Check results for 'ggpicrust2'

using R version 4.5.2 Patched (2026-01-31 r89382)
using platform: aarch64-apple-darwin20
R was compiled by Apple clang version 16.0.0 (clang-1600.0.26.6) GNU Fortran (GCC) 14.2.0
running under: macOS Ventura 13.7.8
using session charset: UTF-8
checking for file ‘ggpicrust2/DESCRIPTION’ ... OK
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this is package ‘ggpicrust2’ version ‘2.5.14’
package encoding: UTF-8
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checking package dependencies ... INFO Packages suggested but not available for checking: 'ALDEx2', 'lefser', 'Maaslin2', 'metagenomeSeq'
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checking whether package ‘ggpicrust2’ can be installed ... [3s/3s] OK See the install log for details.
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checking tests ... [15s/19s] ERROR Running ‘testthat.R’ [15s/18s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > 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") 0 features are filtered! The filtered data has 12 samples and 20 features will be tested! Pseudo-count approach is used. Fit linear models ... Completed. 0 features are filtered! The filtered data has 12 samples and 20 features will be tested! Pseudo-count approach is used. Fit linear models ... Completed. 0 features are filtered! The filtered data has 6 samples and 15 features will be tested! Pseudo-count approach is used. Fit linear models ... Completed. Using column 'sample' as sample identifier 1 constant pathway(s) have zero variance; treated as z-score 0 for clustering. 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 Pathways ordered by hierarchical clustering (complete method, euclidean distance) Row order: Pathway2, Pathway1, Pathway3 Reading input data... Annotating pathways... Creating pathway error bar plots... Plot 1 skipped (no data for method: mock_method) ggpicrust2 analysis completed. 0 features are filtered! The filtered data has 8 samples and 15 features will be tested! Fit linear models ... Completed. Reading input data... Annotating pathways... Creating pathway error bar plots... Plot 1 skipped (no data for method: mock_method) ggpicrust2 analysis completed. 0 features are filtered! The filtered data has 6 samples and 10 features will be tested! Fit linear models ... 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. Using column 'sample_name' as sample identifier Saving _problems/test-pathway_daa-32.R Saving _problems/test-pathway_daa-52.R Saving _problems/test-pathway_daa-86.R Saving _problems/test-pathway_daa-150.R Saving _problems/test-pathway_daa-188.R converting counts to integer mode gene-wise dispersion estimates mean-dispersion relationship gene-wise dispersion estimates mean-dispersion relationship gene-wise dispersion estimates mean-dispersion relationship All dispersion fitting methods failed, using gene-wise estimates... converting counts to integer mode it appears that the last variable in the design formula, 'group', has a factor level, 'control', which is not the reference level. we recommend to use factor(...,levels=...) or relevel() to set this as the reference level before proceeding. for more information, please see the 'Note on factor levels' in vignette('DESeq2'). gene-wise dispersion estimates mean-dispersion relationship gene-wise dispersion estimates mean-dispersion relationship gene-wise dispersion estimates mean-dispersion relationship All dispersion fitting methods failed, using gene-wise estimates... converting counts to integer mode gene-wise dispersion estimates mean-dispersion relationship gene-wise dispersion estimates mean-dispersion relationship gene-wise dispersion estimates mean-dispersion relationship All dispersion fitting methods failed, using gene-wise estimates... Saving _problems/test-pathway_daa-419.R Saving _problems/test-pathway_daa-441.R Saving _problems/test-pathway_daa-499.R Saving _problems/test-pathway_daa-523.R Saving _problems/test-pathway_daa-552.R Saving _problems/test-pathway_daa-577.R 0 features are filtered! The filtered data has 12 samples and 12 features will be tested! Fit linear models ... Completed. 