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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:celaref.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings celaref_1.24.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/celaref.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘celaref/DESCRIPTION’ ... OK
* this is package ‘celaref’ version ‘1.24.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘celaref’ 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
contrast_each_group_to_the_rest: no visible global function definition
  for ‘is’
contrast_the_group_to_the_rest: no visible global function definition
  for ‘is’
contrast_the_group_to_the_rest: no visible global function definition
  for ‘new’
contrast_the_group_to_the_rest: no visible global function definition
  for ‘as<-’
trim_small_groups_and_low_expression_genes: no visible global function
  definition for ‘is’
Undefined global functions or variables:
  as<- is new
Consider adding
  importFrom("methods", "as<-", "is", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
checkRd: (-1) contrast_each_group_to_the_rest_for_norm_ma_with_limma.Rd:54: Lost braces
    54 | from /emph{one single study/experiment} (due to batch effects). 
       |           ^
checkRd: (-1) make_ref_similarity_names.Rd:165: Lost braces
   165 |   e.g. emph{c2:(tc_lymphocytes)}
       |            ^
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* 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 ... OK
* checking LazyData ... OK
* 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
contrast_each_group_to_the_rest                        23.555  1.891  26.000
contrast_each_group_to_the_rest_for_norm_ma_with_limma  9.043  1.258   0.392
* 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 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/celaref.Rcheck/00check.log’
for details.