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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:TimiRGeN.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings TimiRGeN_1.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/TimiRGeN.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TimiRGeN/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘TimiRGeN’ version ‘1.2.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘TimiRGeN’ 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 R 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 ... 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 ... NOTE
  Note: found 3 marked UTF-8 strings
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘TimiRGeN-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: clusterCheck
> ### Title: clusterCheck
> ### Aliases: clusterCheck
> 
> ### ** Examples
> 
> MAE <- MultiAssayExperiment()
> 
> metadata(MAE)[["e_list"]] <- e_list_mouse
> 
> metadata(MAE)[["w_list"]] <- w_list_mouse[1:10]
> 
> MAE <- wikiMatrix(MAE, ID_list = metadata(MAE)[[1]],
+                   wp_list = metadata(MAE)[[2]])
Warning: 'ExperimentList' contains 'data.frame' or 'DataFrame',
  potential for errors with mixed data types
Warning: 'ExperimentList' contains 'data.frame' or 'DataFrame',
  potential for errors with mixed data types
Warning: 'ExperimentList' contains 'data.frame' or 'DataFrame',
  potential for errors with mixed data types
> 
> MAE <- turnPercent(MAE = MAE,
+                    wikiMatrix = assay(MAE, 1))
Warning: 'ExperimentList' contains 'data.frame' or 'DataFrame',
  potential for errors with mixed data types
Warning: 'ExperimentList' contains 'data.frame' or 'DataFrame',
  potential for errors with mixed data types
Warning: 'ExperimentList' contains 'data.frame' or 'DataFrame',
  potential for errors with mixed data types
Warning: 'ExperimentList' contains 'data.frame' or 'DataFrame',
  potential for errors with mixed data types
> 
> MAE <- createClusters(MAE, method = "c",
+                     percentMatrix = assay(MAE, 2),
+                     noClusters = 2, variance = 0.99)
2 genes excluded.
Error in if (res$pathwayInfo["name"] == "") { : 
  argument is of length zero
Calls: createClusters -> <Anonymous>
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/TimiRGeN.Rcheck/00check.log’
for details.