##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data OMA
###
##############################################################################
##############################################################################


* checking for file ‘OMA/DESCRIPTION’ ... OK
* preparing ‘OMA’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘stub.Rmd’ using rmarkdown
[WARNING] This document format requires a nonempty <title> element.
  Please specify either 'title' or 'pagetitle' in the metadata,
  e.g. by using --metadata pagetitle="..." on the command line.
  Falling back to 'stub.knit'
--- finished re-building ‘stub.Rmd’

quarto render ../inst/

[ 1/32] index.qmd


processing file: index.qmd
1/3        
2/3 [intro]
3/3        
output file: index.knit.md

Error adding css vars block SCSSParsingError: SCSS Parsing Error: Expecting punctuation: "}" (13299:53)
    at cssVarsBlock (file:///Applications/quarto/bin/quarto.js:87668:11)
    at file:///Applications/quarto/bin/quarto.js:88117:31
    at file:///Applications/quarto/bin/quarto.js:87850:29
    at eventLoopTick (ext:core/01_core.js:178:7)
    at async handleVarsBlock (file:///Applications/quarto/bin/quarto.js:88130:23)
    at async file:///Applications/quarto/bin/quarto.js:88157:17
    at async SassCache.setFromHash (file:///Applications/quarto/bin/quarto.js:80672:7)
    at async compileSass (file:///Applications/quarto/bin/quarto.js:87960:19)
    at async resolveSassBundles (file:///Applications/quarto/bin/quarto.js:109337:17)
    at async resolveExtras (file:///Applications/quarto/bin/quarto.js:114166:14) {
  name: "SCSSParsingError"
}
The resulting CSS file will not have SCSS color variables exported as CSS.
This is likely a Quarto bug.
Please consider reporting it at https://github.com/quarto-dev/quarto-cli,
along with the _quarto_internal_scss_error.scss file that can be found in the current working directory.

[ 2/32] pages/intro.qmd


processing file: intro.qmd
1/3        
2/3 [setup]
3/3        
output file: intro.knit.md


[ 3/32] pages/miaverse.qmd


processing file: miaverse.qmd
1/19                       
2/19 [setup]               
3/19                       
4/19 [TreeSE-figure]       
2026-05-01 07:35:38.678 R[47322:49730506] XType: Using static font registry.
5/19                       
6/19 [bioc_release]        
7/19                       
8/19 [bioc_devel]          
9/19                       
10/19 [github]              
11/19                       
12/19 [install_function]    
13/19                       
14/19 [install_key_packages]
15/19                       
16/19 [install_packages]    
17/19                       
18/19 [all_packages]        
19/19                       
output file: miaverse.knit.md


[ 4/32] pages/containers.qmd


processing file: containers.qmd
1/41                      
2/41 [setup]              
3/41                      
4/41 [load_pkg_data]      
5/41                      
6/41 [subset_intro]       
7/41                      
8/41 [assay1]             
9/41                      
10/41 [assay2]             
11/41                      
12/41 [assay3]             
13/41                      
14/41 [assay4]             
15/41                      
16/41 [coldata]            
17/41                      
18/41 [rowdata]            
19/41                      
20/41 [rowtree]            
21/41                      
22/41 [rowlinks]           
23/41                      
24/41 [altexp_agglomerate1]
25/41                      
26/41 [altexp_agglomerate2]
27/41                      
28/41 [altexp_agglomerate3]
29/41                      
30/41 [show_mae1]          
31/41                      
32/41 [show_mae2]          
33/41                      
34/41 [show_mae3]          
35/41                      
36/41 [show_holofood_mae]  
37/41                      
38/41 [show_coldata_mae]   
39/41                      
40/41 [show_samplemap_mae] 
41/41                      
output file: containers.knit.md

Warning: stack imbalance in 'vapply', 24 then 26
Warning: stack imbalance in 'vapply', 10 then 12

