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This page was generated on 2023-10-20 09:37:59 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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Package 238/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BRGenomics 1.12.0  (landing page)
Mike DeBerardine
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/BRGenomics
git_branch: RELEASE_3_17
git_last_commit: f73b855
git_last_commit_date: 2023-04-25 13:08:10 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    ERROR    OK  

CHECK results for BRGenomics on kjohnson2


To the developers/maintainers of the BRGenomics package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: BRGenomics
Version: 1.12.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BRGenomics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BRGenomics_1.12.0.tar.gz
StartedAt: 2023-10-17 06:45:36 -0400 (Tue, 17 Oct 2023)
EndedAt: 2023-10-17 06:56:04 -0400 (Tue, 17 Oct 2023)
EllapsedTime: 628.0 seconds
RetCode: 1
Status:   ERROR  
CheckDir: BRGenomics.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:BRGenomics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings BRGenomics_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/BRGenomics.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 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 13.158  0.267  20.666
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/BRGenomics.Rcheck/00check.log’
for details.


Installation output

BRGenomics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL BRGenomics
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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)

Tests output

BRGenomics.Rcheck/tests/testthat.Rout.fail


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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

Example timings

BRGenomics.Rcheck/BRGenomics-Ex.timings

nameusersystemelapsed
applyNFsGRanges0.3160.0160.491
binNdimensions0.4940.0200.790
bootstrap-signal-by-position0.4210.0200.679
genebodies0.2080.0080.332
getCountsByPositions0.5080.0140.796
getCountsByRegions0.2660.0160.434
getDESeqDataSet1.4030.0322.186
getDESeqResults13.158 0.26720.666
getMaxPositionsBySignal0.3230.0090.517
getPausingIndices0.7030.0211.122
getSpikeInCounts0.3860.2190.769
getSpikeInNFs0.6440.1861.194
getStrandedCoverage1.3560.1372.319
import-functions1.1100.0761.805
import_bam0.7270.0381.172
intersectByGene1.1590.0181.780
makeGRangesBRG0.3850.0050.597
mergeGRangesData1.3330.0242.078
mergeReplicates0.8420.0181.320
subsampleBySpikeIn0.8800.2671.638
subsampleGRanges0.0790.0140.137
subsetRegionsBySignal0.7980.0661.306
tidyChromosomes0.7890.1211.388