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### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:chipenrich.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings chipenrich_2.37.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.24-bioc/meat/chipenrich.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-05-05 02:06:49 UTC
* checking for file ‘chipenrich/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘chipenrich’ version ‘2.37.0’
* 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 ‘chipenrich’ 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 ... NOTE
checkRd: (-1) broadenrich.Rd:134: Escaped LaTeX specials: \&
checkRd: (-1) chipenrich.Rd:148: Escaped LaTeX specials: \&
checkRd: (-1) hybridenrich.Rd:111: Escaped LaTeX specials: \&
checkRd: (-1) polyenrich.Rd:148: Escaped LaTeX specials: \&
checkRd: (-1) proxReg.Rd:117: Escaped LaTeX specials: \&
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
             user system elapsed
broadenrich 6.671  0.110   6.782
polyenrich  5.477  0.108   5.585
* 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:
   16. │                   └─DBI (local) .local(conn, statement, ...)
   17. │                     ├─DBI::dbSendQuery(conn, statement, ...)
   18. │                     └─RSQLite::dbSendQuery(conn, statement, ...)
   19. │                       └─RSQLite (local) .local(conn, statement, ...)
   20. │                         ├─methods::new(...)
   21. │                         │ ├─methods::initialize(value, ...)
   22. │                         │ └─methods::initialize(value, ...)
   23. │                         └─RSQLite:::result_create(conn@ptr, statement)
   24. └─base::.handleSimpleError(...)
   25.   └─base (local) h(simpleError(msg, call))
  
  [ FAIL 3 | WARN 0 | SKIP 3 | PASS 162 ]
  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, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.24-bioc/meat/chipenrich.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD INSTALL chipenrich
###
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* installing to library ‘/home/biocbuild/bbs-3.24-bioc/R/site-library’
* installing *source* package ‘chipenrich’ ...
** this is package ‘chipenrich’ version ‘2.37.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (chipenrich)

R version 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 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(chipenrich)





> 
> test_check("chipenrich")
Saving _problems/test_0a_utils-28.R
Saving _problems/test_1_read-52.R
Saving _problems/test_1_read-73.R
[ FAIL 3 | WARN 0 | SKIP 3 | PASS 162 ]

══ Skipped tests (3) ═══════════════════════════════════════════════════════════
• empty test (3): 'test_5_chipenrich.R:200:1', 'test_5_chipenrich.R:233:1',
  'test_5_chipenrich.R:237:1'

