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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:mastR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings mastR_1.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/mastR.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88126)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘mastR/DESCRIPTION’ ... OK
* this is package ‘mastR’ version ‘1.8.0’
* 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 ‘mastR’ 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Non-topic package-anchored link(s) in Rd file 'DEGs_Group.Rd':
  ‘[limma:ebayes]{limma::treat()}’

Non-topic package-anchored link(s) in Rd file 'DEGs_RP.Rd':
  ‘[limma:ebayes]{limma::treat()}’

Non-topic package-anchored link(s) in Rd file 'de_analysis.Rd':
  ‘[limma:ebayes]{limma::treat()}’

Non-topic package-anchored link(s) in Rd file 'process_data.Rd':
  ‘[limma:ebayes]{limma::treat()}’

Non-topic package-anchored link(s) in Rd file 'select_sig.Rd':
  ‘[limma:ebayes]{limma::treat()}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 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
sig_gseaplot      15.672  1.916  17.637
plot_diagnostics  15.588  0.712  17.838
get_panglao_sig   13.233  0.593  22.244
filter_subset_sig  7.753  0.278   8.354
sig_heatmap        6.187  0.539   7.099
de_analysis        6.087  0.331   6.835
pca_matrix_plot    6.222  0.179   6.589
get_degs           5.275  0.150   5.825
plot_mean_var      5.163  0.164   6.093
process_data       4.955  0.131   5.905
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/mastR.Rcheck/00check.log’
for details.