Last updated on 2026-09-03 14:53:00 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.5.17 | 14.87 | 223.44 | 238.31 | NOTE | |
| r-devel-linux-x86_64-debian-gcc | 2.5.17 | 8.41 | 153.61 | 162.02 | NOTE | |
| r-devel-linux-x86_64-fedora-clang | 2.5.17 | 10.00 | 142.72 | 152.72 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 2.5.17 | 10.00 | 170.22 | 180.22 | OK | |
| r-devel-windows-x86_64 | 2.5.17 | 17.00 | 225.00 | 242.00 | ERROR | |
| r-patched-linux-x86_64 | 2.5.17 | 14.22 | 204.83 | 219.05 | OK | |
| r-release-linux-x86_64 | 2.5.17 | 14.30 | 203.29 | 217.59 | OK | |
| r-release-macos-arm64 | 2.5.17 | 4.00 | 71.00 | 75.00 | OK | |
| r-release-macos-x86_64 | 2.5.17 | 11.00 | 291.00 | 302.00 | OK | |
| r-release-windows-x86_64 | 2.5.17 | 16.00 | 218.00 | 234.00 | OK | |
| r-oldrel-macos-arm64 | 2.5.17 | 3.00 | 63.00 | 66.00 | ERROR | |
| r-oldrel-macos-x86_64 | 2.5.17 | 10.00 | 309.00 | 319.00 | OK | |
| r-oldrel-windows-x86_64 | 2.5.17 | 24.00 | 286.00 | 310.00 | OK |
Version: 2.5.17
Check: Rd contents
Result: NOTE
Rd files without \usage:
‘compare_daa_results.Rd’ ‘pathway_errorbar.Rd’ ‘pathway_heatmap.Rd’
\arguments should not be documented without \usage.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 2.5.17
Check: tests
Result: ERROR
Running 'testthat.R' [75s]
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.
Saving _problems/test-core-audit-followup-101.R
Saving _problems/test-core-audit-followup-118.R
Saving _problems/test-core-audit-followup-119.R
Saving _problems/test-core-audit-followup-125.R
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
conditions vector supplied
operating in serial mode
computing center with all features
conditions vector supplied
operating in serial mode
computing center with all features
calcNormFactors has been renamed to normLibSizes
calcNormFactors has been renamed to normLibSizes
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
calcNormFactors has been renamed to normLibSizes
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...
Default value being used.
conditions vector supplied
operating in serial mode
computing center with all features
conditions vector supplied
operating in serial mode
computing center with all features
calcNormFactors has been renamed to normLibSizes
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
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"
2026-09-01 18:10:53.823084 INFO::Writing function arguments to log file
2026-09-01 18:10:53.8438 INFO::Verifying options selected are valid
2026-09-01 18:10:53.846396 INFO::Determining format of input files
2026-09-01 18:10:53.84895 INFO::Input format is data samples as rows and metadata samples as rows
2026-09-01 18:10:53.855745 INFO::Formula for fixed effects: expr ~ Env
2026-09-01 18:10:53.857927 INFO::Filter data based on min abundance and min prevalence
2026-09-01 18:10:53.859681 INFO::Total samples in data: 12
2026-09-01 18:10:53.861258 INFO::Min samples required with min abundance for a feature not to be filtered: 1.200000
2026-09-01 18:10:53.864055 INFO::Total filtered features: 0
2026-09-01 18:10:53.86615 INFO::Filtered feature names from abundance and prevalence filtering:
2026-09-01 18:10:53.868461 INFO::Total filtered features with variance filtering: 0
2026-09-01 18:10:53.870344 INFO::Filtered feature names from variance filtering:
2026-09-01 18:10:53.872066 INFO::Running selected normalization method: TSS
2026-09-01 18:10:53.874281 INFO::Applying z-score to standardize continuous metadata
