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### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:ClustIRR.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings ClustIRR_1.3.8.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/ClustIRR.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘ClustIRR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ClustIRR’ version ‘1.3.8’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ClustIRR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plot_graph: no visible global function definition for ‘adjustcolor’
Undefined global functions or variables:
  adjustcolor
Consider adding
  importFrom("grDevices", "adjustcolor")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) clust_irr-class.Rd:30-80: Lost braces in \itemize; meant \describe ?
checkRd: (-1) clust_irr-class.Rd:81: Lost braces in \itemize; meant \describe ?
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from Rd file 'plot_graph.Rd':
plot_graph
  Code: function(g, select_by = "Ag_species", as_visnet = FALSE,
                 show_singletons = TRUE, node_opacity = 1)
  Docs: function(g, select_by = "Ag_species", as_visnet = FALSE,
                 show_singletons = TRUE)
  Argument names in code not in docs:
    node_opacity

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... WARNING
  Warning: found non-ASCII strings
  'LGTGNQFYF<a0>' in object 'mcpas'
  'YQLTF<a0>' in object 'mcpas'
  'PYSSASKIIF<a0>' in object 'mcpas'
  'STSFGSNYGQNFVF<a0>' in object 'mcpas'
  'Inflammatory bowel disease (IBD)<a0>' in object 'mcpas'
  'Flagellin<a0>' in object 'mcpas'
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                user system elapsed
clust_irr-class 6.62  0.104   3.593
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/ClustIRR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL ClustIRR
###
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘ClustIRR’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ClustIRR)

R version 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(ClustIRR)
> test_check("ClustIRR")


Analyze database: 100.0% (500.0)                    
  Index database: 100.0% (500.0)                    
    Read queries: 100.0% (10231.0 Bytes)                    
    Read queries: 100.0% (10231.0 Bytes)                    
    Read queries: 100.0% (10231.0 Bytes)                    
    Read queries: 100.0% (10231.0 Bytes)                    
    Read queries: 100.0% (10231.0 Bytes)                    
    Read queries: 100.0% (10231.0 Bytes)                    
    Read queries: 100.0% (10231.0 Bytes)                    
    Read queries: 100.0% (10231.0 Bytes)                    
 Search database: 23.2% (116.0)                    
 Search database: 100.0% (500.0)                    
      Write hits: 100.0% (597.0)                    
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 87 ]
> 
> proc.time()
   user  system elapsed 
 21.918   0.836  21.942