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### Running command:
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###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:chromVAR.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings chromVAR_1.24.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/chromVAR.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 ‘chromVAR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘chromVAR’ 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 ‘chromVAR’ can be installed ... OK
* used C++ compiler: ‘g++ (GCC) 10.3.1’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
  installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘chromVAR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: computeDeviations
> ### Title: computeDeviations
> ### Aliases: computeDeviations
> ###   computeDeviations,SummarizedExperiment,SummarizedExperiment-method
> ###   computeDeviations,SummarizedExperiment,MatrixOrmatrix-method
> ###   computeDeviations,SummarizedExperiment,list-method
> ###   computeDeviations,SummarizedExperiment,missingOrNULL-method
> ###   computeDeviations,MatrixOrmatrix,SummarizedExperiment-method
> ###   computeDeviations,MatrixOrmatrix,MatrixOrmatrix-method
> ###   computeDeviations,MatrixOrmatrix,list-method
> ###   computeDeviations,MatrixOrmatrix,missingOrNULL-method
> 
> ### ** Examples
> 
> # Register BiocParallel
> BiocParallel::register(BiocParallel::SerialParam())
> # Load very small example counts (already filtered)
> data(mini_counts, package = "chromVAR")
> # load annotation matrix; result from matchMotifs
> data(mini_ix, package = "chromVAR")
> 
> # computing deviations
> dev <- computeDeviations(object = mini_counts,
+                          annotations = mini_ix)
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’/home/biocbuild/R/R-4.3.1/bin/BATCH: line 60: 539744 Killed                  ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1

 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(chromVAR)
  
  > BiocParallel::register(BiocParallel::SerialParam())
  > test_check("chromVAR")
* 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, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/chromVAR.Rcheck/00check.log’
for details.