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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:dominatR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings dominatR_0.99.5.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/dominatR.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘dominatR/DESCRIPTION’ ... OK
* this is package ‘dominatR’ version ‘0.99.5’
* 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 ‘dominatR’ 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 ... NOTE
2025-12-02 19:41:10.716 R[12872:246897818] XType: Using static font registry.
* checking S3 generic/method consistency ... WARNING
2025-12-02 19:41:14.555 R[13240:246898632] XType: Using static font registry.
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* checking replacement functions ... WARNING
2025-12-02 19:41:18.160 R[13626:246899455] XType: Using static font registry.
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
* checking foreign function calls ... NOTE
2025-12-02 19:41:21.844 R[14031:246900256] XType: Using static font registry.
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
2025-12-02 19:41:26.007 R[14874:246901790] XType: Using static font registry.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
2025-12-02 19:41:33.902 R[16198:246904434] XType: Using static font registry.
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
2025-12-02 19:41:37.422 R[16537:246905263] XType: Using static font registry.
2025-12-02 19:41:40.850 R[17365:246906787] XType: Using static font registry.
2025-12-02 19:41:44.318 R[18041:246908107] XType: Using static font registry.
* checking Rd \usage sections ... NOTE
2025-12-02 19:41:47.996 R[18644:246909416] XType: Using static font registry.
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
plot_circle           11.043  0.493  12.117
plot_circle_frequency  4.917  0.070   5.364
* 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: 4 WARNINGs, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/dominatR.Rcheck/00check.log’
for details.