[ 5/32] pages/import.qmd


processing file: import.qmd
1/47                         
2/47 [setup]                 
3/47                         
4/47 [import1]               
5/47                         
6/47 [import2]               
7/47                         
8/47 [import3]               
9/47                         
10/47 [import4]               
11/47                         
12/47 [import5]               
13/47                         
14/47 [import6]               
15/47                         
16/47 [import7]               
17/47                         
18/47 [import8]               
19/47                         
20/47 [import9]               
21/47                         
22/47 [import10]              
23/47                         
24/47 [import_csv1]           
25/47                         
26/47 [import_csv2]           
27/47                         
28/47 [import_csv3]           
29/47                         
30/47 [import_csv4]           
31/47                         
32/47 [import_mae1]           
33/47                         
34/47 [import_mae2]           
35/47                         
36/47 [pkg_data1]             
Data sets in package 'mia':

dmn_se                 Twins' microbiome data from 278 individuals
enterotype             Human gut microbiome dataset from 22 subjects
                       based on shotgun DNA sequencing
esophagus              Human esophageal community from 3 individuals
GlobalPatterns         Global patterns of 16S rRNA diversity at a
                       depth of millions of sequences per sample.
HintikkaXOData         Multiomics dataset from 40 rat samples
ibdmdb                 IBDMDB 2-omic demo dataset (MGX + MTX)
peerj13075             Skin microbial profiles 58 genetically
                       unrelated individuals
Tengeler2020           Gut microbiota profiles of 27 individuals
                       with ADHD and healthy controls
Tito2024QMP            Fecal microbiota samples from 589 patients
                       across different colorectal cancer stages

37/47                         
38/47 [pkg_data2]             
39/47                         
40/47 [experimenthub_datasets]
41/47                         
42/47 [package_datasets]      
43/47                         
44/47 [metagenome_datasets]   
45/47                         
46/47 [microbiome_compendium] 
47/47                         
output file: import.knit.md

Warning: stack imbalance in 'vapply', 24 then 26
Registered S3 method overwritten by 'bit64':
  method          from 
  print.bitstring tools
Warning: stack imbalance in 'vapply', 10 then 12

[ 6/32] pages/convert.qmd


processing file: convert.qmd
1/17                    
2/17 [setup]            
3/17                    
4/17 [load_pkg_data]    
5/17                    
6/17 [convert_phyloseq1]
7/17                    
8/17 [convert_phyloseq2]
9/17                    
10/17 [write_feather]    
11/17                    
12/17 [write_csv]        
13/17                    
14/17 [write_feater_mae] 
15/17                    
16/17 [write_csv_mae]    
17/17                    
output file: convert.knit.md

Warning: stack imbalance in 'vapply', 24 then 26
Warning: stack imbalance in 'vapply', 10 then 12

[ 7/32] pages/taxonomy.qmd


processing file: taxonomy.qmd
1/45                    
2/45 [setup]            
3/45                    
4/45 [load_pkg_data]    
5/45                    
6/45 [check_tax]        
7/45                    
8/45 [tax_ranks]        
9/45                    
10/45 [subset_rowData]   
11/45                    
12/45 [check_empty]      
13/45                    
14/45 [get_taxa_labels1] 
15/45                    
16/45 [get_taxa_labels2] 
17/45                    
18/45 [get_taxa_labels3] 
19/45                    
20/45 [getUnique]        
21/45                    
22/45 [mapTaxonomy]      
23/45                    
24/45 [subset_tse]       
25/45                    
26/45 [subset_tree]      
27/45                    
28/45 [getHierarchyTree] 
29/45                    
30/45 [addHierarchyTree] 
31/45                    
32/45 [get_default_ranks]
33/45                    
34/45 [get_ranks]        
35/45                    
36/45 [set_ranks]        
37/45                    
38/45 [set_default_ranks]
39/45                    
40/45 [plot_phylogeny1]  
41/45                    
42/45 [plot_phylogeny2]  
2026-05-01 07:37:57.586 R[48618:49735537] XType: Using static font registry.
43/45                    
44/45 [plot_phylogeny3]  
45/45                    
output file: taxonomy.knit.md

