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### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:BRGenomics.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings BRGenomics_1.12.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/BRGenomics.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘BRGenomics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BRGenomics’ version ‘1.12.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BRGenomics’ 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 R 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 ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
getDESeqResults 9.753  0.676   10.43
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   14. │               └─GenomicRanges:::combine_seqinfo_from_GenomicRanges_objects(all_objects)
   15. │                 ├─BiocGenerics::do.call(merge, lapply(seq_len(x_len), function(i) seqinfo(x[[i]])))
   16. │                 ├─base::do.call(merge, lapply(seq_len(x_len), function(i) seqinfo(x[[i]])))
   17. │                 ├─base (local) `<stndrdGn>`(`<Seqinfo>`, `<Seqinfo>`, `<Seqinfo>`)
   18. │                 └─GenomeInfoDb (local) `<stndrdGn>`(`<Seqinfo>`, `<Seqinfo>`, `<Seqinfo>`)
   19. │                   └─GenomeInfoDb:::.merge_Seqinfo_objects(x, y, ...)
   20. │                     └─GenomeInfoDb:::.merge_two_Seqinfo_objects(x, y)
   21. │                       └─GenomeInfoDb:::mergeNamedAtomicVectors(...)
   22. │                         └─base::stop(msg)
   23. └─base::.handleSimpleError(...)
   24.   └─base (local) h(simpleError(msg, call))
  
  [ FAIL 2 | WARN 0 | SKIP 0 | PASS 572 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘AnalyzingMultipleDatasets.Rmd’ using ‘UTF-8’... OK
  ‘DESeq2WithGlobalPerturbations.Rmd’ using ‘UTF-8’... OK
  ‘GettingStarted.Rmd’ using ‘UTF-8’... OK
  ‘ImportingModifyingAnnotations.Rmd’ using ‘UTF-8’... OK
  ‘ImportingProcessingData.Rmd’ using ‘UTF-8’... OK
  ‘Overview.Rmd’ using ‘UTF-8’... OK
  ‘ProfilePlotsAndBootstrapping.Rmd’ using ‘UTF-8’... OK
  ‘SequenceExtraction.Rmd’ using ‘UTF-8’... OK
  ‘SignalCounting.Rmd’ using ‘UTF-8’... OK
  ‘SpikeInNormalization.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/BRGenomics.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL BRGenomics
###
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* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘BRGenomics’ ...
** using staged installation
** R
** data
** 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 (BRGenomics)

R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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.

> Sys.setenv("R_TESTS" = "")
> library(testthat)
> library(BRGenomics)
Loading required package: rtracklayer
Loading required package: GenomicRanges
Loading required package: stats4
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, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

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
> 
> test_check("BRGenomics")
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 572 ]

