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### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:deltaCaptureC.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings deltaCaptureC_1.23.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/deltaCaptureC.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘deltaCaptureC/DESCRIPTION’ ... OK
* this is package ‘deltaCaptureC’ version ‘1.23.0’
* package encoding: UTF-8
* 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 ‘deltaCaptureC’ 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 ... NOTE
Namespace in Imports field not imported from: ‘tictoc’
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getDeltaSE: warning in SummarizedExperiment(assay = list(delta =
  delta), colData = colData): partial argument match of 'assay' to
  'assays'
plotSignificantRegions: no visible binding for global variable ‘ctr’
plotSignificantRegions: no visible binding for global variable ‘delta’
plotSignificantRegions: no visible binding for global variable
  ‘significance’
Undefined global functions or variables:
  ctr delta significance
* 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 ‘deltaCaptureC-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: binSummarizedExperiment
> ### Title: Bin a Summarized experiment into a set of bins given by a
> ###   GRanges object
> ### Aliases: binSummarizedExperiment
> 
> ### ** Examples
> 
> binnedSummarizedExperiment = binSummarizedExperiment(smallSetOfSmallBins,smallerDeltaSE)
Loading required namespace: GenomeInfoDb
Failed with error:  ‘there is no package called ‘GenomeInfoDb’’
Error in .requirePackage(package) : 
  unable to load required package ‘GenomeInfoDb’
Calls: binSummarizedExperiment ... vapply -> FUN -> is -> getClassDef -> .requirePackage
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘deltaCaptureC.Rmd’ using rmarkdown
Failed with error:  'there is no package called 'GenomeInfoDb''

Quitting from deltaCaptureC.Rmd:238-245 [unnamed-chunk-6]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.requirePackage()`:
! unable to load required package 'GenomeInfoDb'
---
Backtrace:
     ▆
  1. └─deltaCaptureC::binSummarizedExperiment(smallSetOfSmallBins, smallerDeltaSE)
  2.   └─deltaCaptureC::getOverlapWeights(bins, rowRanges(se))
  3.     ├─IRanges::findOverlaps(bins, gr)
  4.     └─GenomicRanges::findOverlaps(bins, gr)
  5.       └─GenomicRanges (local) .local(query, subject, maxgap, minoverlap, type, select, ...)
  6.         └─GenomicRanges:::findOverlaps_GNCList(...)
  7.           ├─base::merge(seqinfo(query), seqinfo(subject))
  8.           └─Seqinfo::merge(seqinfo(query), seqinfo(subject))
  9.             └─Seqinfo:::.merge_Seqinfo_objects(x, y, ...)
 10.               └─base::vapply(args, function(arg) is(arg, class(x)), logical(1))
 11.                 └─Seqinfo (local) FUN(X[[i]], ...)
 12.                   └─methods::is(arg, class(x))
 13.                     └─methods::getClassDef(...)
 14.                       └─methods:::.requirePackage(package)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'deltaCaptureC.Rmd' failed with diagnostics:
unable to load required package 'GenomeInfoDb'
--- failed re-building ‘deltaCaptureC.Rmd’

SUMMARY: processing the following file failed:
  ‘deltaCaptureC.Rmd’

Error: Vignette re-building failed.
Execution halted

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

Status: 2 ERRORs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/deltaCaptureC.Rcheck/00check.log’
for details.