Warning: stack imbalance in 'vapply', 24 then 26
Warning: stack imbalance in 'vapply', 10 then 12

[ 8/32] pages/wrangling.qmd


processing file: wrangling.qmd
1/31                 
2/31 [setup]         
3/31                 
4/31 [splitOn]       
5/31                 
6/31 [modify_coldata]
7/31                 
8/31 [add-coldata1]  
9/31                 
10/31 [add-coldata2]  
11/31                 
12/31 [add_assay]     
13/31                 
14/31 [combine-cols]  
15/31                 
16/31 [merge1]        
17/31                 
18/31 [merge2]        
19/31                 
20/31 [merge3]        
21/31                 
22/31 [melt-data]     
23/31                 
24/31 [melt-mae-data] 
25/31                 
26/31 [tidy1]         
27/31                 
28/31 [tidy2]         
29/31                 
30/31 [tidy3]         
2026-05-01 07:38:39.255 R[48828:49736951] XType: Using static font registry.
31/31                 
output file: wrangling.knit.md

Warning: stack imbalance in 'vapply', 24 then 26
Warning: stack imbalance in 'vapply', 10 then 12

[ 9/32] pages/preprocess.qmd


processing file: preprocess.qmd
1/3        
2/3 [setup]
3/3        
output file: preprocess.knit.md


[10/32] pages/quality_control.qmd


processing file: quality_control.qmd
1/53                         
2/53 [setup]                 
3/53                         
4/53 [load_data]             
5/53                         
6/53 [explore1]              
7/53                         
8/53 [explore2]              
9/53                         
10/53 [explore3]              
11/53                         
12/53 [explore4]              
13/53                         
14/53 [explore5]              
15/53                         
16/53 [explore6]              
17/53                         
18/53 [explore7]              
19/53                         
20/53 [outlier1]              
21/53                         
22/53 [outlier2]              
2026-05-01 07:39:26.794 R[50283:49742690] XType: Using static font registry.
23/53                         
24/53 [replace_missing_values]
25/53                         
26/53 [show_metadata]         
27/53                         
28/53 [detect_contaminant]    
29/53                         
30/53 [filter_contaminants]   
31/53                         
32/53 [add_control_info]      
33/53                         
34/53 [contaminant_prevalence]
35/53                         
36/53 [distribution1]         
37/53                         
38/53 [distribution2]         
39/53                         
40/53 [plot_abundance1]       
41/53                         
42/53 [plot_abundance2]       
43/53                         
44/53 [plot_abundance3]       
45/53                         
46/53 [plot_prevalence1]      
47/53                         
48/53 [plot_prevalence2]      
49/53                         
50/53 [plot_prevalence3]      
51/53                         
52/53 [plot_prevalence4]      
53/53                         
output file: quality_control.knit.md

Registered S3 method overwritten by 'bit64':
  method          from 
  print.bitstring tools
Warning: stack imbalance in 'vapply', 24 then 26
Warning: stack imbalance in 'vapply', 10 then 12

[11/32] pages/subsetting.qmd


processing file: subsetting.qmd
1/27                          
2/27 [setup]                  
3/27                          
4/27 [load_data]              
5/27                          
6/27 [show_data]              
7/27                          
8/27 [filter_samples]         
9/27                          
10/27 [show_phyla]             
11/27                          
12/27 [subset_features]        
13/27                          
14/27 [subset_samples_and_feat]
15/27                          
16/27 [select_archaea]         
17/27                          
18/27 [subset_empty]           
19/27                          
20/27 [subset_empty2]          
21/27                          
22/27 [standard_deviation]     
2026-05-01 07:41:11.010 R[50571:49744043] XType: Using static font registry.
23/27                          
24/27 [filter_sd]              
25/27                          
26/27 [subset_by_rare]         
27/27                          
output file: subsetting.knit.md

