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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:RCAS.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings RCAS_1.26.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/RCAS.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 ‘RCAS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RCAS’ version ‘1.26.0’
* 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 ‘RCAS’ 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 ‘RCAS-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: checkSeqDb
> ### Title: checkSeqDb
> ### Aliases: checkSeqDb
> 
> ### ** Examples
> 
> checkSeqDb('hg19')
Error in get_data_annotation_contrib_url(type) : 
  Install 'BiocManager' from CRAN to get 'BioCann' contrib.url
Calls: checkSeqDb -> <Anonymous> -> get_data_annotation_contrib_url
Execution halted
* 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:
  Backtrace:
      ▆
   1. ├─testthat::expect_error(runReport(genomeVersion = "9"), regexp = "match the genome version to an unambigous genome sequence") at test_report.R:7:2
   2. │ └─testthat:::quasi_capture(...)
   3. │   ├─testthat (local) .capture(...)
   4. │   │ └─base::withCallingHandlers(...)
   5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   6. └─RCAS::runReport(genomeVersion = "9")
   7.   └─RCAS::checkSeqDb(genomeVersion)
   8.     └─BSgenome::available.genomes()
   9.       └─BSgenome:::get_data_annotation_contrib_url(type)
  
  [ FAIL 5 | WARN 9 | SKIP 0 | PASS 39 ]
  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 ...
  ‘RCAS.metaAnalysis.vignette.Rmd’ using ‘UTF-8’... OK
  ‘RCAS.vignette.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘RCAS.metaAnalysis.vignette.Rmd’ using rmarkdown
--- finished re-building ‘RCAS.metaAnalysis.vignette.Rmd’

--- re-building ‘RCAS.vignette.Rmd’ using rmarkdown
Error in x$.self$finalize() : attempt to apply non-function
Warning: call dbDisconnect() when finished working with a connection

Quitting from lines 223-229 [motif_analysis] (RCAS.vignette.Rmd)
Error: processing vignette 'RCAS.vignette.Rmd' failed with diagnostics:
Install 'BiocManager' from CRAN to get 'BioCann' contrib.url
--- failed re-building ‘RCAS.vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘RCAS.vignette.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 3 ERRORs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/RCAS.Rcheck/00check.log’
for details.