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### Running command:
###
###   /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD check --install=check:geneAttribution.install-out.txt --library=/home/biocbuild/bbs-3.24-bioc/R/site-library --timings geneAttribution_1.39.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.24-bioc/meat/geneAttribution.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 03:48:33 UTC
* checking for file ‘geneAttribution/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘geneAttribution’ version ‘1.39.0’
* 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 ‘geneAttribution’ 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘geneAttribution-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: geneAttribution
> ### Title: geneAttribution: Identification of candidate genes associated
> ###   with noncoding genetic variation
> ### Aliases: geneAttribution geneAttribution-package
> 
> ### ** Examples
> 
> geneLocs <- geneModels()
  2169 genes were dropped because they have exons located on both strands of
  the same reference sequence or on more than one reference sequence, so cannot
  be represented by a single genomic range.
  Use 'single.strand.genes.only=FALSE' to get all the genes in a GRangesList
  object, or use suppressMessages() to suppress this message.
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 'toTable': unable to open database file
Calls: geneModels ... dbFetch -> .local -> result_fetch -> .handleSimpleError -> h
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:
   14. │               └─AnnotationDbi:::dbQuery(conn, SQL, 1)
   15. │                 ├─DBI::dbGetQuery(conn, SQL)
   16. │                 └─DBI::dbGetQuery(conn, SQL)
   17. │                   └─DBI (local) .local(conn, statement, ...)
   18. │                     ├─DBI::dbFetch(rs, n = n, ...)
   19. │                     └─RSQLite::dbFetch(rs, n = n, ...)
   20. │                       └─RSQLite (local) .local(res, n, ...)
   21. │                         └─RSQLite:::result_fetch(res@ptr, n = n)
   22. └─base::.handleSimpleError(...)
   23.   └─base (local) h(simpleError(msg, call))
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 5 ]
  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: 2 ERRORs
See
  ‘/home/biocbuild/bbs-3.24-bioc/meat/geneAttribution.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD INSTALL geneAttribution
###
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* installing to library ‘/home/biocbuild/bbs-3.24-bioc/R/site-library’
* installing *source* package ‘geneAttribution’ ...
** this is package ‘geneAttribution’ version ‘1.39.0’
** 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 (geneAttribution)

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(geneAttribution)

> 
> test_check("geneAttribution")
Saving _problems/testGeneAttribution-5.R
Saving _problems/testGeneAttribution-25.R
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 5 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('testGeneAttribution.R:5:8'): geneModels() output is a GenomicRanges object with the required fields ──
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. ├─geneAttribution::geneModels() at testGeneAttribution.R:5:15
  2. │ ├─BiocGenerics::as.data.frame(org.Hs.eg.db::org.Hs.egSYMBOL2EG)
  3. │ └─BiocGenerics::as.data.frame(org.Hs.eg.db::org.Hs.egSYMBOL2EG)
  4. │   ├─BiocGenerics::toTable(x)
  5. │   └─AnnotationDbi::toTable(x)
  6. │     └─AnnotationDbi (local) .local(x, ...)
  7. │       ├─BiocGenerics::toTable(flatten(x, fromKeys.only = TRUE))
  8. │       ├─AnnotationDbi:::flatten(x, fromKeys.only = TRUE)
  9. │       └─AnnotationDbi:::flatten(x, fromKeys.only = TRUE)
 10. │         └─AnnotationDbi (local) .local(x, ...)
 11. │           ├─AnnotationDbi::Rkeys(x)
 12. │           └─AnnotationDbi::Rkeys(x)
 13. │             └─AnnotationDbi:::dbUniqueVals(...)
 14. │               └─AnnotationDbi:::dbQuery(conn, SQL, 1)
 15. │                 ├─DBI::dbGetQuery(conn, SQL)
 16. │                 └─DBI::dbGetQuery(conn, SQL)
 17. │                   └─DBI (local) .local(conn, statement, ...)
 18. │                     ├─DBI::dbFetch(rs, n = n, ...)
 19. │                     └─RSQLite::dbFetch(rs, n = n, ...)
 20. │                       └─RSQLite (local) .local(res, n, ...)
 21. │                         └─RSQLite:::result_fetch(res@ptr, n = n)
 22. └─base::.handleSimpleError(...)
 23.   └─base (local) h(simpleError(msg, call))
── Error ('testGeneAttribution.R:25:8'): geneAttribution output is a named vector that adds up to 1 ──
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. ├─geneAttribution::geneModels() at testGeneAttribution.R:25:15
  2. │ ├─BiocGenerics::as.data.frame(org.Hs.eg.db::org.Hs.egSYMBOL2EG)
  3. │ └─BiocGenerics::as.data.frame(org.Hs.eg.db::org.Hs.egSYMBOL2EG)
  4. │   ├─BiocGenerics::toTable(x)
  5. │   └─AnnotationDbi::toTable(x)
  6. │     └─AnnotationDbi (local) .local(x, ...)
  7. │       ├─BiocGenerics::toTable(flatten(x, fromKeys.only = TRUE))
  8. │       ├─AnnotationDbi:::flatten(x, fromKeys.only = TRUE)
  9. │       └─AnnotationDbi:::flatten(x, fromKeys.only = TRUE)
 10. │         └─AnnotationDbi (local) .local(x, ...)
 11. │           ├─AnnotationDbi::Rkeys(x)
 12. │           └─AnnotationDbi::Rkeys(x)
 13. │             └─AnnotationDbi:::dbUniqueVals(...)
 14. │               └─AnnotationDbi:::dbQuery(conn, SQL, 1)
 15. │                 ├─DBI::dbGetQuery(conn, SQL)
 16. │                 └─DBI::dbGetQuery(conn, SQL)
 17. │                   └─DBI (local) .local(conn, statement, ...)
 18. │                     ├─DBI::dbFetch(rs, n = n, ...)
 19. │                     └─RSQLite::dbFetch(rs, n = n, ...)
 20. │                       └─RSQLite (local) .local(res, n, ...)
 21. │                         └─RSQLite:::result_fetch(res@ptr, n = n)
 22. └─base::.handleSimpleError(...)
 23.   └─base (local) h(simpleError(msg, call))

[ FAIL 2 | WARN 0 | SKIP 0 | PASS 5 ]
Error:
! Test failures.
Execution halted