Warning: stack imbalance in 'vapply', 24 then 26
Warning: stack imbalance in 'vapply', 10 then 12

[12/32] pages/agglomeration.qmd


processing file: agglomeration.qmd
1/27                     
2/27 [setup]             
3/27                     
4/27 [load_data]         
5/27                     
6/27 [agg_phylum]        
7/27                     
8/27 [agg_phylum_rowdata]
9/27                     
10/27 [agg_phylum_rowtree]
11/27                     
12/27 [agg_phylum_assay]  
13/27                     
14/27 [select_phyla]      
15/27                     
16/27 [agg_family]        
17/27                     
18/27 [add_agg]           
19/27                     
20/27 [agglomerateranks]  
21/27                     
22/27 [aggregate_samples] 
23/27                     
24/27 [agg_prevalence]    
25/27                     
26/27 [agg_prev_phylum]   
27/27                     
output file: agglomeration.knit.md

Warning: stack imbalance in 'vapply', 24 then 26
Warning: stack imbalance in 'vapply', 10 then 12

[13/32] pages/transformation.qmd


processing file: transformation.qmd
1/17          
2/17 [setup]  
3/17          
4/17 [transf1]
5/17          
6/17 [transf2]
7/17          
8/17 [transf3]
9/17          
10/17 [transf4]
11/17          
12/17 [transf5]
13/17          
14/17 [transf6]
15/17          
16/17 [transf7]
17/17          
output file: transformation.knit.md

Warning: stack imbalance in 'vapply', 24 then 26
Warning: stack imbalance in 'vapply', 10 then 12

[14/32] pages/composition.qmd


processing file: composition.qmd
1/11               
2/11 [setup]       
3/11               
4/11 [composition] 
2026-05-01 07:42:44.669 R[50794:49747411] XType: Using static font registry.
5/11               
6/11 [heatmap_prep]
7/11               
8/11 [heatmap]     
9/11               
10/11 [neatmap]     
11/11               
output file: composition.knit.md

Warning: stack imbalance in 'vapply', 24 then 26
Registered S3 method overwritten by 'seriation':
  method         from 
  reorder.hclust vegan
Warning: stack imbalance in 'vapply', 10 then 12

[15/32] pages/alpha_diversity.qmd


processing file: alpha_diversity.qmd
1/19                       
2/19 [setup]               
3/19                       
4/19 [alpha_table]         
5/19                       
6/19 [calc_diversity]      
7/19                       
8/19 [plot_richness]       
2026-05-01 07:43:15.168 R[50874:49747838] XType: Using static font registry.
9/19                       
10/19 [compare_diversities] 
11/19                       
12/19 [compare_indices]     
13/19                       
14/19 [plot_all_diversities]
15/19                       
16/19 [test_alpha]          
17/19                       
18/19 [visualize_shannon]   
19/19                       
output file: alpha_diversity.knit.md

Warning: stack imbalance in 'vapply', 24 then 26
Warning: stack imbalance in 'vapply', 10 then 12