0 features are filtered! The filtered data has 12 samples and 12 features will be tested! Fit linear models ... Completed. Disp = 1e-04 , BCV = 0.01 Disp = 1e-04 , BCV = 0.01 Saving _problems/test-pathway_daa-858.R Excluded 1 pathways with missing annotations. Use 'pathway_annotation' to add them. Excluded 1 rows with missing 'pathway_name' annotations. Saving _problems/test-pathway_errorbar-232.R 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) 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' as sample identifier 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 'sample_name' as sample identifier [ FAIL 13 | WARN 3 | SKIP 17 | PASS 414 ] ══ Skipped tests (17) ══════════════════════════════════════════════════════════ • 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:111:3' • 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. (2): 'test-pathway_annotation.R:65:3', 'test-pathway_annotation.R:84:3' • empty test (1): 'test-pathway_annotation.R:218:1' • {ALDEx2} is not installed (1): 'test-pathway_daa.R:906:3' • {Maaslin2} is not installed (2): 'test-pathway_daa.R:300:3', 'test-pathway_daa.R:683:3' • {lefser} is not installed (1): 'test-pathway_daa.R:625:3' • {metagenomeSeq} is not installed (4): 'test-pathway_daa.R:335:3', 'test-pathway_daa.R:371:3', 'test-pathway_daa.R:757:3', 'test-pathway_daa.R:795:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-pathway_daa.R:32:3'): pathway_daa works with basic inputs ────── Error in `require_package(method_packages[[daa_method]], purpose = daa_method)`: Package 'ALDEx2' is required for ALDEx2. Install with: BiocManager::install('ALDEx2') Backtrace: ▆ 1. └─ggpicrust2::pathway_daa(td$abundance, td$metadata, "group", daa_method = "ALDEx2") at test-pathway_daa.R:32:3 2. └─ggpicrust2:::require_package(method_packages[[daa_method]], purpose = daa_method) ── Error ('test-pathway_daa.R:49:3'): pathway_daa validates inputs correctly ─── Error in `require_package(method_packages[[daa_method]], purpose = daa_method)`: Package 'ALDEx2' is required for ALDEx2. Install with: BiocManager::install('ALDEx2') Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-pathway_daa.R:49:3 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. └─ggpicrust2::pathway_daa(...) 8. └─ggpicrust2:::require_package(method_packages[[daa_method]], purpose = daa_method) ── Error ('test-pathway_daa.R:86:5'): pathway_daa core methods produce expected results ── Error in `require_package(method_packages[[daa_method]], purpose = daa_method)`: Package 'ALDEx2' is required for ALDEx2. Install with: BiocManager::install('ALDEx2') Backtrace: ▆ 1. ├─base::suppressWarnings(...) at test-pathway_daa.R:86:5 2. │ └─base::withCallingHandlers(...) 3. └─ggpicrust2::pathway_daa(abundance, metadata, "group", daa_method = method) 4. └─ggpicrust2:::require_package(method_packages[[daa_method]], purpose = daa_method) ── Error ('test-pathway_daa.R:149:3'): pathway_daa handles sample selection correctly ── Error in `require_package(method_packages[[daa_method]], purpose = daa_method)`: Package 'ALDEx2' is required for ALDEx2. Install with: BiocManager::install('ALDEx2') Backtrace: ▆ 1. └─ggpicrust2::pathway_daa(...) at test-pathway_daa.R:149:3 2. └─ggpicrust2:::require_package(method_packages[[daa_method]], purpose = daa_method) ── Error ('test-pathway_daa.R:187:3'): pathway_daa select= keeps metadata rows aligned with abundance columns ── Error in `require_package(method_packages[[daa_method]], purpose = daa_method)`: Package 'ALDEx2' is required for ALDEx2. Install with: BiocManager::install('ALDEx2') Backtrace: ▆ 1. └─ggpicrust2::pathway_daa(...) at test-pathway_daa.R:187:3 2. └─ggpicrust2:::require_package(method_packages[[daa_method]], purpose = daa_method) ── Error ('test-pathway_daa.R:416:3'): pathway_daa