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_0a_utils.R:28:5'): Genome to eg2symbol ─────────────────────────
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'toTable': unable to open database file
Backtrace:
     ▆
  1. ├─testthat::expect_equal(class(genome_to_orgdb("hg19")), "data.frame") at test_0a_utils.R:28:5
  2. │ └─testthat::quasi_label(enquo(object), label)
  3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
  4. ├─chipenrich:::genome_to_orgdb("hg19")
  5. │ ├─BiocGenerics::as.data.frame(egSYMBOL[mapped_genes])
  6. │ └─AnnotationDbi::as.data.frame(egSYMBOL[mapped_genes])
  7. │   ├─BiocGenerics::toTable(x)
  8. │   └─AnnotationDbi::toTable(x)
  9. │     └─AnnotationDbi (local) .local(x, ...)
 10. │       ├─BiocGenerics::toTable(flatten(x, fromKeys.only = TRUE))
 11. │       ├─AnnotationDbi:::flatten(x, fromKeys.only = TRUE)
 12. │       └─AnnotationDbi:::flatten(x, fromKeys.only = TRUE)
 13. │         └─AnnotationDbi (local) .local(x, ...)
 14. │           └─AnnotationDbi:::dbSelectFromL2Rchain(...)
 15. │             └─AnnotationDbi:::dbQuery(conn, SQL)
 16. │               ├─DBI::dbGetQuery(conn, SQL)
 17. │               └─DBI::dbGetQuery(conn, SQL)
 18. │                 └─DBI (local) .local(conn, statement, ...)
 19. │                   ├─DBI::dbSendQuery(conn, statement, ...)
 20. │                   └─RSQLite::dbSendQuery(conn, statement, ...)
 21. │                     └─RSQLite (local) .local(conn, statement, ...)
 22. │                       ├─methods::new(...)
 23. │                       │ ├─methods::initialize(value, ...)
 24. │                       │ └─methods::initialize(value, ...)
 25. │                       └─RSQLite:::result_create(conn@ptr, statement)
 26. └─base::.handleSimpleError(...)
 27.   └─base (local) h(simpleError(msg, call))
── Error ('test_1_read.R:52:2'): Test renaming geneid to gene_id and hg19 genome ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'toTable': unable to open database file
Backtrace:
     ▆
  1. ├─chipenrich:::read_ldef(ldef_geneid_file, genome = "hg19") at test_1_read.R:52:9
  2. │ └─chipenrich:::genome_to_orgdb(genome)
  3. │   ├─BiocGenerics::as.data.frame(egSYMBOL[mapped_genes])
  4. │   └─AnnotationDbi::as.data.frame(egSYMBOL[mapped_genes])
  5. │     ├─BiocGenerics::toTable(x)
  6. │     └─AnnotationDbi::toTable(x)
  7. │       └─AnnotationDbi (local) .local(x, ...)
  8. │         ├─BiocGenerics::toTable(flatten(x, fromKeys.only = TRUE))
  9. │         ├─AnnotationDbi:::flatten(x, fromKeys.only = TRUE)
 10. │         └─AnnotationDbi:::flatten(x, fromKeys.only = TRUE)
 11. │           └─AnnotationDbi (local) .local(x, ...)
 12. │             └─AnnotationDbi:::dbSelectFromL2Rchain(...)
 13. │               └─AnnotationDbi:::dbQuery(conn, SQL)
 14. │                 ├─DBI::dbGetQuery(conn, SQL)
 15. │                 └─DBI::dbGetQuery(conn, SQL)
 16. │                   └─DBI (local) .local(conn, statement, ...)
 17. │                     ├─DBI::dbSendQuery(conn, statement, ...)
 18. │                     └─RSQLite::dbSendQuery(conn, statement, ...)
 19. │                       └─RSQLite (local) .local(conn, statement, ...)
 20. │                         ├─methods::new(...)
 21. │                         │ ├─methods::initialize(value, ...)
 22. │                         │ └─methods::initialize(value, ...)
 23. │                         └─RSQLite:::result_create(conn@ptr, statement)
 24. └─base::.handleSimpleError(...)
 25.   └─base (local) h(simpleError(msg, call))
── Error ('test_1_read.R:73:2'): Test nosymbol and hg19 genome ─────────────────
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'toTable': unable to open database file
Backtrace:
     ▆
  1. ├─chipenrich:::read_ldef(ldef_nosymbol_file, genome = "hg19") at test_1_read.R:73:9
  2. │ └─chipenrich:::genome_to_orgdb(genome)
  3. │   ├─BiocGenerics::as.data.frame(egSYMBOL[mapped_genes])
  4. │   └─AnnotationDbi::as.data.frame(egSYMBOL[mapped_genes])
  5. │     ├─BiocGenerics::toTable(x)
  6. │     └─AnnotationDbi::toTable(x)
  7. │       └─AnnotationDbi (local) .local(x, ...)
  8. │         ├─BiocGenerics::toTable(flatten(x, fromKeys.only = TRUE))
  9. │         ├─AnnotationDbi:::flatten(x, fromKeys.only = TRUE)
 10. │         └─AnnotationDbi:::flatten(x, fromKeys.only = TRUE)
 11. │           └─AnnotationDbi (local) .local(x, ...)
 12. │             └─AnnotationDbi:::dbSelectFromL2Rchain(...)
 13. │               └─AnnotationDbi:::dbQuery(conn, SQL)
 14. │                 ├─DBI::dbGetQuery(conn, SQL)
 15. │                 └─DBI::dbGetQuery(conn, SQL)
 16. │                   └─DBI (local) .local(conn, statement, ...)
 17. │                     ├─DBI::dbSendQuery(conn, statement, ...)
 18. │                     └─RSQLite::dbSendQuery(conn, statement, ...)
 19. │                       └─RSQLite (local) .local(conn, statement, ...)
 20. │                         ├─methods::new(...)
 21. │                         │ ├─methods::initialize(value, ...)
 22. │                         │ └─methods::initialize(value, ...)
 23. │                         └─RSQLite:::result_create(conn@ptr, statement)
 24. └─base::.handleSimpleError(...)
 25.   └─base (local) h(simpleError(msg, call))

[ FAIL 3 | WARN 0 | SKIP 3 | PASS 162 ]
Error:
! Test failures.
Execution halted