[16/32] pages/community_similarity.qmd


processing file: community_similarity.qmd
1/67                                                                
2/67 [setup1]                                                       
3/67                                                                
4/67 [setup2]                                                       
5/67                                                                
6/67 [prep_tse]                                                     
7/67                                                                
8/67 [diss_matrix]                                                  
9/67                                                                
10/67 [diss_matrix_plot]                                             
11/67                                                                
12/67 [add_divergence]                                               
13/67                                                                
14/67 [permanova]                                                    
15/67                                                                
16/67 [addMDS]                                                       
17/67                                                                
18/67 [MDS_plot_based_on_the_Bray-Curtis_distances]                  
19/67                                                                
20/67 [add_box_to_mds]                                               
21/67                                                                
22/67 [mds-nmds_comparison1]                                         
23/67                                                                
24/67 [mds-nmds_comparison2]                                         
25/67                                                                
26/67 [plot_unifrac]                                                 
27/67                                                                
28/67 [rarefaction]                                                  
29/67                                                                
30/67 [Aitchison_distance_without_rarefaction]                       
31/67                                                                
32/67 [rarefied_mds]                                                 
33/67                                                                
34/67 [MDS_plot_based_on_the_Bray-Curtis_distances_using_rarefaction]
35/67                                                                
36/67 [PC_correlation]                                               
37/67                                                                
38/67 [plot_pca]                                                     
39/67                                                                
40/67 [plot_umap]                                                    
41/67                                                                
42/67 [relstress]                                                    
43/67                                                                
44/67 [plot_shepard]                                                 
45/67                                                                
46/67 [import_rda_dataset]                                           
47/67                                                                
48/67 [run_rda]                                                      
49/67                                                                
50/67 [rda_permanova_results]                                        
51/67                                                                
52/67 [plot_rda]                                                     
53/67                                                                
54/67 [plot_top_coef_anova]                                          
55/67                                                                
56/67 [get_top_taxa]                                                 
57/67                                                                
58/67 [rda_homogeneity_results]                                      
59/67                                                                
60/67 [case_study1]                                                  
61/67                                                                
62/67 [case_study2]                                                  
63/67                                                                
64/67 [case_study3]                                                  
65/67                                                                
66/67 [case_study4]                                                  
67/67                                                                
output file: community_similarity.knit.md

Warning: stack imbalance in 'vapply', 24 then 26
Warning: stack imbalance in 'vapply', 10 then 12

[17/32] pages/clustering.qmd


processing file: clustering.qmd
1/45                             
2/45 [setup]                     
3/45                             
4/45 [load_bluster]              
5/45                             
6/45 [load_pkg_data]             
7/45                             
8/45 [hclust1]                   
9/45                             
10/45 [hclust2]                   
2026-05-01 07:45:04.975 R[51216:49749859] XType: Using static font registry.
11/45                             
12/45 [hclust3]                   
13/45                             
14/45 [hclust4]                   
15/45                             
16/45 [taxa_clustering]           
17/45                             
18/45 [taxa_clustering_histrogram]
19/45                             
20/45 [taxa_clustering_row_merge] 
21/45                             
22/45 [dmm1]                      
23/45                             
24/45 [dmm2]                      
25/45                             
26/45 [dmm3]                      
27/45                             
28/45 [dmm4]                      
29/45                             
30/45 [nmf1]                      
31/45                             
32/45 [nmf2]                      
33/45                             
34/45 [pheatmap1]                 
35/45                             
36/45 [pheatmap2]                 
37/45                             
38/45 [pheatmap3]                 
39/45                             
40/45 [pheatmap4]                 
41/45                             
42/45 [pheatmap5]                 
43/45                             
44/45 [pheatmap6]                 
45/45                             
output file: clustering.knit.md

Warning: stack imbalance in 'vapply', 24 then 26
Registered S3 method overwritten by 'dendextend':
  method     from 
  rev.hclust vegan
Warning: stack imbalance in 'vapply', 10 then 12

[18/32] pages/differential_abundance.qmd


processing file: differential_abundance.qmd
1/35                         
2/35 [setup]                 
3/35                         
4/35 [load_packages_and_data]
5/35                         
6/35 [prepare_data]          
7/35                         
8/35 [run_daa_basic]         
Error in `library()`:
! there is no package called 'Maaslin2'
Backtrace:
    ▆
 1. └─base::library(Maaslin2)

Quitting from differential_abundance.qmd:202-217 [run_daa_basic]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `library()`:
! there is no package called 'Maaslin2'
---
Backtrace:
    ▆
 1. └─base::library(Maaslin2)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Execution halted
WARN: Error encountered when rendering files
make: *** [render] Error 1
Error in tools::buildVignettes(dir = ".", tangle = TRUE) : 
  running 'make' failed
Execution halted