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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:EWCE.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings EWCE_1.18.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/EWCE.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* 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 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘EWCE/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘EWCE’ version ‘1.18.0’
* 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 ‘EWCE’ 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 ... NOTE
checkRd: (-1) compute_gene_scores.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_gene_scores.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) drop_uninformative_genes.Rd:186-187: Lost braces in \itemize; meant \describe ?
checkRd: (-1) drop_uninformative_genes.Rd:188-189: Lost braces in \itemize; meant \describe ?
checkRd: (-1) drop_uninformative_genes.Rd:190-192: Lost braces in \itemize; meant \describe ?
* 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 ... NOTE
Documented arguments not in \usage in Rd file 'get_exp_data_for_bootstrapped_genes.Rd':
  ‘full_results’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
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
controlled_geneset_enrichment              7.960  1.220   9.715
merged_ewce                                7.866  0.455   8.696
filter_nonorthologs                        6.900  0.180   7.104
generate_bootstrap_plots_for_transcriptome 6.489  0.315   7.126
filter_genes_without_1to1_homolog          6.561  0.175   6.684
generate_bootstrap_plots                   5.094  0.272   5.629
bootstrap_enrichment_test                  5.132  0.201   5.609
* 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-3.22-bioc/meat/EWCE.Rcheck/00check.log’
for details.