##############################################################################
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###
### Running command:
###
###   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.

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###
### Running command:
###
###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL gDNAx
###
##############################################################################
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* installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library'
* installing *source* package 'gDNAx' ...
** this is package 'gDNAx' version '1.5.1'
** 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 (gDNAx)

R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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.

> require("gDNAx") || stop("unable to load gDNAx package")
Loading required package: gDNAx
[1] TRUE
> BiocGenerics:::testPackage("gDNAx")
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")'.

see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for documentation
downloading 1 resources
retrieving 1 resource
loading from cache
require("Rsamtools")
see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for documentation
loading from cache
see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for documentation
downloading 1 resources
retrieving 1 resource
loading from cache
see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for documentation
downloading 2 resources
retrieving 2 resources
Error loading resource.
 attempting to re-download
downloading 2 resources
retrieving 2 resources
loading from cache
see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for documentation
loading from cache
see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for documentation
loading from cache
see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for documentation
downloading 1 resources
retrieving 1 resource
Error loading resource.
 attempting to re-download
downloading 2 resources
retrieving 2 resources
loading from cache
see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for documentation
loading from cache
see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for documentation
downloading 1 resources
retrieving 1 resource
Error loading resource.
 attempting to re-download
downloading 2 resources
retrieving 2 resources
Error : failed to load resource
  name: EH8087
  title: RNA-seq data BAM file subset of HRR589625 contaminated with 10% gDNA
  reason: 2 resources failed to download
In addition: There were 15 warnings (use warnings() to see them)
see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for documentation
loading from cache
see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for documentation
downloading 1 resources
retrieving 1 resource
loading from cache
see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for documentation
loading from cache
see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for documentation
downloading 1 resources
retrieving 1 resource
loading from cache
see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for documentation
loading from cache
see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for documentation
loading from cache
see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for documentation
loading from cache
see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for documentation
loading from cache
see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for documentation
loading from cache
[E::hts_idx_load3] Could not load local index file 'E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp2F1Kb1/s32gDNA0.bai' : Invalid argument
[E::hts_idx_load3] Could not load local index file 'E:\biocbuild\bbs-3.21-bioc\tmpdir\Rtmp2F1Kb1/s32gDNA0' : No such file or directory
Timing stopped at: 0.05 0 0.05
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'obj' in selecting a method for function 'unname': isOpen(<BamFile>) is not 'TRUE'


RUNIT TEST PROTOCOL -- Sat Feb 15 01:32:38 2025 
*********************************************** 
Number of test functions: 4 
Number of errors: 2 
Number of failures: 0 

 
1 Test Suite : 
gDNAx RUnit Tests - 4 test functions, 2 errors, 0 failures
ERROR in E:/biocbuild/bbs-3.21-bioc/R/library/gDNAx/unitTests/test_dx.R: Error while sourcing  E:/biocbuild/bbs-3.21-bioc/R/library/gDNAx/unitTests/test_dx.R : Error : failed to load resource
  name: EH8087
  title: RNA-seq data BAM file subset of HRR589625 contaminated with 10% gDNA
  reason: 2 resources failed to download
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