• using R Under development (unstable) (2026-08-31 r90457 ucrt)
• using platform: x86_64-w64-mingw32
• R was compiled by     gcc.exe (GCC) 14.3.0     GNU Fortran (GCC) 14.3.0
• running under: Windows Server 2022 x64 (build 20348)
• using session charset: UTF-8 * current time: 2026-09-01 16:08:04 UTC
• checking for file 'ggpicrust2/DESCRIPTION' ... OK
• checking extension type ... Package
• this is package 'ggpicrust2' version '2.5.17'
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking whether package 'ggpicrust2' can be installed ... OK See the install log for details.
• checking installed package size ... INFO   installed size is 5.7Mb   sub-directories of 1Mb or more:     data 2.6Mb     extdata 1.0Mb     help 1.4Mb
• checking package directory ... OK
• checking 'build' directory ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• checking for left-over files ... OK
• checking index information ... OK
• checking package subdirectories ... OK
• checking code files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... [2s] OK
• checking whether the package can be loaded with stated dependencies ... [2s] OK
• checking whether the package can be unloaded cleanly ... [2s] OK
• checking whether the namespace can be loaded with stated dependencies ... [2s] OK
• checking whether the namespace can be unloaded cleanly ... [3s] OK
• checking loading without being on the library search path ... [2s] OK
• checking whether startup messages can be suppressed ... [2s] OK
• checking use of S3 registration ... OK
• checking dependencies in R code ... OK
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... [16s] OK
• checking Rd files ... [2s] OK
• checking Rd metadata ... OK
• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking contents of 'data' directory ... OK
• checking data for non-ASCII characters ... [1s] OK
• checking LazyData ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking installed files from 'inst/doc' ... OK
• checking files in 'vignettes' ... OK
• checking examples ... [11s] OK
• checking for unstated dependencies in 'tests' ... OK
• checking tests ... [75s] 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
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [6s] OK
• checking PDF version of manual ... [23s] OK
• checking HTML version of manual ... [4s] OK
• DONE

Status: 1 ERROR