R Under development (unstable) (2026-02-10 r89394 ucrt) -- "Unsuffered Consequences" Copyright (C) 2026 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(ggpicrust2) Loading required package: ggpicrust2 To cite ggpicrust2 in publications use: Chen Yang, Jiahao Mai, Xuan Cao, Aaron Burberry, Fabio Cominelli, Liangliang Zhang, ggpicrust2: an R package for PICRUSt2 predicted functional profile analysis and visualization, Bioinformatics, Volume 39, Issue 8, August 2023, btad470, https://doi.org/10.1093/bioinformatics/btad470 > > test_check("ggpicrust2") Reading input data... Performing pathway differential abundance analysis... Annotating pathways... Creating pathway error bar plots... Plot 1 skipped (no data for method: mock_method) ggpicrust2 analysis completed. Note: Preranked GSEA methods (fgsea, clusterProfiler) do not account for inter-gene correlations, which may lead to unreliable p-values (Wu et al., 2012). Consider using method='camera' or method='fry' for more reliable statistical inference. 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computing center with all features Disp = 1e-04 , BCV = 0.01 conditions vector supplied operating in serial mode computing center with all features conditions vector supplied operating in serial mode computing center with all features conditions vector supplied operating in serial mode computing center with all features conditions vector supplied operating in serial mode computing center with all features conditions vector supplied operating in serial mode computing center with all features conditions vector supplied operating in serial mode computing center with all features Excluded 1 pathways with missing annotations. Use 'pathway_annotation' to add them. Excluded 1 rows with missing 'pathway_name' annotations. conditions vector supplied operating in serial mode computing center with all features Note: Preranked GSEA methods (fgsea, clusterProfiler) do not account for inter-gene correlations, which may lead to unreliable p-values (Wu et al., 2012). Consider using method='camera' or method='fry' for more reliable statistical inference. Using column 'sample_name' as sample identifier Using column 'sample_name' as sample identifier Testing 2 gene sets (filtered from 2 by size constraints) Using column 'sample' as sample identifier The Sample Names in order from left to right are: S1, S2, S3, S4 The Group Levels in order from left to right are: A, A, B, B Using column 'sample' as sample identifier The Sample Names in order from left to right are: S1, S2, S3, S4 The Group Levels in order from left to right are: A, A, B, B Using column 'sample' as sample identifier The Sample Names in order from left to right are: S1, S2, S3, S4 The Group Levels in order from left to right are: A, A, B, B Using column 'sample_name' as sample identifier Using column 'sample_name' as sample identifier Using column 'sample_name' as sample identifier Too few points to calculate an ellipse Too few points to calculate an ellipse Using column 'sample_name' as sample identifier Using column 'sample_name' as sample identifier Using column 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|==================================================================== | 98% | |===================================================================== | 98% | |===================================================================== | 99% | |======================================================================| 99% | |======================================================================| 100% [ FAIL 0 | WARN 2 | SKIP 7 | PASS 198 ] ══ Skipped tests (7) ═══════════════════════════════════════════════════════════ • On CRAN (4): 'test-pathway_ridgeplot.R:25:3', 'test-pathway_ridgeplot.R:42:3', 'test-pathway_ridgeplot.R:65:3', 'test-pathway_volcano.R:82:3' • Set GGPICRUST2_RUN_E2E_TESTS=true to run full ggpicrust2 end-to-end tests. (1): 'test-ggpicrust2-return-structure.R:4:3' • Set GGPICRUST2_RUN_EXTENDED_DAA_TESTS=true to run extended DAA method tests. (1): 'test-pathway_daa.R:102:3' • Set GGPICRUST2_RUN_NETWORK_TESTS=true to run network-dependent KEGG tests. (1): 'test-pathway_annotation.R:36:3' [ FAIL 0 | WARN 2 | SKIP 7 | PASS 198 ] > > proc.time() user system elapsed 23.06 1.65 27.67