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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:RCAS.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings RCAS_1.36.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/RCAS.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘RCAS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RCAS’ version ‘1.36.0’
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 24 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 code 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                  user system elapsed
runMotifDiscovery               35.047  0.981  31.654
getMotifSummaryTable            12.188  0.461  47.557
getFeatureBoundaryCoverageMulti 11.939  0.703  12.643
calculateCoverageProfileList    10.333  0.263  10.597
calculateCoverageProfile         8.123  0.271   8.395
findDifferentialMotifs           7.127  0.362   6.846
getTargetedGenesTable            6.832  0.560   7.342
summarizeQueryRegionsMulti       6.670  0.192  20.378
getTxdbFeaturesFromGRanges       6.001  0.387   6.385
summarizeQueryRegions            6.107  0.176   6.284
createDB                         2.583  0.212  15.657
checkSeqDb                       0.799  0.098 450.940
findEnrichedFunctions            0.540  0.108   5.509
* 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:
    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)
    8.         ├─utils::contrib.url(BiocManager::repositories()["BioCann"], type = type)
    9.         └─BiocManager::repositories()
   10.           └─BiocManager:::.version_validate(version)
   11.             ├─base::ifelse(.is_CRAN_check(), .message(txt), .stop(txt))
   12.             └─BiocManager:::.stop(txt)
  
  [ FAIL 2 | WARN 9941 | SKIP 0 | PASS 44 ]
  Error:
  ! Test failures.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/RCAS.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL RCAS
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘RCAS’ ...
** this is package ‘RCAS’ version ‘1.36.0’
** 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 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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")
Saving _problems/test_database_functions-13.R
Saving _problems/test_motif-15.R
[ FAIL 2 | WARN 9941 | SKIP 0 | PASS 44 ]

══ 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: "Bioconductor version cannot be validated; no internet connection?  See\n  #troubleshooting section in vignette"
Backtrace:
     ▆
  1. ├─testthat::expect_error(...) at test_database_functions.R:10:3
  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)
 10.         ├─utils::contrib.url(BiocManager::repositories()["BioCann"], type = type)
 11.         └─BiocManager::repositories()
 12.           └─BiocManager:::.version_validate(version)
 13.             ├─base::ifelse(.is_CRAN_check(), .message(txt), .stop(txt))
 14.             └─BiocManager:::.stop(txt)
── Error ('test_motif.R:15:3'): Extracting sequences of a GRanges object from a BSGenome object ──
Error: Bioconductor version cannot be validated; no internet connection?  See
  #troubleshooting section in vignette
Backtrace:
     ▆
  1. ├─testthat::expect_is(extractSequences(peaks[1:5], "hg19"), "DNAStringSet") at test_motif.R:15:3
  2. │ └─testthat::quasi_label(enquo(object), label)
  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)
  8.         ├─utils::contrib.url(BiocManager::repositories()["BioCann"], type = type)
  9.         └─BiocManager::repositories()
 10.           └─BiocManager:::.version_validate(version)
 11.             ├─base::ifelse(.is_CRAN_check(), .message(txt), .stop(txt))
 12.             └─BiocManager:::.stop(txt)

[ FAIL 2 | WARN 9941 | SKIP 0 | PASS 44 ]
Error:
! Test failures.
Execution halted