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### Running command:
###
###   /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.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL RCAS
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘RCAS’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘Biostrings::pattern’ by ‘grid::pattern’ when loading ‘genomation’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘Biostrings::pattern’ by ‘grid::pattern’ when loading ‘genomation’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘Biostrings::pattern’ by ‘grid::pattern’ when loading ‘genomation’
** testing if installed package keeps a record of temporary installation path
* DONE (RCAS)

R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(RCAS)
Loading required package: plotly
Loading required package: ggplot2

Attaching package: 'plotly'

The following object is masked from 'package:ggplot2':

    last_plot

The following object is masked from 'package:stats':

    filter

The following object is masked from 'package:graphics':

    layout

Loading required package: DT
Loading required package: data.table
Warning message:
replacing previous import 'Biostrings::pattern' by 'grid::pattern' when loading 'genomation' 
> 
> test_check("RCAS")
[ FAIL 5 | WARN 9 | SKIP 0 | PASS 39 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_database_functions.R:10:3'): Testing createDB function ───────
`createDB(dbPath = dbPath, genomeVersion = "hg19", update = FALSE)` threw an error with unexpected message.
Expected match: "A database already exists"
Actual message: "Install 'BiocManager' from CRAN to get 'BioCann' contrib.url"
Backtrace:
    ▆
 1. ├─testthat::expect_error(...) at test_database_functions.R:10:2
 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::createDB(dbPath = dbPath, genomeVersion = "hg19", update = FALSE)
 7.   └─RCAS::checkSeqDb(genomeVersion)
 8.     └─BSgenome::available.genomes()
 9.       └─BSgenome:::get_data_annotation_contrib_url(type)
── Error ('test_motif.R:15:3'): Extracting sequences of a GRanges object from a BSGenome object ──
Error in `get_data_annotation_contrib_url(type)`: Install 'BiocManager' from CRAN to get 'BioCann' contrib.url
Backtrace:
    ▆
 1. ├─testthat::expect_is(extractSequences(peaks[1:5], "hg19"), "DNAStringSet") at test_motif.R:15:2
 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
 3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
 4. └─RCAS::extractSequences(peaks[1:5], "hg19")
 5.   └─RCAS::checkSeqDb(genomeVersion)
 6.     └─BSgenome::available.genomes()
 7.       └─BSgenome:::get_data_annotation_contrib_url(type)
── Error ('test_motif.R:20:1'): (code run outside of `test_that()`) ────────────
Error in `get_data_annotation_contrib_url(type)`: Install 'BiocManager' from CRAN to get 'BioCann' contrib.url
Backtrace:
    ▆
 1. └─RCAS::runMotifDiscovery(...) at test_motif.R:20:0
 2.   └─RCAS::extractSequences(queryRegions, genomeVersion)
 3.     └─RCAS::checkSeqDb(genomeVersion)
 4.       └─BSgenome::available.genomes()
 5.         └─BSgenome:::get_data_annotation_contrib_url(type)
── Failure ('test_report.R:5:3'): Testing runReport function ───────────────────
`runReport(genomeVersion = "foo")` threw an error with unexpected message.
Expected match: "Can't find a genome sequence"
Actual message: "Install 'BiocManager' from CRAN to get 'BioCann' contrib.url"
Backtrace:
    ▆
 1. ├─testthat::expect_error(runReport(genomeVersion = "foo"), regexp = "Can't find a genome sequence") at test_report.R:5:2
 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 = "foo")
 7.   └─RCAS::checkSeqDb(genomeVersion)
 8.     └─BSgenome::available.genomes()
 9.       └─BSgenome:::get_data_annotation_contrib_url(type)
── Failure ('test_report.R:7:3'): Testing runReport function ───────────────────
`runReport(genomeVersion = "9")` threw an error with unexpected message.
Expected match: "match the genome version to an unambigous genome sequence"
Actual message: "Install 'BiocManager' from CRAN to get 'BioCann' contrib.url"
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