* using log directory ‘/home/hornik/tmp/CRAN_special_donttest/ggpicrust2.Rcheck’
* using R Under development (unstable) (2026-02-10 r89394)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-15 (Debian 15.2.0-12) 15.2.0
    GNU Fortran (Debian 15.2.0-12) 15.2.0
* running under: Debian GNU/Linux forky/sid
* using session charset: UTF-8
* current time: 2026-02-11 15:52:38 UTC
* using option ‘--run-donttest’
* checking for file ‘ggpicrust2/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ggpicrust2’ version ‘2.5.8’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [6s/8s] NOTE
Maintainer: ‘Chen Yang <cafferychen7850@gmail.com>’

Suggests or Enhances not in mainstream repositories:
  Maaslin2
Availability using Additional_repositories specification:
  Maaslin2   no   ?                                             
  ?           ?   https://bioconductor.org/packages/release/bioc
* checking package namespace information ... OK
* checking package dependencies ... INFO
Package suggested but not available for checking: ‘Maaslin2’
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* 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 ... [9s/9s] 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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [27s/27s] OK
  Running ‘testthat.R’ [27s/27s]
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* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR, 1 NOTE