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### Running command:
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###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:goSorensen.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings goSorensen_1.4.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/goSorensen.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 ‘goSorensen/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘goSorensen’ version ‘1.4.0’
* 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 ‘goSorensen’ 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 data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘goSorensen-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: hclustThreshold
> ### Title: From a Sorensen-Dice threshold dissimilarity matrix, generate an
> ###   object of class "hclust"
> ### Aliases: hclustThreshold
> 
> ### ** Examples
> 
> # Gene lists to analyse:
> data("allOncoGeneLists")
> # Gene universe:
> data("humanEntrezIDs")
> # First, compute the Sorensen-Dice threshold equivalence dissimilarity
> # for ontology BP at level 4:
> # # Very time consuming, it requires building all joint enrichment contingency tables
> dOncBP4 <- sorenThreshold(allOncoGeneLists, onto = "BP", GOLevel = 4,
+                           geneUniverse = humanEntrezIDs, orgPackg = "org.Hs.eg.db")

 Thu Nov  2 11:14:22 2023   Building all enrichment contingency tables...
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test_gosorensen_funcs.R’/home/biocbuild/R/R-4.3.1/bin/BATCH: line 60: 1250566 Killed                  ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1

 ERROR
Running the tests in ‘tests/test_gosorensen_funcs.R’ failed.
Last 13 lines of output:
       a "character" vector of gene identifiers.
  
  _S_o_u_r_c_e:
  
       <http://www.bushmanlab.org/links/genelists>
  
  
  > data(humanEntrezIDs)
  > # First, the mutual GO node enrichment tables are built, then computations
  > # proceed from these contingency tables.
  > # Building the contingency tables is a slow process (many enrichment tests)
  > normTest <- equivTestSorensen(allOncoGeneLists[["atlas"]], allOncoGeneLists[["sanger"]],
  +                               listNames = c("atlas", "sanger"),
  +                               onto = "BP", GOLevel = 5,
  +                               geneUniverse = humanEntrezIDs, orgPackg = "org.Hs.eg.db")
* 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: 2 ERRORs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/goSorensen.Rcheck/00check.log’
for details.