2026-09-01 18:10:53.87839 INFO::Running selected transform method: AST
2026-09-01 18:10:53.880611 INFO::Running selected analysis method: LM
2026-09-01 18:10:53.882597 INFO::Fitting model to feature number 1, f1
2026-09-01 18:10:53.889127 INFO::Fitting model to feature number 2, f2
2026-09-01 18:10:53.894393 INFO::Fitting model to feature number 3, f3
2026-09-01 18:10:53.899249 INFO::Fitting model to feature number 4, f4
2026-09-01 18:10:53.903309 INFO::Fitting model to feature number 5, f5
2026-09-01 18:10:53.906517 INFO::Fitting model to feature number 6, f6
2026-09-01 18:10:53.909408 INFO::Fitting model to feature number 7, f7
2026-09-01 18:10:53.912325 INFO::Fitting model to feature number 8, f8
2026-09-01 18:10:53.916842 INFO::Fitting model to feature number 9, f9
2026-09-01 18:10:53.920393 INFO::Fitting model to feature number 10, f10
2026-09-01 18:10:53.923551 INFO::Fitting model to feature number 11, f11
2026-09-01 18:10:53.926626 INFO::Fitting model to feature number 12, f12
2026-09-01 18:10:53.932716 INFO::Counting total values for each feature
2026-09-01 18:10:53.935384 INFO::Writing filtered data to file D:\temp\2026_09_01_01_50_00_22259\Rtmp8e5EaA\ggpicrust2_maaslin2_25f285a6369bd/features/filtered_data.tsv
2026-09-01 18:10:53.937835 INFO::Writing filtered, normalized data to file D:\temp\2026_09_01_01_50_00_22259\Rtmp8e5EaA\ggpicrust2_maaslin2_25f285a6369bd/features/filtered_data_norm.tsv
2026-09-01 18:10:53.940539 INFO::Writing filtered, normalized, transformed data to file D:\temp\2026_09_01_01_50_00_22259\Rtmp8e5EaA\ggpicrust2_maaslin2_25f285a6369bd/features/filtered_data_norm_transformed.tsv
2026-09-01 18:10:53.943281 INFO::Writing residuals to file D:\temp\2026_09_01_01_50_00_22259\Rtmp8e5EaA\ggpicrust2_maaslin2_25f285a6369bd/fits/residuals.rds
2026-09-01 18:10:53.94515 INFO::Writing fitted values to file D:\temp\2026_09_01_01_50_00_22259\Rtmp8e5EaA\ggpicrust2_maaslin2_25f285a6369bd/fits/fitted.rds
2026-09-01 18:10:53.946989 INFO::Writing all results to file (ordered by increasing q-values): D:\temp\2026_09_01_01_50_00_22259\Rtmp8e5EaA\ggpicrust2_maaslin2_25f285a6369bd/all_results.tsv
2026-09-01 18:10:53.949574 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_09_01_01_50_00_22259\Rtmp8e5EaA\ggpicrust2_maaslin2_25f285a6369bd/significant_results.tsv
[1] "Creating output feature tables folder"
[1] "Creating output fits folder"
2026-09-01 18:10:53.961625 INFO::Writing function arguments to log file
2026-09-01 18:10:53.977803 INFO::Verifying options selected are valid
2026-09-01 18:10:53.980908 INFO::Determining format of input files
2026-09-01 18:10:53.98358 INFO::Input format is data samples as rows and metadata samples as rows
2026-09-01 18:10:53.990352 INFO::Formula for fixed effects: expr ~ Env
2026-09-01 18:10:53.993775 INFO::Filter data based on min abundance and min prevalence
2026-09-01 18:10:53.996272 INFO::Total samples in data: 12
2026-09-01 18:10:53.998529 INFO::Min samples required with min abundance for a feature not to be filtered: 1.200000
2026-09-01 18:10:54.001234 INFO::Total filtered features: 0
2026-09-01 18:10:54.003486 INFO::Filtered feature names from abundance and prevalence filtering:
2026-09-01 18:10:54.005686 INFO::Total filtered features with variance filtering: 0
2026-09-01 18:10:54.007216 INFO::Filtered feature names from variance filtering:
2026-09-01 18:10:54.008583 INFO::Running selected normalization method: TSS
2026-09-01 18:10:54.010507 INFO::Applying z-score to standardize continuous metadata
2026-09-01 18:10:54.014166 INFO::Running selected transform method: AST
