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### Running command:
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###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:gDNAx.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings gDNAx_1.5.1.tar.gz
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* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/gDNAx.Rcheck'
* using R Under development (unstable) (2025-01-21 r87610 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'gDNAx/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'gDNAx' version '1.5.1'
* 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 whether package 'gDNAx' 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 dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  'GenomicAlignments:::.make_GAlignmentPairs_from_GAlignments'
  'GenomicAlignments:::.normargParam' 'S4Vectors:::makePowersOfTwo'
  See the note in ?`:::` about the use of this operator.
* 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 'gDNAx-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: filterBAMtx
> ### Title: Filter alignments in a BAM file using a transcriptome
> ### Aliases: filterBAMtx filterBAMtxFlag testBAMtxFlag
> 
> ### ** Examples
> 
> library(gDNAinRNAseqData)
> 
> library(TxDb.Hsapiens.UCSC.hg38.knownGene)
Loading required package: GenomicFeatures
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

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene
> 
> # Getting the 'gDNAx' object
> bamfiles <- LiYu22subsetBAMfiles()
see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for documentation
loading from cache
require("Rsamtools")
see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for documentation
downloading 2 resources
retrieving 2 resources
Warning: download failed
  web resource path: 'https://experimenthub.bioconductor.org/fetch/8132'
  local file path: 'E:\biocbuild\ExperimentHub_cache\file127381dc27984'
  reason: Internal Server Error (HTTP 500).
Warning: bfcdownload() failed
  rid: BFC140
  file: 'https://experimenthub.bioconductor.org/fetch/8132'
  reason: download failed
Warning: download failed
  hub path: 'https://experimenthub.bioconductor.org/fetch/8132'
  cache resource: 'EH8080 : 8132'
  reason: download failed; see warnings()
Error loading resource.
 attempting to re-download
downloading 2 resources
retrieving 2 resources
Warning: download failed
  web resource path: 'https://experimenthub.bioconductor.org/fetch/8131'
  local file path: 'E:\biocbuild\ExperimentHub_cache\file12738e1f72dc'
  reason: Internal Server Error (HTTP 500).
Warning: bfcdownload() failed
  rid: BFC139
  file: 'https://experimenthub.bioconductor.org/fetch/8131'
  reason: download failed
Warning: download failed
  hub path: 'https://experimenthub.bioconductor.org/fetch/8131'
  cache resource: 'EH8080 : 8131'
  reason: download failed; see warnings()
Warning: download failed
  web resource path: 'https://experimenthub.bioconductor.org/fetch/8132'
  local file path: 'E:\biocbuild\ExperimentHub_cache\file127384e6ba1a'
  reason: Internal Server Error (HTTP 500).
Warning: bfcdownload() failed
  rid: BFC140
  file: 'https://experimenthub.bioconductor.org/fetch/8132'
  reason: download failed
Warning: download failed
  hub path: 'https://experimenthub.bioconductor.org/fetch/8132'
  cache resource: 'EH8080 : 8132'
  reason: download failed; see warnings()
Error: failed to load resource
  name: EH8080
  title: RNA-seq data BAM file subset of HRR589633 contaminated with 0% gDNA
  reason: 2 resources failed to download
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'runTests.R'
 ERROR
Running the tests in 'tests/runTests.R' failed.
Last 13 lines of output:
  ERROR in test_output_strandedness: Error in h(simpleError(msg, call)) : 
    error in evaluating the argument 'obj' in selecting a method for function 'unname': isOpen(<BamFile>) is not 'TRUE'
  
  Test files with failing tests
  
     test_dx.R 
       E:/biocbuild/bbs-3.21-bioc/R/library/gDNAx/unitTests/test_dx.R 
  
     test_strandedness.R 
       test_output_strandedness 
  
  
  Error in BiocGenerics:::testPackage("gDNAx") : 
    unit tests failed for package gDNAx
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 1 NOTE
See
  'E:/biocbuild/bbs-3.21-bioc/meat/gDNAx.Rcheck/00check.log'
for details.