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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BiocGenerics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BiocGenerics_0.51.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/BiocGenerics.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* 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 12.7.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BiocGenerics/DESCRIPTION’ ... OK
* this is package ‘BiocGenerics’ version ‘0.51.0’
* 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 ‘BiocGenerics’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’ ‘utils’ ‘graphics’ ‘stats’
A package should be listed in only one of these fields.
* 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 ... NOTE
'library' or 'require' call to ‘RUnit’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in Rd file 'as.data.frame.Rd':
  ‘[IRanges]{as.data.frame,IntegerRanges-method}’

Missing link or links in Rd file 'order.Rd':
  ‘[IRanges]{order,IntegerRanges-method}’

Missing link or links in Rd file 'type.Rd':
  ‘[DelayedArray]{type,ANY-method}’
  ‘[Biostrings]{type,PairwiseAlignments-method}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from Rd file 'funprog.Rd':
Reduce
  Code: function(f, x, init, right = FALSE, accumulate = FALSE,
                 simplify = TRUE)
  Docs: function(f, x, init, right = FALSE, accumulate = FALSE)
  Argument names in code not in docs:
    simplify

Codoc mismatches from Rd file 'xtabs.Rd':
xtabs
  Code: function(formula = ~., data = parent.frame(), subset, sparse =
                 FALSE, na.action, na.rm = FALSE, addNA = FALSE,
                 exclude = if (!addNA) c(NA, NaN), drop.unused.levels =
                 FALSE)
  Docs: function(formula = ~., data = parent.frame(), subset, sparse =
                 FALSE, na.action, addNA = FALSE, exclude = if (!addNA)
                 c(NA, NaN), drop.unused.levels = FALSE)
  Argument names in code not in docs:
    na.rm
  Mismatches in argument names:
    Position: 6 Code: na.rm Docs: addNA
    Position: 7 Code: addNA Docs: exclude
    Position: 8 Code: exclude Docs: drop.unused.levels

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
fileName 16.853  0.800  19.236
Ontology  7.148  0.394   8.350
plotMA    6.396  0.315   7.210
plotPCA   4.574  0.075   5.188
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘run_unitTests.R’
 OK
* checking PDF version of manual ... OK
* DONE

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