2026-09-01 18:10:54.015935 INFO::Running selected analysis method: LM
2026-09-01 18:10:54.017397 INFO::Fitting model to feature number 1, f1
2026-09-01 18:10:54.021349 INFO::Fitting model to feature number 2, f2
2026-09-01 18:10:54.024561 INFO::Fitting model to feature number 3, f3
2026-09-01 18:10:54.02768 INFO::Fitting model to feature number 4, f4
2026-09-01 18:10:54.030555 INFO::Fitting model to feature number 5, f5
2026-09-01 18:10:54.033517 INFO::Fitting model to feature number 6, f6
2026-09-01 18:10:54.036399 INFO::Fitting model to feature number 7, f7
2026-09-01 18:10:54.039373 INFO::Fitting model to feature number 8, f8
2026-09-01 18:10:54.042306 INFO::Fitting model to feature number 9, f9
2026-09-01 18:10:54.04522 INFO::Fitting model to feature number 10, f10
2026-09-01 18:10:54.04807 INFO::Fitting model to feature number 11, f11
2026-09-01 18:10:54.050974 INFO::Fitting model to feature number 12, f12
2026-09-01 18:10:54.05773 INFO::Counting total values for each feature
2026-09-01 18:10:54.060524 INFO::Writing filtered data to file D:\temp\2026_09_01_01_50_00_22259\Rtmp8e5EaA\ggpicrust2_maaslin2_25f28721933f9/features/filtered_data.tsv
2026-09-01 18:10:54.063777 INFO::Writing filtered, normalized data to file D:\temp\2026_09_01_01_50_00_22259\Rtmp8e5EaA\ggpicrust2_maaslin2_25f28721933f9/features/filtered_data_norm.tsv
2026-09-01 18:10:54.068071 INFO::Writing filtered, normalized, transformed data to file D:\temp\2026_09_01_01_50_00_22259\Rtmp8e5EaA\ggpicrust2_maaslin2_25f28721933f9/features/filtered_data_norm_transformed.tsv
2026-09-01 18:10:54.072299 INFO::Writing residuals to file D:\temp\2026_09_01_01_50_00_22259\Rtmp8e5EaA\ggpicrust2_maaslin2_25f28721933f9/fits/residuals.rds
2026-09-01 18:10:54.07502 INFO::Writing fitted values to file D:\temp\2026_09_01_01_50_00_22259\Rtmp8e5EaA\ggpicrust2_maaslin2_25f28721933f9/fits/fitted.rds
2026-09-01 18:10:54.07752 INFO::Writing all results to file (ordered by increasing q-values): D:\temp\2026_09_01_01_50_00_22259\Rtmp8e5EaA\ggpicrust2_maaslin2_25f28721933f9/all_results.tsv
2026-09-01 18:10:54.081739 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_09_01_01_50_00_22259\Rtmp8e5EaA\ggpicrust2_maaslin2_25f28721933f9/significant_results.tsv
Disp = 1e-04 , BCV = 0.01
Disp = 1e-04 , BCV = 0.01
Saving _problems/test-pathway_errorbar-41.R
Saving _problems/test-pathway_errorbar-61.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-88.R
Saving _problems/test-pathway_errorbar-103.R
Saving _problems/test-pathway_errorbar-115.R
Saving _problems/test-pathway_errorbar-131.R
Saving _problems/test-pathway_errorbar-168.R
Saving _problems/test-pathway_errorbar-192.R
Saving _problems/test-pathway_errorbar-204.R
conditions vector supplied
operating in serial mode
computing center with all features
Saving _problems/test-pathway_errorbar-279.R
Saving _problems/test-pathway_errorbar-359.R
Saving _problems/test-pathway_errorbar-384.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 16 | WARN 3 | SKIP 9 | PASS 509 ]
══ Skipped tests (9) ═══════════════════════════════════════════════════════════
• 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'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-core-audit-followup.R:91:3'): pathway_errorbar order='group' resolves tied groups deterministically ──
Error: object 'ggcoef_multinom' is not exported by 'namespace:ggstats'
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-core-audit-followup.R:91:3
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_errorbar(...)
