Package check result: ERROR Check: CRAN incoming feasibility, Result: NOTE Maintainer: ‘Chen Yang ’ Suggests or Enhances not in mainstream repositories: Maaslin2 Availability using Additional_repositories specification: Maaslin2 no ? ? ? https://bioconductor.org/packages/release/bioc Check: examples, Result: ERROR Running examples in ‘ggpicrust2-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: compare_daa_results > ### Title: Compare the Consistency of Statistically Significant Features > ### Aliases: compare_daa_results > > ### ** Examples > > ## No test: > library(magrittr) > library(ggpicrust2) > library(tibble) > data("metacyc_abundance") > data("metadata") > > # Run pathway_daa function for multiple methods > methods <- c("DESeq2", "edgeR","Maaslin2") > daa_results_list <- lapply(methods, function(method) { + pathway_daa(abundance = metacyc_abundance %>% column_to_rownames("pathway"), + metadata = metadata, group = "Environment", daa_method = method) + }) converting counts to integer mode Note: levels of factors in the design contain characters other than letters, numbers, '_' and '.'. It is recommended (but not required) to use only letters, numbers, and delimiters '_' or '.', as these are safe characters for column names in R. [This is a message, not a warning or an error] Note: levels of factors in the design contain characters other than letters, numbers, '_' and '.'. It is recommended (but not required) to use only letters, numbers, and delimiters '_' or '.', as these are safe characters for column names in R. [This is a message, not a warning or an error] gene-wise dispersion estimates mean-dispersion relationship -- note: fitType='parametric', but the dispersion trend was not well captured by the function: y = a/x + b, and a local regression fit was automatically substituted. specify fitType='local' or 'mean' to avoid this message next time. Note: levels of factors in the design contain characters other than letters, numbers, '_' and '.'. It is recommended (but not required) to use only letters, numbers, and delimiters '_' or '.', as these are safe characters for column names in R. [This is a message, not a warning or an error] final dispersion estimates Disp = 0.69705 , BCV = 0.8349 Error in require_package(method_packages[[daa_method]], purpose = daa_method) : Package 'Maaslin2' is required for Maaslin2. Install with: BiocManager::install('Maaslin2') Calls: lapply -> FUN -> pathway_daa -> require_package Execution halted