Last updated on 2026-05-03 11:51:31 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.5.12 | 13.30 | 186.38 | 199.68 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.5.12 | 9.32 | 125.63 | 134.95 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.5.14 | 28.00 | 373.22 | 401.22 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 2.5.14 | 24.00 | 366.91 | 390.91 | OK | |
| r-devel-windows-x86_64 | 2.5.14 | 23.00 | 249.00 | 272.00 | OK | |
| r-patched-linux-x86_64 | 2.5.12 | 12.35 | 166.42 | 178.77 | OK | |
| r-release-linux-x86_64 | 2.5.14 | 12.79 | 161.24 | 174.03 | ERROR | |
| r-release-macos-arm64 | 2.5.14 | 3.00 | 69.00 | 72.00 | OK | |
| r-release-macos-x86_64 | 2.5.14 | 10.00 | 274.00 | 284.00 | OK | |
| r-release-windows-x86_64 | 2.5.12 | 15.00 | 188.00 | 203.00 | OK | |
| r-oldrel-macos-arm64 | 2.5.14 | 3.00 | 61.00 | 64.00 | ERROR | |
| r-oldrel-macos-x86_64 | 2.5.14 | 10.00 | 283.00 | 293.00 | OK | |
| r-oldrel-windows-x86_64 | 2.5.14 | 24.00 | 300.00 | 324.00 | OK |
Version: 2.5.14
Check: tests
Result: ERROR
Running ‘testthat.R’ [52s/64s]
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
calcNormFactors has been renamed to normLibSizes
Default value being used.
Saving _problems/test-pathway_daa-419.R
Saving _problems/test-pathway_daa-441.R
calcNormFactors has been renamed to normLibSizes
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.
[1] "Creating output feature tables folder"
[1] "Creating output fits folder"
2026-05-02 13:53:03.366368 INFO::Writing function arguments to log file
2026-05-02 13:53:03.381895 INFO::Verifying options selected are valid
2026-05-02 13:53:03.383388 INFO::Determining format of input files
2026-05-02 13:53:03.384461 INFO::Input format is data samples as rows and metadata samples as rows
2026-05-02 13:53:03.387616 INFO::Formula for fixed effects: expr ~ Env
2026-05-02 13:53:03.389215 INFO::Filter data based on min abundance and min prevalence
2026-05-02 13:53:03.390351 INFO::Total samples in data: 12
2026-05-02 13:53:03.391338 INFO::Min samples required with min abundance for a feature not to be filtered: 1.200000
2026-05-02 13:53:03.39294 INFO::Total filtered features: 0
2026-05-02 13:53:03.394042 INFO::Filtered feature names from abundance and prevalence filtering:
2026-05-02 13:53:03.395754 INFO::Total filtered features with variance filtering: 0
2026-05-02 13:53:03.396859 INFO::Filtered feature names from variance filtering:
2026-05-02 13:53:03.397745 INFO::Running selected normalization method: TSS
2026-05-02 13:53:03.39939 INFO::Applying z-score to standardize continuous metadata
2026-05-02 13:53:03.403739 INFO::Running selected transform method: AST
2026-05-02 13:53:03.405366 INFO::Running selected analysis method: LM
2026-05-02 13:53:03.406473 INFO::Fitting model to feature number 1, f1
2026-05-02 13:53:03.411019 INFO::Fitting model to feature number 2, f2
2026-05-02 13:53:03.419899 INFO::Fitting model to feature number 3, f3
2026-05-02 13:53:03.444934 INFO::Fitting model to feature number 4, f4
2026-05-02 13:53:03.453992 INFO::Fitting model to feature number 5, f5
2026-05-02 13:53:03.460414 INFO::Fitting model to feature number 6, f6
2026-05-02 13:53:03.465618 INFO::Fitting model to feature number 7, f7
2026-05-02 13:53:03.471014 INFO::Fitting model to feature number 8, f8
2026-05-02 13:53:03.476052 INFO::Fitting model to feature number 9, f9
2026-05-02 13:53:03.480924 INFO::Fitting model to feature number 10, f10
2026-05-02 13:53:03.485658 INFO::Fitting model to feature number 11, f11
2026-05-02 13:53:03.490842 INFO::Fitting model to feature number 12, f12
2026-05-02 13:53:03.50237 INFO::Counting total values for each feature
2026-05-02 13:53:03.505465 INFO::Writing filtered data to file /home/hornik/tmp/scratch/RtmpFIWCYR/ggpicrust2_maaslin2_8472f41fed4c3/features/filtered_data.tsv
2026-05-02 13:53:03.507489 INFO::Writing filtered, normalized data to file /home/hornik/tmp/scratch/RtmpFIWCYR/ggpicrust2_maaslin2_8472f41fed4c3/features/filtered_data_norm.tsv
2026-05-02 13:53:03.509272 INFO::Writing filtered, normalized, transformed data to file /home/hornik/tmp/scratch/RtmpFIWCYR/ggpicrust2_maaslin2_8472f41fed4c3/features/filtered_data_norm_transformed.tsv
2026-05-02 13:53:03.511264 INFO::Writing residuals to file /home/hornik/tmp/scratch/RtmpFIWCYR/ggpicrust2_maaslin2_8472f41fed4c3/fits/residuals.rds
2026-05-02 13:53:03.512584 INFO::Writing fitted values to file /home/hornik/tmp/scratch/RtmpFIWCYR/ggpicrust2_maaslin2_8472f41fed4c3/fits/fitted.rds
