R Under development (unstable) (2026-02-03 r89375 ucrt) -- "Unsuffered Consequences"
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> 
> # Load testthat
> library(testthat)
> 
> # #Test our package
> test_check("MTaP")
Loading required package: MTaP
MTaP (Microbial Taxonomy Profiler) - Usage Help
===============================================

Main Functions:
  * mtap_config()     - Create analysis configuration
  * mtap_analyze()    - Execute complete analysis
  * mtap_quick()      - Quick analysis (one-step)
  * mtap_cli()        - Command line interface

Data Reading Functions:
  * mtap_read_otu()       - Read OTU table
  * mtap_read_taxonomy()  - Read taxonomy table
  * mtap_detect_levels()  - Detect taxonomy levels

Data Processing Functions:
  * mtap_merge_data()     - Merge data
  * mtap_fill_missing()   - Fill missing values
  * mtap_aggregate()      - Aggregate abundance

Utility Functions:
  * mtap_validate_config() - Validate configuration
  * mtap_validate_data()   - Validate data
  * mtap_help()            - Display this help information

Usage Examples:
  # Basic analysis
  config <- mtap_config("otu.csv", "tax.csv")
  result <- mtap_analyze(config)

  # Quick analysis
  result <- mtap_quick("otu.csv", "tax.csv", 
                      output_prefix = "my_result")

  # Command line usage
  # Rscript -e "MTaP::mtap_cli()" otu.csv tax.csv output
MTaP (Microbial Taxonomy Profiler) - Usage Help
===============================================

Main Functions:
  * mtap_config()     - Create analysis configuration
  * mtap_analyze()    - Execute complete analysis
  * mtap_quick()      - Quick analysis (one-step)
  * mtap_cli()        - Command line interface

Data Reading Functions:
  * mtap_read_otu()       - Read OTU table
  * mtap_read_taxonomy()  - Read taxonomy table
  * mtap_detect_levels()  - Detect taxonomy levels

Data Processing Functions:
  * mtap_merge_data()     - Merge data
  * mtap_fill_missing()   - Fill missing values
  * mtap_aggregate()      - Aggregate abundance

Utility Functions:
  * mtap_validate_config() - Validate configuration
  * mtap_validate_data()   - Validate data
  * mtap_help()            - Display this help information

Usage Examples:
  # Basic analysis
  config <- mtap_config("otu.csv", "tax.csv")
  result <- mtap_analyze(config)

  # Quick analysis
  result <- mtap_quick("otu.csv", "tax.csv", 
                      output_prefix = "my_result")

  # Command line usage
  # Rscript -e "MTaP::mtap_cli()" otu.csv tax.csv output
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 112 ]
> 
> proc.time()
   user  system elapsed 
   1.37    0.26    1.64