Multiple errors when following tutorial using my own dataset

[lingvv]

Hello!
Thank you for creating this helpful tool; it has been truly beneficial.
I've encountered a few error messages, and I'm seeking assistance to address them.

I've imported my phyloseq object from QIIME2, as demonstrated below.

> ps
phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 1663 taxa and 48 samples ]
sample_data() Sample Data:       [ 48 samples by 4 sample variables ]
tax_table()   Taxonomy Table:    [ 1663 taxa by 7 taxonomic ranks ]
phy_tree()    Phylogenetic Tree: [ 1663 tips and 1656 internal nodes ]

\

(A) Similar to issue #107

mg_anova <- run_test_multiple_groups( 
  ps, 
  group = "TreatmentType", 
  method = "anova" 
) 

Error Message:

Also defined by ‘tidytree’ 
Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq' 
Also defined by ‘tidytree’ 
Error in `purrr::map()`: 
ℹ In index: 136. 
Caused by error in `str2lang()`: 
! <text>:1:87: unexpected input 
1: k__d__Bacteria___p__Firmicutes___c__Clostridia___o__Oscillospirales___f__[Clostridium]_ 
                                                                                          ^ 
Run `rlang::last_trace()` to see where the error occurred.

> rlang::last_trace() 
<error/purrr_error_indexed> 
Error in `purrr::map()`: 
ℹ In index: 136. 
Caused by error in `str2lang()`: 
! <text>:1:87: unexpected input 
1: k__d__Bacteria___p__Firmicutes___c__Clostridia___o__Oscillospirales___f__[Clostridium]_ 
                                                                                          ^ 
--- 
Backtrace: 
     ▆ 
  1. ├─microbiomeMarker::run_test_multiple_groups(...) 
  2. │ ├─... %>% purrr::map_dbl(~ .x[[1]][["Pr(>F)"]][1]) 
  3. │ └─purrr::map(formula_char, ~aov(as.formula(.x), aov_df) %>% summary(.)) 
  4. │   └─purrr:::map_("list", .x, .f, ..., .progress = .progress) 
  5. │     ├─purrr:::with_indexed_errors(...) 
  6. │     │ └─base::withCallingHandlers(...) 
  7. │     ├─purrr:::call_with_cleanup(...) 
  8. │     └─microbiomeMarker (local) .f(.x[[i]], ...) 
  9. │       ├─aov(as.formula(.x), aov_df) %>% summary(.) 
 10. │       ├─stats::aov(as.formula(.x), aov_df) 
 11. │       │ └─stats::terms(formula, "Error", data = data) 
 12. │       └─stats::as.formula(.x) 
 13. │         ├─stats::formula(object, env = baseenv()) 
 14. │         └─stats:::formula.character(object, env = baseenv()) 
 15. │           └─base::str2lang(x) 
 16. ├─purrr::map_dbl(., ~.x[[1]][["Pr(>F)"]][1]) 
 17. │ └─purrr:::map_("double", .x, .f, ..., .progress = .progress) 
 18. │   └─purrr:::vctrs_vec_compat(.x, .purrr_user_env) 
 19. └─base::summary(.) 
Run rlang::last_trace(drop = FALSE) to see 4 hidden frames. 

(B)

mm_lefse <- run_lefse( 
  ps, 
  wilcoxon_cutoff = 0.01, 
  group = "TreatmentType", 
  kw_cutoff = 0.01, 
  multigrp_strat = TRUE, 
  lda_cutoff = 4 
) 

Error Message:
Error: Too small samples in each class or the variance of feature abundances within a class too small (zero or near zero)

(C)

mm_lv_pair <- run_limma_voom( 
  ps, 
  "TreatmentType", 
  contrast = c("Cecum_COS_CH", "Cecum_COS_CL"), 
  pvalue_cutoff = 0.05, 
  p_adjust = "fdr" 
) 

Error Message:

Also defined by ‘tidytree’ 
Coefficients not estimable: groupCecum_COS_CL groupIleum_UC  
Coefficients not estimable: groupCecum_COS_CL groupIleum_UC  
Warning messages: 
1: Partial NA coefficients for 627 probe(s)  
2: Partial NA coefficients for 627 probe(s)  
3: In .ebayes(fit = fit, proportion = proportion, stdev.coef.lim = stdev.coef.lim,  : 
  Estimation of var.prior failed - set to default value 
4: No marker was identified 

I appreciate any assistance and feedback regarding the error message I mentioned earlier. Thank you for taking the time to help!