)
4. └─withr::with_tempfile(...) at test-read_npx_zip.R:847:9
5. └─base::eval(substitute(code), envir = env)
6. └─base::eval(substitute(code), envir = env)
7. ├─testthat::expect_true(inherits(x = df_out_arrow, what = "ArrowObject")) at test-read_npx_zip.R:878:13
8. │ └─testthat::quasi_label(enquo(object), label)
9. │ └─rlang::eval_bare(expr, quo_get_env(quo))
10. └─base::inherits(x = df_out_arrow, what = "ArrowObject")
── Failure ('test-read_npx_zip.R:978:13'): read NPX zip - NPX and SHA256 checksum ──
Expected `expect_no_warning(...)` not to throw any errors.
Actually got a <rlang_error> with message:
Key error: No function registered with name: match_substring_regex
Backtrace:
▆
1. └─withr::with_tempfile(...) at test-read_npx_zip.R:915:5
2. └─base::eval(substitute(code), envir = env)
3. └─base::eval(substitute(code), envir = env)
4. └─withr::with_tempfile(...) at test-read_npx_zip.R:961:9
5. └─base::eval(substitute(code), envir = env)
6. └─base::eval(substitute(code), envir = env)
7. └─testthat::expect_no_error(...) at test-read_npx_zip.R:978:13
── Error ('test-utils.R:142:5'): remove_all_na_cols - works - olink_class and arrow ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! Invalid Error: std::exception
i Context: rapi_execute
i Error type: INVALID
── Failure ('test-utils.R:376:5'): convert_read_npx_output - works - df: arrow; out: tibble ──
Expected `expect_no_message(...)` not to throw any errors.
Actually got a <rlang_error> with message:
Key error: No function registered with name: match_substring_regex
── Failure ('test-utils.R:389:5'): convert_read_npx_output - works - df: arrow; out: tibble ──
Expected `... <- NULL` not to throw any conditions.
Actually got a <objectNotFoundError> with message:
object 'npx_data1_arrow' not found
── Error ('test-utils.R:396:5'): convert_read_npx_output - works - df: arrow; out: tibble ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'npx_data1_tibble' not found
Backtrace:
▆
1. └─testthat::expect_s3_class(object = npx_data1_tibble, class = "tbl_df") at test-utils.R:396:5
2. └─testthat::quasi_label(enquo(object))
3. └─rlang::eval_bare(expr, quo_get_env(quo))
── Failure ('test-utils.R:433:5'): convert_read_npx_output - works - df: arrow; out: arrow ──
Expected `expect_no_message(...)` not to throw any errors.
Actually got a <rlang_error> with message:
Key error: No function registered with name: match_substring_regex
── Failure ('test-utils.R:446:5'): convert_read_npx_output - works - df: arrow; out: arrow ──
Expected `... <- NULL` not to throw any conditions.
Actually got a <objectNotFoundError> with message:
object 'npx_data1_arrow' not found
── Error ('test-utils.R:453:5'): convert_read_npx_output - works - df: arrow; out: arrow ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'npx_data1_arrow_v2' not found
Backtrace:
▆
1. └─testthat::expect_r6_class(object = npx_data1_arrow_v2, class = "ArrowObject") at test-utils.R:453:5
2. └─testthat::quasi_label(enquo(object))
3. └─rlang::eval_bare(expr, quo_get_env(quo))
── Error ('test-utils.R:483:5'): convert_read_npx_output - works - df: tibble; out: arrow ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! Invalid Error: std::exception
i Context: rapi_execute
i Error type: INVALID
── Error ('test-utils.R:539:5'): convert_read_npx_output - works df: tibble; out: tibble ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! Invalid Error: std::exception
i Context: rapi_execute
i Error type: INVALID
── Error ('test-utils.R:654:5'): get_read_npx_output - works - returns tibble for olink_class input ──
Error in `dplyr::collect(dplyr::filter(dplyr::summarise(arrow::to_duckdb(dplyr::mutate(dplyr::group_by(dplyr::select(df, dplyr::all_of(c(col_names[["olink_id"]], col_names[["quant"]]))), .data[[col_names[["olink_id"]]]]), is_na = dplyr::if_else(is.na(.data[[col_names[["quant"]]]]), 1L, 0L))), n = dplyr::n(), n_na = sum(.data[["is_na"]], na.rm = TRUE), .groups = "drop"), .data[["n"]] == .data[["n_na"]]))`: Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! Invalid Error: std::exception
i Context: rapi_execute
i Error type: INVALID
── Failure ('test-utils.R:695:5'): get_read_npx_output - works - returns arrow for olink_class arrow input ──
Expected `expect_no_message(...)` not to throw any errors.
Actually got a <rlang_error> with message:
Key error: No function registered with name: match_substring_regex
── Error ('test-utils.R:708:5'): get_read_npx_output - works - returns arrow for olink_class arrow input ──
<objectNotFoundError/error/condition>
Error in `eval(code, test_env)`: object 'npx_data1_arrow' not found
Backtrace:
▆
1. ├─testthat::expect_identical(...) at test-utils.R:708:5
2. │ └─testthat::quasi_label(enquo(object), label)
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─OlinkAnalyze:::get_read_npx_output(df = npx_data1_arrow)
5. └─OlinkAnalyze:::check_is_dataset(x = df, error = TRUE)
6. └─OlinkAnalyze:::check_is_arrow_object(x = x, error = FALSE)
[ FAIL 165 | WARN 0 | SKIP 266 | PASS 974 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc