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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:BRGenomics.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings BRGenomics_1.12.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/BRGenomics.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘BRGenomics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BRGenomics’ version ‘1.12.0’
* 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:
  .travis.yml
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 ‘BRGenomics’ 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
getDESeqResults 9.753  0.676   10.43
* 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:
   14. │               └─GenomicRanges:::combine_seqinfo_from_GenomicRanges_objects(all_objects)
   15. │                 ├─BiocGenerics::do.call(merge, lapply(seq_len(x_len), function(i) seqinfo(x[[i]])))
   16. │                 ├─base::do.call(merge, lapply(seq_len(x_len), function(i) seqinfo(x[[i]])))
   17. │                 ├─base (local) `<stndrdGn>`(`<Seqinfo>`, `<Seqinfo>`, `<Seqinfo>`)
   18. │                 └─GenomeInfoDb (local) `<stndrdGn>`(`<Seqinfo>`, `<Seqinfo>`, `<Seqinfo>`)
   19. │                   └─GenomeInfoDb:::.merge_Seqinfo_objects(x, y, ...)
   20. │                     └─GenomeInfoDb:::.merge_two_Seqinfo_objects(x, y)
   21. │                       └─GenomeInfoDb:::mergeNamedAtomicVectors(...)
   22. │                         └─base::stop(msg)
   23. └─base::.handleSimpleError(...)
   24.   └─base (local) h(simpleError(msg, call))
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 572 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘AnalyzingMultipleDatasets.Rmd’ using ‘UTF-8’... OK
  ‘DESeq2WithGlobalPerturbations.Rmd’ using ‘UTF-8’... OK
  ‘GettingStarted.Rmd’ using ‘UTF-8’... OK
  ‘ImportingModifyingAnnotations.Rmd’ using ‘UTF-8’... OK
  ‘ImportingProcessingData.Rmd’ using ‘UTF-8’... OK
  ‘Overview.Rmd’ using ‘UTF-8’... OK
  ‘ProfilePlotsAndBootstrapping.Rmd’ using ‘UTF-8’... OK
  ‘SequenceExtraction.Rmd’ using ‘UTF-8’... OK
  ‘SignalCounting.Rmd’ using ‘UTF-8’... OK
  ‘SpikeInNormalization.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/BRGenomics.Rcheck/00check.log’
for details.