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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ClustIRR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ClustIRR_1.3.8.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/ClustIRR.Rcheck’
* using R version 4.4.1 RC (2024-06-06 r86719)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 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 7.347  0.209   4.885
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

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