8. └─base::loadNamespace(x)
9. └─base::namespaceImportFrom(...)
10. └─base::importIntoEnv(impenv, impnames, ns, impvars)
── Failure ('test-core-audit-followup.R:107:3'): pathway_errorbar normalizes logical flags and rejects invalid p_adjust ──
Expected `... <- NULL` not to throw any errors.
Actually got a <simpleError> with message:
object 'ggcoef_multinom' is not exported by 'namespace:ggstats'
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-core-audit-followup.R:107:3
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_errorbar(...)
8. └─base::loadNamespace(x)
9. └─base::namespaceImportFrom(...)
10. └─base::importIntoEnv(impenv, impnames, ns, impvars)
── Failure ('test-core-audit-followup.R:119:3'): pathway_errorbar normalizes logical flags and rejects invalid p_adjust ──
Expected `plot` to be an S3 object.
Actual OO type: none.
── Error ('test-core-audit-followup.R:122:3'): pathway_errorbar normalizes logical flags and rejects invalid p_adjust ──
Error: object 'ggcoef_multinom' is not exported by 'namespace:ggstats'
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-core-audit-followup.R:122:3
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_errorbar(...)
8. └─base::loadNamespace(x)
9. └─base::namespaceImportFrom(...)
10. └─base::importIntoEnv(impenv, impnames, ns, impvars)
── Error ('test-pathway_errorbar.R:34:3'): pathway_errorbar basic functionality works ──
Error: object 'ggcoef_multinom' is not exported by 'namespace:ggstats'
Backtrace:
▆
1. ├─ggpicrust2::pathway_errorbar(...) at test-pathway_errorbar.R:34:3
2. └─base::loadNamespace(x)
3. └─base::namespaceImportFrom(...)
4. └─base::importIntoEnv(impenv, impnames, ns, impvars)
── Error ('test-pathway_errorbar.R:53:3'): pathway_errorbar pathway_names_text_size parameter works ──
Error: object 'ggcoef_multinom' is not exported by 'namespace:ggstats'
Backtrace:
▆
1. ├─ggpicrust2::pathway_errorbar(...) at test-pathway_errorbar.R:53:3
2. └─base::loadNamespace(x)
3. └─base::namespaceImportFrom(...)
4. └─base::importIntoEnv(impenv, impnames, ns, impvars)
── Error ('test-pathway_errorbar.R:83:3'): pathway_errorbar handles missing annotations ──
Error: object 'ggcoef_multinom' is not exported by 'namespace:ggstats'
Backtrace:
▆
1. ├─ggpicrust2::pathway_errorbar(...) at test-pathway_errorbar.R:83:3
2. └─base::loadNamespace(x)
3. └─base::namespaceImportFrom(...)
4. └─base::importIntoEnv(impenv, impnames, ns, impvars)
── Error ('test-pathway_errorbar.R:95:3'): pathway_errorbar handles too many features ──
Error: object 'ggcoef_multinom' is not exported by 'namespace:ggstats'
Backtrace:
▆
1. ├─testthat::expect_warning(...) at test-pathway_errorbar.R:95:3
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_errorbar(...)
8. └─base::loadNamespace(x)
9. └─base::namespaceImportFrom(...)
10. └─base::importIntoEnv(impenv, impnames, ns, impvars)
── Error ('test-pathway_errorbar.R:109:3'): pathway_errorbar handles custom colors correctly ──
Error: object 'ggcoef_multinom' is not exported by 'namespace:ggstats'
Backtrace:
▆
1. ├─ggpicrust2::pathway_errorbar(...) at test-pathway_errorbar.R:109:3
2. └─base::loadNamespace(x)
3. └─base::namespaceImportFrom(...)
