* using log directory ‘/Volumes/Builds/packages/big-sur-arm64/results/4.5/bulkAnalyseR.Rcheck’
* using R Under development (unstable) (2025-01-24 r87627)
* using platform: aarch64-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 Ventura 13.4
* using session charset: UTF-8
* checking for file ‘bulkAnalyseR/DESCRIPTION’ ... OK
* this is package ‘bulkAnalyseR’ version ‘1.1.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Packages suggested but not available for checking:
  'org.Hs.eg.db', 'org.Mm.eg.db'
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘bulkAnalyseR’ can be installed ... [4s/4s] OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-macos-arm64/bulkAnalyseR-00install.html' for details.
* checking installed package size ... INFO
  installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc       2.3Mb
    extdata   3.4Mb
* 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 ... [1s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/1s] OK
* checking whether the package can be unloaded cleanly ... [0s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/1s] OK
* checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
* checking loading without being on the library search path ... [1s/1s] 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 ... [4s/4s] OK
* checking Rd files ... [0s/0s] OK
* 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 ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [2s/2s] ERROR
Running examples in ‘bulkAnalyseR-Ex.R’ failed
The error most likely occurred in:

> ### Name: DEanalysis
> ### Title: Perform differential expression (DE) analysis on an expression
> ###   matrix
> ### Aliases: DEanalysis DEanalysis_edger DEanalysis_deseq2
> 
> ### ** Examples
> 
> expression.matrix.preproc <- as.matrix(read.csv(
+   system.file("extdata", "expression_matrix_preprocessed.csv", package = "bulkAnalyseR"), 
+   row.names = 1
+ ))[1:100, 1:4]
> 
> anno <- AnnotationDbi::select(
+   getExportedValue('org.Mm.eg.db', 'org.Mm.eg.db'),
+   keys = rownames(expression.matrix.preproc),
+   keytype = 'ENSEMBL',
+   columns = 'SYMBOL'
+ ) %>%
+   dplyr::distinct(ENSEMBL, .keep_all = TRUE) %>%
+   dplyr::mutate(NAME = ifelse(is.na(SYMBOL), ENSEMBL, SYMBOL))
Error in (function (cond)  : 
  error in evaluating the argument 'x' in selecting a method for function 'select': there is no package called ‘org.Mm.eg.db’
Calls: %>% ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [1s/1s] OK
  Running ‘testthat.R’ [1s/1s]
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [21s/29s] OK
* checking PDF version of manual ... [4s/5s] OK
* DONE
Status: 1 ERROR
* using check arguments '--no-clean-on-error '

* elapsed time (check, wall clock): 1:10