2026-05-02 13:53:03.51372 INFO::Writing all results to file (ordered by increasing q-values): /home/hornik/tmp/scratch/RtmpFIWCYR/ggpicrust2_maaslin2_8472f41fed4c3/all_results.tsv
2026-05-02 13:53:03.516064 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): /home/hornik/tmp/scratch/RtmpFIWCYR/ggpicrust2_maaslin2_8472f41fed4c3/significant_results.tsv
[1] "Creating output feature tables folder"
[1] "Creating output fits folder"
2026-05-02 13:53:03.524399 INFO::Writing function arguments to log file
2026-05-02 13:53:03.532866 INFO::Verifying options selected are valid
2026-05-02 13:53:03.53396 INFO::Determining format of input files
2026-05-02 13:53:03.535467 INFO::Input format is data samples as rows and metadata samples as rows
2026-05-02 13:53:03.538337 INFO::Formula for fixed effects: expr ~ Env
2026-05-02 13:53:03.539877 INFO::Filter data based on min abundance and min prevalence
2026-05-02 13:53:03.540843 INFO::Total samples in data: 12
2026-05-02 13:53:03.541764 INFO::Min samples required with min abundance for a feature not to be filtered: 1.200000
2026-05-02 13:53:03.543338 INFO::Total filtered features: 0
2026-05-02 13:53:03.544384 INFO::Filtered feature names from abundance and prevalence filtering:
2026-05-02 13:53:03.545893 INFO::Total filtered features with variance filtering: 0
2026-05-02 13:53:03.546878 INFO::Filtered feature names from variance filtering:
2026-05-02 13:53:03.547779 INFO::Running selected normalization method: TSS
2026-05-02 13:53:03.549317 INFO::Applying z-score to standardize continuous metadata
2026-05-02 13:53:03.553263 INFO::Running selected transform method: AST
2026-05-02 13:53:03.554878 INFO::Running selected analysis method: LM
2026-05-02 13:53:03.55584 INFO::Fitting model to feature number 1, f1
2026-05-02 13:53:03.560375 INFO::Fitting model to feature number 2, f2
2026-05-02 13:53:03.564987 INFO::Fitting model to feature number 3, f3
2026-05-02 13:53:03.569612 INFO::Fitting model to feature number 4, f4
2026-05-02 13:53:03.57421 INFO::Fitting model to feature number 5, f5
2026-05-02 13:53:03.578858 INFO::Fitting model to feature number 6, f6
2026-05-02 13:53:03.583513 INFO::Fitting model to feature number 7, f7
2026-05-02 13:53:03.588006 INFO::Fitting model to feature number 8, f8
2026-05-02 13:53:03.600668 INFO::Fitting model to feature number 9, f9
2026-05-02 13:53:03.605597 INFO::Fitting model to feature number 10, f10
2026-05-02 13:53:03.610215 INFO::Fitting model to feature number 11, f11
2026-05-02 13:53:03.614745 INFO::Fitting model to feature number 12, f12
2026-05-02 13:53:03.626449 INFO::Counting total values for each feature
2026-05-02 13:53:03.63016 INFO::Writing filtered data to file /home/hornik/tmp/scratch/RtmpFIWCYR/ggpicrust2_maaslin2_8472f8cb9bf8/features/filtered_data.tsv
2026-05-02 13:53:03.632517 INFO::Writing filtered, normalized data to file /home/hornik/tmp/scratch/RtmpFIWCYR/ggpicrust2_maaslin2_8472f8cb9bf8/features/filtered_data_norm.tsv
2026-05-02 13:53:03.634807 INFO::Writing filtered, normalized, transformed data to file /home/hornik/tmp/scratch/RtmpFIWCYR/ggpicrust2_maaslin2_8472f8cb9bf8/features/filtered_data_norm_transformed.tsv
2026-05-02 13:53:03.637434 INFO::Writing residuals to file /home/hornik/tmp/scratch/RtmpFIWCYR/ggpicrust2_maaslin2_8472f8cb9bf8/fits/residuals.rds
2026-05-02 13:53:03.639201 INFO::Writing fitted values to file /home/hornik/tmp/scratch/RtmpFIWCYR/ggpicrust2_maaslin2_8472f8cb9bf8/fits/fitted.rds
2026-05-02 13:53:03.640819 INFO::Writing all results to file (ordered by increasing q-values): /home/hornik/tmp/scratch/RtmpFIWCYR/ggpicrust2_maaslin2_8472f8cb9bf8/all_results.tsv
2026-05-02 13:53:03.643636 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): /home/hornik/tmp/scratch/RtmpFIWCYR/ggpicrust2_maaslin2_8472f8cb9bf8/significant_results.tsv
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 13 | PASS 435 ]
══ Skipped tests (13) ══════════════════════════════════════════════════════════
• 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'
• {DESeq2} is not installed (2): 'test-pathway_daa.R:243:3',
'test-pathway_daa.R:281:3'
• {lefser} is not installed (1): 'test-pathway_daa.R:625:3'
══ 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 13 | PASS 435 ]
Error:
! Test failures.
Execution halted
Flavor: r-release-linux-x86_64
Version: 2.5.14
Check: tests
Result: ERROR
Running ‘testthat.R’ [16s/19s]
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
Flavor: r-oldrel-macos-arm64