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### Running command:
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###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:ClusterJudge.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings ClusterJudge_1.24.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/ClusterJudge.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ClusterJudge/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ClusterJudge’ version ‘1.24.0’
* 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 ‘ClusterJudge’ 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 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 ... 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘ClusterJudge-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: clusterJudge_z_score
> ### Title: calculates the 'cluster judge' z-score
> ### Aliases: clusterJudge_z_score
> ### Keywords: clusterJudge Yeast.GO.assocs
> 
> ### ** Examples
> 
> 
> library('yeastExpData')
Loading required package: graph
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

> data(ccyclered)
> 
> clusters <- ccyclered$Cluster
> ###  convert from Gene names to the new standard of Saccharomyces Genome Database (SGD) gene ids
> ccyclered$SGDID <- sub('^S','S00',ccyclered$SGDID)
> names(clusters) <- ccyclered$SGDID
> 
> data(Yeast.GO.assocs)  #### obtain associations and consolidate them at uncertainty level 0.001
> Yeast.GO.assocs.cons <- consolidate_entity_attribute(entity.attribute = Yeast.GO.assocs
+                                                    , min.entities.per.attr =3
+                                                    , mut.inf=mi.GO.Yeast
+                                                    , U.limit = c(0.001)) 
......
* 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
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/ClusterJudge.Rcheck/00check.log’
for details.