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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:gDNAx.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings gDNAx_1.3.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/gDNAx.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gDNAx/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gDNAx’ version ‘1.3.0’
* 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 ‘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 loading without being on the library search path ... 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

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, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
    union, 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: 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
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
see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for documentation
loading from cache
see ?gDNAinRNAseqData and browseVignettes('gDNAinRNAseqData') for documentation
loading from cache
> bamfiles <- bamfiles[c(1,7)] # using a subset of samples
> gdnax <- gDNAdx(bamfiles, txdb, singleEnd=FALSE, strandMode=NA)
ℹ Library layout: paired-end, 2 (2x50nt).
ℹ Fetching gene-level annotations for hg38
ℹ Fetching RepeatMasker annotations for hg38
Warning: download failed
  web resource path: ‘https://annotationhub.bioconductor.org/fetch/118079’
  local file path: ‘/home/biocbuild/.cache/R/AnnotationHub/file229d093e4fdf11’
  reason: Internal Server Error (HTTP 500).
Warning: bfcdownload() failed
  rid: BFC37
  file: ‘https://annotationhub.bioconductor.org/fetch/118079’
  reason: download failed
Warning: download failed
  hub path: ‘https://annotationhub.bioconductor.org/fetch/118079’
  cache resource: ‘AH111333 : 118079’
  reason: download failed; see warnings()
Error: failed to load resource
  name: AH111333
  title: UCSC RepeatMasker annotations (Oct2022) for Human (hg38)
  reason: 1 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:
  gDNAx RUnit Tests - 7 test functions, 1 error, 0 failures
  ERROR in test_gDNAdx: Error : failed to load resource
    name: AH111333
    title: UCSC RepeatMasker annotations (Oct2022) for Human (hg38)
    reason: 1 resources failed to download
  
  Test files with failing tests
  
     test_dx.R 
       test_gDNAdx 
  
  
  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
  ‘/home/biocbuild/bbs-3.20-bioc/meat/gDNAx.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL gDNAx
###
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* installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’
* installing *source* package ‘gDNAx’ ...
** 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 version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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.

> 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

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, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
    union, 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: 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
Could not check id: EH8079 for updates.
  Using previously cached version.
loading from cache
require("Rsamtools")
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
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
! 2 BAM files had < 200000 alignments overlapping exonic regions
Timing stopped at: 25.64 1.561 42.11
Error : failed to load resource
  name: AH111333
  title: UCSC RepeatMasker annotations (Oct2022) for Human (hg38)
  reason: 1 resources failed to download
In addition: Warning messages:
1: download failed
  web resource path: 'https://annotationhub.bioconductor.org/fetch/118079'
  local file path: '/home/biocbuild/.cache/R/AnnotationHub/file22c137661f3862'
  reason: Internal Server Error (HTTP 500). 
2: bfcdownload() failed
  rid: BFC37
  file: 'https://annotationhub.bioconductor.org/fetch/118079'
  reason: download failed 
3: download failed
  hub path: 'https://annotationhub.bioconductor.org/fetch/118079'
  cache resource: 'AH111333 : 118079'
  reason: download failed; see warnings() 
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
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
Estimating strandedness ■■■■■■■■■■■■■■■■                  50% | ETA:  2s
Estimating strandedness ■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■■  100% | ETA:  0s
! 2 BAM files had < 200000 alignments overlapping exonic regions


RUNIT TEST PROTOCOL -- Sat Jul  6 05:19:04 2024 
*********************************************** 
Number of test functions: 7 
Number of errors: 1 
Number of failures: 0 

 
1 Test Suite : 
gDNAx RUnit Tests - 7 test functions, 1 error, 0 failures
ERROR in test_gDNAdx: Error : failed to load resource
  name: AH111333
  title: UCSC RepeatMasker annotations (Oct2022) for Human (hg38)
  reason: 1 resources failed to download

Test files with failing tests

   test_dx.R 
     test_gDNAdx 


Error in BiocGenerics:::testPackage("gDNAx") : 
  unit tests failed for package gDNAx
Execution halted