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### Running command:
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###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GeDi.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings GeDi_1.1.1.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/GeDi.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'GeDi/DESCRIPTION' ... OK
* this is package 'GeDi' version '1.1.1'
* 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 whether package 'GeDi' 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 whether startup messages can be suppressed ... 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 ... 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 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 'GeDi-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: kNN_clustering
> ### Title: Calculate clusters based on kNN clustering
> ### Aliases: kNN_clustering
> 
> ### ** Examples
> 
> ## Mock example showing how the data should look like
> scores <- Matrix::Matrix(stats::runif(100, min = 0, max = 1), 10, 10)
> rownames(scores) <- colnames(scores) <- c("a", "b", "c", "d", "e",
+                                 "f", "g", "h", "i", "j")
> cluster <- kNN_clustering(scores, k = 3)
Error: unable to find an inherited method for function 'findKNN' for signature 'X = "dgeMatrix"'
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  preparing gene to GO mapping data...
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 181 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-clustering.R:143:3'): kNN clustering works correctly ───────────
  Error: unable to find an inherited method for function 'findKNN' for signature 'X = "dsyMatrix"'
  Backtrace:
      ▆
   1. └─GeDi::kNN_clustering(distances, 3) at test-clustering.R:143:3
   2.   └─BiocNeighbors::findKNN(scores, k, warn.ties = FALSE)
   3.     └─methods (local) `<fn>`(`<list>`, `<nnstndGF>`, `<env>`)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 181 ]
  Error: Test failures
  Execution halted
* 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 ERRORs
See
  'F:/biocbuild/bbs-3.20-bioc/meat/GeDi.Rcheck/00check.log'
for details.