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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:bsseq.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings bsseq_1.35.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/bsseq.Rcheck’
* using R version 4.3.0 alpha (2023-04-03 r84154)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘bsseq/DESCRIPTION’ ... OK
* this is package ‘bsseq’ version ‘1.35.0’
* 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 ‘bsseq’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* 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 ... NOTE
Unexported objects imported by ':::' calls:
  ‘BiocGenerics:::replaceSlots’
  ‘DelayedArray:::get_verbose_block_processing’
  ‘DelayedArray:::normarg_grid’
  ‘GenomicRanges:::.extract_groups_from_GenomicRanges’
  ‘GenomicRanges:::.get_circle_length’
  ‘GenomicRanges:::extraColumnSlotNames’
  ‘IRanges:::.shift_ranges_in_groups_to_first_circle’
  ‘S4Vectors:::normarg_names’ ‘S4Vectors:::numeric2integer’
  ‘S4Vectors:::sapply_isNULL’ ‘data.table:::funique’
  See the note in ?`:::` about the use of this operator.
* 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 ... WARNING
Missing link or links in documentation object 'BSmooth.Rd':
  ‘BatchJobsParam-class’

Missing link or links in documentation object 'read.bismark.Rd':
  ‘BatchJobsParam-class’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
getMeth       6.667  3.308   9.976
BSmooth.tstat 7.712  0.504   8.224
getCoverage   6.042  0.104   6.146
BSseq-class   4.532  0.540   4.758
* 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:
  • Skipping tests that require SnowParam with multiple machines (1)
  • TODO: Remove these tests if no longer required (1)
  • empty test (4)
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_BSmooth.R:64:9'): Expected parallelisation backends work with in-memory realization backend ──
  Error in `BatchJobsParam(2, progressbar = FALSE)`: could not find function "BatchJobsParam"
  Backtrace:
      ▆
   1. └─bsseq::BSmooth(bsseq_test, BPPARAM = BatchJobsParam(2, progressbar = FALSE)) at test_BSmooth.R:64:8
   2.   └─methods::is(BPPARAM, "SnowParam")
  
  [ FAIL 1 | WARN 4 | SKIP 6 | PASS 131 ]
  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 ...
  ‘bsseq.Rmd’ using ‘UTF-8’... OK
  ‘bsseq_analysis.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/bsseq.Rcheck/00check.log’
for details.