4. └─base::importIntoEnv(impenv, impnames, ns, impvars)
── Error ('test-pathway_errorbar.R:125:5'): pathway_errorbar handles different ordering options ──
Error: object 'ggcoef_multinom' is not exported by 'namespace:ggstats'
Backtrace:
▆
1. ├─ggpicrust2::pathway_errorbar(...) at test-pathway_errorbar.R:125:5
2. └─base::loadNamespace(x)
3. └─base::namespaceImportFrom(...)
4. └─base::importIntoEnv(impenv, impnames, ns, impvars)
── Failure ('test-pathway_errorbar.R:157:3'): pathway_errorbar regression: ko_to_kegg TRUE with pathway_class order ──
Expected `pathway_errorbar(...)` not to throw any errors.
Actually got a <simpleError> with message:
object 'ggcoef_multinom' is not exported by 'namespace:ggstats'
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-pathway_errorbar.R:157:3
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_errorbar(...)
8. └─base::loadNamespace(x)
9. └─base::namespaceImportFrom(...)
10. └─base::importIntoEnv(impenv, impnames, ns, impvars)
── Failure ('test-pathway_errorbar.R:181:3'): pathway_errorbar aligns Group by names when provided ──
Expected `pathway_errorbar(...)` not to throw any errors.
Actually got a <simpleError> with message:
object 'ggcoef_multinom' is not exported by 'namespace:ggstats'
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-pathway_errorbar.R:181:3
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_errorbar(...)
8. └─base::loadNamespace(x)
9. └─base::namespaceImportFrom(...)
10. └─base::importIntoEnv(impenv, impnames, ns, impvars)
── Error ('test-pathway_errorbar.R:198:3'): pathway_errorbar handles p_value_bar parameter correctly ──
Error: object 'ggcoef_multinom' is not exported by 'namespace:ggstats'
Backtrace:
▆
1. ├─ggpicrust2::pathway_errorbar(...) at test-pathway_errorbar.R:198:3
2. └─base::loadNamespace(x)
3. └─base::namespaceImportFrom(...)
4. └─base::importIntoEnv(impenv, impnames, ns, impvars)
── Error ('test-pathway_errorbar.R:273:3'): pathway_errorbar and pathway_errorbar_table share the same mean/sd source ──
Error: object 'ggcoef_multinom' is not exported by 'namespace:ggstats'
Backtrace:
▆
1. ├─ggpicrust2::pathway_errorbar(...) at test-pathway_errorbar.R:273:3
2. └─base::loadNamespace(x)
3. └─base::namespaceImportFrom(...)
4. └─base::importIntoEnv(impenv, impnames, ns, impvars)
── Error ('test-pathway_errorbar.R:353:3'): pathway_errorbar preserves a method-native log2_fold_change instead of overwriting it with a mean-ratio ──
Error: object 'ggcoef_multinom' is not exported by 'namespace:ggstats'
Backtrace:
▆
1. ├─ggpicrust2::pathway_errorbar(...) at test-pathway_errorbar.R:353:3
2. └─base::loadNamespace(x)
3. └─base::namespaceImportFrom(...)
4. └─base::importIntoEnv(impenv, impnames, ns, impvars)
── Error ('test-pathway_errorbar.R:378:3'): pathway_errorbar falls back to mean-ratio log2_fold_change when the column is absent ──
Error: object 'ggcoef_multinom' is not exported by 'namespace:ggstats'
Backtrace:
▆
1. ├─ggpicrust2::pathway_errorbar(...) at test-pathway_errorbar.R:378:3
2. └─base::loadNamespace(x)
3. └─base::namespaceImportFrom(...)
4. └─base::importIntoEnv(impenv, impnames, ns, impvars)
[ FAIL 16 | WARN 3 | SKIP 9 | PASS 509 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-windows-x86_64
Version: 2.5.17
Check: tests
Result: 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.
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
Flavor: r-oldrel-macos-arm64