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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD check --install=check:mastR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings mastR_1.8.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/mastR.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS-SP1)
* 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 loading without being on the library search path ... 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 ... ERROR
Running examples in ‘mastR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_diagnostics
> ### Title: plot diagnostics before and after 'process_data()'
> ### Aliases: plot_diagnostics
> 
> ### ** Examples
> 
> data("im_data_6")
> dge <- edgeR::DGEList(
+   counts = Biobase::exprs(im_data_6),
+   samples = Biobase::pData(im_data_6)
+ )
> dge$logCPM <- edgeR::cpm(dge, log = TRUE)
> proc_data <- process_data(dge,
+   group_col = "celltype.ch1",
+   target_group = "NK"
+ )
       NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
Down             4009         3944       3146   2694   2153
NotSig           1476         2678       4405   4985   6183
Up               4926         3789       2860   2732   2075
> plot_diagnostics(proc_data$logCPM, proc_data$vfit$E,
+   group_col = proc_data$samples$group
+ )
Error: Can't find method for generic `*(e1, e2)`:
- e1: <patchwork>
- e2: <theme>
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
pca_matrix_plot   5.550  0.371   5.933
get_panglao_sig   5.558  0.243  10.762
filter_subset_sig 5.255  0.219   5.485
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’