rejects negative abundance values ── Error in `require_package(method_packages[[daa_method]], purpose = daa_method)`: Package 'ALDEx2' is required for ALDEx2. Install with: BiocManager::install('ALDEx2') Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-pathway_daa.R:416:3 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. └─ggpicrust2::pathway_daa(abundance, metadata, "group", daa_method = "ALDEx2") 8. └─ggpicrust2:::require_package(method_packages[[daa_method]], purpose = daa_method) ── Error ('test-pathway_daa.R:440:3'): pathway_daa handles factor levels correctly with subset ── Error in `require_package(method_packages[[daa_method]], purpose = daa_method)`: Package 'ALDEx2' is required for ALDEx2. Install with: BiocManager::install('ALDEx2') Backtrace: ▆ 1. └─ggpicrust2::pathway_daa(...) at test-pathway_daa.R:440:3 2. └─ggpicrust2:::require_package(method_packages[[daa_method]], purpose = daa_method) ── Error ('test-pathway_daa.R:498:3'): pathway_daa handles p-value adjustment correctly ── Error in `require_package(method_packages[[daa_method]], purpose = daa_method)`: Package 'ALDEx2' is required for ALDEx2. Install with: BiocManager::install('ALDEx2') Backtrace: ▆ 1. └─ggpicrust2::pathway_daa(...) at test-pathway_daa.R:498:3 2. └─ggpicrust2:::require_package(method_packages[[daa_method]], purpose = daa_method) ── Error ('test-pathway_daa.R:520:3'): pathway_daa include_abundance_stats parameter works correctly ── Error in `require_package(method_packages[[daa_method]], purpose = daa_method)`: Package 'ALDEx2' is required for ALDEx2. Install with: BiocManager::install('ALDEx2') Backtrace: ▆ 1. └─ggpicrust2::pathway_daa(...) at test-pathway_daa.R:520:3 2. └─ggpicrust2:::require_package(method_packages[[daa_method]], purpose = daa_method) ── Error ('test-pathway_daa.R:551:3'): ALDEx2 returns effect size columns by default ── Error in `require_package(method_packages[[daa_method]], purpose = daa_method)`: Package 'ALDEx2' is required for ALDEx2. Install with: BiocManager::install('ALDEx2') Backtrace: ▆ 1. └─ggpicrust2::pathway_daa(td$abundance, td$metadata, "group", daa_method = "ALDEx2") at test-pathway_daa.R:551:3 2. └─ggpicrust2:::require_package(method_packages[[daa_method]], purpose = daa_method) ── Error ('test-pathway_daa.R:574:3'): include_abundance_stats does not collide with method-native log2FC ── Error in `require_package(method_packages[[daa_method]], purpose = daa_method)`: Package 'ALDEx2' is required for ALDEx2. Install with: BiocManager::install('ALDEx2') Backtrace: ▆ 1. └─ggpicrust2::pathway_daa(...) at test-pathway_daa.R:574:3 2. └─ggpicrust2:::require_package(method_packages[[daa_method]], purpose = daa_method) ── Error ('test-pathway_daa.R:849:3'): pathway_daa re-validates group count after align/select ── Error in `require_package(method_packages[[daa_method]], purpose = daa_method)`: Package 'ALDEx2' is required for ALDEx2. Install with: BiocManager::install('ALDEx2') Backtrace: ▆ 1. ├─testthat::expect_error(...) at test-pathway_daa.R:849:3 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. └─ggpicrust2::pathway_daa(...) 8. └─ggpicrust2:::require_package(method_packages[[daa_method]], purpose = daa_method) ── Error ('test-pathway_errorbar.R:227:3'): pathway_errorbar_table function works correctly ── Error in `require_package(method_packages[[daa_method]], purpose = daa_method)`: Package 'ALDEx2' is required for ALDEx2. Install with: BiocManager::install('ALDEx2') Backtrace: ▆ 1. └─ggpicrust2::pathway_daa(...) at test-pathway_errorbar.R:227:3 2. └─ggpicrust2:::require_package(method_packages[[daa_method]], purpose = daa_method) [ FAIL 13 | WARN 3 | SKIP 17 | PASS 414 ] Error: ! Test failures. Execution halted
checking for unstated dependencies in vignettes ... OK
checking package vignettes ... OK
checking re-building of vignette outputs ... [4s/4s] OK
checking PDF version of manual ... [3s/3s] OK
DONE Status: 1 ERROR
using check arguments '--no-clean-on-error '