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### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BadRegionFinder.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BadRegionFinder_1.38.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BadRegionFinder.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 ‘BadRegionFinder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BadRegionFinder’ version ‘1.38.0’
* 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 ‘BadRegionFinder’ 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 ... NOTE
determineCoverage: no visible global function definition for ‘path’
Undefined global functions or variables:
  path
* 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 ‘BadRegionFinder-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotDetailed
> ### Title: Plots a more detailed overview of the coverage quality
> ### Aliases: plotDetailed 'plot Detailed'
> 
> ### ** Examples
> 
> library("BSgenome.Hsapiens.UCSC.hg19")
Loading required package: BSgenome
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: ‘generics’

The following objects are masked from ‘package:base’:

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:utils’:

    findMatches

The following objects are masked from ‘package:base’:

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: Seqinfo
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector

Attaching package: ‘Biostrings’

The following object is masked from ‘package:base’:

    strsplit

Loading required package: BiocIO
Loading required package: rtracklayer
> threshold1 <- 20
> threshold2 <- 100
> percentage1 <- 0.80
> percentage2 <- 0.90
> sample_file <- system.file("extdata", "SampleNames.txt", 
+                            package = "BadRegionFinder")
> samples <- read.table(sample_file)
> bam_input <- system.file("extdata", package = "BadRegionFinder")
> output <- system.file("extdata", package = "BadRegionFinder")
> target_regions <- system.file("extdata", "targetRegions.bed",
+                               package = "BadRegionFinder")
> targetRegions <- read.table(target_regions, header = FALSE,
+                             stringsAsFactors = FALSE)
> 
> coverage_summary <- determineCoverage(samples, bam_input, targetRegions, output,
+                                       TRonly = FALSE)
Determine Coverage
Sample Test_454
Sample Test_ion
Determine target bases
Combine Information
Chromosome: 1
Chromosome: 2
Chromosome: 3
Chromosome: 4
Chromosome: 5
Chromosome: 6
Chromosome: 7
Chromosome: 8
Chromosome: 9
Chromosome: 10
Chromosome: 11
Chromosome: 12
Chromosome: 13
Chromosome: 14
Chromosome: 15
Chromosome: 16
Chromosome: 17
Chromosome: 18
Chromosome: 19
Chromosome: 20
Chromosome: 21
Chromosome: 22
Chromosome: X
Chromosome: Y
Chromosome: MT
> coverage_indicators <- determineCoverageQuality(threshold1, threshold2,
+                                                 percentage1, percentage2,
+                                                 coverage_summary)
Analyzing Chromosome 1
Analyzing Chromosome 2
Analyzing Chromosome 3
Analyzing Chromosome 4
Analyzing Chromosome 5
Analyzing Chromosome 6
Analyzing Chromosome 7
Analyzing Chromosome 8
Analyzing Chromosome 9
Analyzing Chromosome 10
Analyzing Chromosome 11
Analyzing Chromosome 12
Analyzing Chromosome 13
Analyzing Chromosome 14
Analyzing Chromosome 15
Analyzing Chromosome 16
Analyzing Chromosome 17
Analyzing Chromosome 18
Analyzing Chromosome 19
Analyzing Chromosome 20
Analyzing Chromosome 21
Analyzing Chromosome 22
Analyzing Chromosome 23
Analyzing Chromosome 24
Analyzing Chromosome 25
> coverage_indicators_temp <- reportBadRegionsDetailed(threshold1, threshold2,
+                                                      percentage1, percentage2,
+                                                      coverage_indicators, "",
+                                                      samples, output)
Analyzing Chromosome 1
Analyzing Chromosome 2
Error: Your query has been redirected to https://status.ensembl.org indicating this Ensembl service is currently unavailable.
Look at ?useEnsembl for details on how to try a mirror site.
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 ‘BadRegionFinder.Rnw’ using Sweave
Determine Coverage
Sample Test2_454
Sample Test2_ion
Determine target bases
Combine Information
Chromosome: 1
Chromosome: 2
Chromosome: 3
Chromosome: 4
Chromosome: 5
Chromosome: 6
Chromosome: 7
Chromosome: 8
Chromosome: 9
Chromosome: 10
Chromosome: 11
Chromosome: 12
Chromosome: 13
Chromosome: 14
Chromosome: 15
Chromosome: 16
Chromosome: 17
Chromosome: 18
Chromosome: 19
Chromosome: 20
Chromosome: 21
Chromosome: 22
Chromosome: X
Chromosome: Y
Chromosome: MT
Analyzing Chromosome 1
Analyzing Chromosome 2
Analyzing Chromosome 3
Analyzing Chromosome 4
Analyzing Chromosome 5
Analyzing Chromosome 6
Analyzing Chromosome 7
Analyzing Chromosome 8
Analyzing Chromosome 9
Analyzing Chromosome 10
Analyzing Chromosome 11
Analyzing Chromosome 12
Analyzing Chromosome 13
Analyzing Chromosome 14
Analyzing Chromosome 15
Analyzing Chromosome 16
Analyzing Chromosome 17
Analyzing Chromosome 18
Analyzing Chromosome 19
Analyzing Chromosome 20
Analyzing Chromosome 21
Analyzing Chromosome 22
Analyzing Chromosome 23
Analyzing Chromosome 24
Analyzing Chromosome 25
Analyze Chromosome 1
Analyze Chromosome 2
Analyze Chromosome 3
Analyze Chromosome 4
Analyze Chromosome 5
Analyze Chromosome 6
Analyze Chromosome 7
Analyze Chromosome 8
Analyze Chromosome 9
Analyze Chromosome 10
Analyze Chromosome 11
Analyze Chromosome 12
Analyze Chromosome 13
Analyze Chromosome 14
Analyze Chromosome 15
Analyze Chromosome 16
Analyze Chromosome 17
Analyze Chromosome 18
Analyze Chromosome 19
Analyze Chromosome 20
Analyze Chromosome 21
Analyze Chromosome 22
Analyze Chromosome 23
Analyze Chromosome 24
Analyze Chromosome 25

Error: processing vignette 'BadRegionFinder.Rnw' failed with diagnostics:
 chunk 10 (label = 10) 
Error : Your query has been redirected to https://status.ensembl.org indicating this Ensembl service is currently unavailable.
Look at ?useEnsembl for details on how to try a mirror site.

--- failed re-building ‘BadRegionFinder.Rnw’

SUMMARY: processing the following file failed:
  ‘BadRegionFinder.Rnw’

Error: Vignette re-building failed.
Execution halted

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

Status: 2 ERRORs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/BadRegionFinder.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL BadRegionFinder
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘BadRegionFinder’ ...
** this is package ‘BadRegionFinder’ version ‘1.38.0’
** 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 (BadRegionFinder)