Running ‘testthat.R’ [15s/20s]
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.
  Samples ordered by group (4 samples, 2 groups)
  Pathways ordered by hierarchical clustering (complete method, euclidean distance)
  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
  Samples ordered by group (4 samples, 2 groups)
  Using column 'sample' as sample identifier
  Samples ordered by group (4 samples, 2 groups)
  Using column 'sample' as sample identifier
  Samples ordered by group (4 samples, 2 groups)
  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 453 ]
  
  ══ 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:120:3', 'test-pathway_annotation.R:139:3'
  • empty test (1): 'test-pathway_annotation.R:273:1'
  • {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 453 ]
  Error:
  ! Test failures.
  Execution halted