══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_spikein_and_normalization.R:214:5'): can spike-in normalize a GRanges with field = NULL ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'sort': sequences chr1, chr2, spikechr1, spikechr2 have incompatible seqlengths:
  - in 'x': 1, 2, 3, 4
  - in 'y': 0, 0, 0, 0
Backtrace:
     ▆
  1. ├─testthat::expect_message(...) at test_spikein_and_normalization.R:214:4
  2. │ └─testthat:::quasi_capture(enquo(object), label, capture_messages)
  3. │   ├─testthat (local) .capture(...)
  4. │   │ └─base::withCallingHandlers(...)
  5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  6. ├─BRGenomics::spikeInNormGRanges(...)
  7. │ └─BRGenomics::applyNFsGRanges(...)
  8. │   └─parallel::mclapply(...)
  9. │     └─base::lapply(X = X, FUN = FUN, ...)
 10. │       └─BRGenomics (local) FUN(X[[i]], ...)
 11. │         ├─BiocGenerics::sort(do.call(c, cvg_ls))
 12. │         ├─BiocGenerics::do.call(c, cvg_ls)
 13. │         ├─base::do.call(c, cvg_ls)
 14. │         ├─methods (local) `<fn>`(`<GRanges>`, `<GRanges>`, `<GRanges>`)
 15. │         └─S4Vectors (local) `<fn>`(`<GRanges>`, `<GRanges>`, `<GRanges>`)
 16. │           └─S4Vectors (local) .local(x, ...)
 17. │             ├─S4Vectors::bindROWS(x, list(...), ignore.mcols = ignore.mcols)
 18. │             └─GenomicRanges::bindROWS(x, list(...), ignore.mcols = ignore.mcols)
 19. │               └─GenomicRanges:::combine_seqinfo_from_GenomicRanges_objects(all_objects)
 20. │                 ├─BiocGenerics::do.call(merge, lapply(seq_len(x_len), function(i) seqinfo(x[[i]])))
 21. │                 ├─base::do.call(merge, lapply(seq_len(x_len), function(i) seqinfo(x[[i]])))
 22. │                 ├─base (local) `<stndrdGn>`(`<Seqinfo>`, `<Seqinfo>`, `<Seqinfo>`)
 23. │                 └─GenomeInfoDb (local) `<stndrdGn>`(`<Seqinfo>`, `<Seqinfo>`, `<Seqinfo>`)
 24. │                   └─GenomeInfoDb:::.merge_Seqinfo_objects(x, y, ...)
 25. │                     └─GenomeInfoDb:::.merge_two_Seqinfo_objects(x, y)
 26. │                       └─GenomeInfoDb:::mergeNamedAtomicVectors(...)
 27. │                         └─base::stop(msg)
 28. └─base::.handleSimpleError(...)
 29.   └─base (local) h(simpleError(msg, call))
── Error ('test_spikein_and_normalization.R:280:5'): can subsample with field = NULL and RPM_units ──
Error in `h(simpleError(msg, call))`: error in evaluating the argument 'x' in selecting a method for function 'sort': sequences chr1, chr2 have incompatible seqlengths:
  - in 'x': 1, 2
  - in 'y': 0, 0
Backtrace:
     ▆
  1. ├─BRGenomics::subsampleBySpikeIn(...) at test_spikein_and_normalization.R:280:4
  2. │ └─BRGenomics::applyNFsGRanges(...)
  3. │   └─parallel::mclapply(...)
  4. │     └─base::lapply(X = X, FUN = FUN, ...)
  5. │       └─BRGenomics (local) FUN(X[[i]], ...)
  6. │         ├─BiocGenerics::sort(do.call(c, cvg_ls))
  7. │         ├─BiocGenerics::do.call(c, cvg_ls)
  8. │         ├─base::do.call(c, cvg_ls)
  9. │         ├─methods (local) `<fn>`(`<GRanges>`, `<GRanges>`, `<GRanges>`)
 10. │         └─S4Vectors (local) `<fn>`(`<GRanges>`, `<GRanges>`, `<GRanges>`)
 11. │           └─S4Vectors (local) .local(x, ...)
 12. │             ├─S4Vectors::bindROWS(x, list(...), ignore.mcols = ignore.mcols)
 13. │             └─GenomicRanges::bindROWS(x, list(...), ignore.mcols = ignore.mcols)
 14. │               └─GenomicRanges:::combine_seqinfo_from_GenomicRanges_objects(all_objects)
 15. │                 ├─BiocGenerics::do.call(merge, lapply(seq_len(x_len), function(i) seqinfo(x[[i]])))
 16. │                 ├─base::do.call(merge, lapply(seq_len(x_len), function(i) seqinfo(x[[i]])))
 17. │                 ├─base (local) `<stndrdGn>`(`<Seqinfo>`, `<Seqinfo>`, `<Seqinfo>`)
 18. │                 └─GenomeInfoDb (local) `<stndrdGn>`(`<Seqinfo>`, `<Seqinfo>`, `<Seqinfo>`)
 19. │                   └─GenomeInfoDb:::.merge_Seqinfo_objects(x, y, ...)
 20. │                     └─GenomeInfoDb:::.merge_two_Seqinfo_objects(x, y)
 21. │                       └─GenomeInfoDb:::mergeNamedAtomicVectors(...)
 22. │                         └─base::stop(msg)
 23. └─base::.handleSimpleError(...)
 24.   └─base (local) h(simpleError(msg, call))

[ FAIL 2 | WARN 0 | SKIP 0 | PASS 572 ]
Error: Test failures
Execution halted