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") 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 converting counts to integer mode gene-wise dispersion estimates mean-dispersion relationship -- note: fitType='parametric', but the dispersion trend was not well captured by the function: y = a/x + b, and a local regression fit was automatically substituted. specify fitType='local' or 'mean' to avoid this message next time. final dispersion estimates Disp = 1e-04 , BCV = 0.01 0 features are filtered! The filtered data has 10 samples and 3 features will be tested! Fit linear models ... Completed. 2026-02-11 16:07:08.955542 WARNING::Input is a matrix, passing through as.data.frame() . [1] "Creating output feature tables folder" [1] "Creating output fits folder" 2026-02-11 16:07:08.966661 INFO::Writing function arguments to log file 2026-02-11 16:07:08.98458 INFO::Verifying options selected are valid 2026-02-11 16:07:09.027172 INFO::Determining format of input files 2026-02-11 16:07:09.028525 INFO::Input format is data samples as rows and metadata samples as rows 2026-02-11 16:07:09.031669 INFO::Formula for fixed effects: expr ~ group 2026-02-11 16:07:09.033146 INFO::Filter data based on min abundance and min prevalence 2026-02-11 16:07:09.034375 INFO::Total samples in data: 10 2026-02-11 16:07:09.03556 INFO::Min samples required with min abundance for a feature not to be filtered: 1.000000 2026-02-11 16:07:09.036986 INFO::Total filtered features: 0 2026-02-11 16:07:09.038304 INFO::Filtered feature names from abundance and prevalence filtering: 2026-02-11 16:07:09.03975 INFO::Total filtered features with variance filtering: 0 2026-02-11 16:07:09.041012 INFO::Filtered feature names from variance filtering: 2026-02-11 16:07:09.042185 INFO::Running selected normalization method: TSS 2026-02-11 16:07:09.097876 INFO::Applying z-score to standardize continuous metadata 2026-02-11 16:07:09.19718 INFO::Running selected transform method: AST 2026-02-11 16:07:09.199592 INFO::Running selected analysis method: LM 2026-02-11 16:07:09.208772 INFO::Fitting model to feature number 1, pathway1 2026-02-11 16:07:09.21293 INFO::Fitting model to feature number 2, pathway2 2026-02-11 16:07:09.216098 INFO::Fitting model to feature number 3, pathway3 2026-02-11 16:07:09.224058 INFO::Counting total values for each feature 2026-02-11 16:07:09.226148 INFO::Writing filtered data to file D:\temp\2026_02_11_16_05_16_27802\RtmpGk6rvN/features/filtered_data.tsv 2026-02-11 16:07:09.228202 INFO::Writing filtered, normalized data to file D:\temp\2026_02_11_16_05_16_27802\RtmpGk6rvN/features/filtered_data_norm.tsv 2026-02-11 16:07:09.230213 INFO::Writing filtered, normalized, transformed data to file D:\temp\2026_02_11_16_05_16_27802\RtmpGk6rvN/features/filtered_data_norm_transformed.tsv 2026-02-11 16:07:09.232325 INFO::Writing residuals to file D:\temp\2026_02_11_16_05_16_27802\RtmpGk6rvN/fits/residuals.rds 2026-02-11 16:07:09.23393 INFO::Writing fitted values to file D:\temp\2026_02_11_16_05_16_27802\RtmpGk6rvN/fits/fitted.rds 2026-02-11 16:07:09.235417 INFO::Writing all results to file (ordered by increasing q-values): D:\temp\2026_02_11_16_05_16_27802\RtmpGk6rvN/all_results.tsv 2026-02-11 16:07:09.237799 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.250000 ) to file (ordered by increasing q-values): D:\temp\2026_02_11_16_05_16_27802\RtmpGk6rvN/significant_results.tsv 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 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_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 'sample_name' as sample identifier Using column 'sample_name' as sample identifier | | | 0% | | | 1% | |= | 1% | |= | 2% | |== | 2% | |== | 3% | |== | 4% | |=== | 4% | |=== | 5% | |==== | 5% | |==== | 6% | |===== | 7% | |===== | 8% | |====== | 8% | |====== | 9% | |======= | 9% | |======= | 10% | |======= | 11% | |======== | 11% | |======== | 12% | |========= | 12% | |========= | 13% | |========== | 14% | |========== | 15% | |=========== | 15% | |=========== | 16% | |============ | 17% | |============ | 18% | 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═══════════════════════════════════════════════════════════ • On CRAN (6): 'test-ggpicrust2-return-structure.R:4:3', 'test-pathway_annotation.R:36:3', 'test-pathway_ridgeplot.R:25:3', 'test-pathway_ridgeplot.R:42:3', 'test-pathway_ridgeplot.R:65:3', 'test-pathway_volcano.R:82:3' [ FAIL 0 | WARN 4 | SKIP 6 | PASS 196 ] > > proc.time() user system elapsed 28.35 1.90 33.15