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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:VplotR.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings VplotR_1.18.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/VplotR.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘VplotR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘VplotR’ version ‘1.18.0’
* 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 ‘VplotR’ can be installed ... OK
* checking installed package size ... INFO
  installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data      2.9Mb
    figures   2.1Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... 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
nucleosomeEnrichment.GRanges 10.699  1.745  12.445
nucleosomeEnrichment.Vmat     6.289  1.052   7.343
nucleosomeEnrichment          5.418  1.062   6.481
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘VplotR.Rmd’ using rmarkdown

Quitting from VplotR.Rmd:214-224 [unnamed-chunk-11]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `do.call()`:
! replacement has length zero
---
Backtrace:
     ▆
  1. ├─VplotR::plotVmat(...)
  2. └─VplotR:::plotVmat.list(...)
  3.   └─parallel::mclapply(...)
  4.     └─base::lapply(X = X, FUN = FUN, ...)
  5.       └─VplotR (local) FUN(X[[i]], ...)
  6.         ├─VplotR::plotVmat(...)
  7.         └─VplotR:::plotVmat.GRanges(...)
  8.           └─VplotR::computeVmat(...)
  9.             ├─methods (local) `[<-`(`*tmp*`, filt, value = `<GRanges>`)
 10.             └─S4Vectors (local) `[<-`(`*tmp*`, filt, value = `<GRanges>`)
 11.               ├─methods::callNextMethod(x, i, value = value)
 12.               │ └─base::eval(call, callEnv)
 13.               │   └─base::eval(call, callEnv)
 14.               └─S4Vectors (local) .nextMethod(x, i, value = value)
 15.                 ├─S4Vectors::mergeROWS(x, i, value)
 16.                 └─S4Vectors::mergeROWS(x, i, value)
 17.                   ├─S4Vectors::replaceROWS(x, nsbs, value)
 18.                   └─GenomicRanges (local) replaceROWS(x, nsbs, value)
 19.                     ├─S4Vectors::replaceROWS(...)
 20.                     └─S4Vectors::replaceROWS(...)
 21.                       └─S4Vectors:::.subassign_columns(x, nsbs, value)
 22.                         ├─BiocGenerics::lapply(...)
 23.                         └─base::lapply(...)
 24.                           └─S4Vectors (local) FUN(X[[i]], ...)
 25.                             ├─S4Vectors (local) FUN(x[[j]], nsbs, value[[((j - 1L)%%value_ncol) + 1L]])
 26.                             └─S4Vectors (local) FUN(x[[j]], nsbs, value[[((j - 1L)%%value_ncol) + 1L]])
 27.                               ├─S4Vectors::mergeROWS(x, i, value)
 28.                               └─S4Vectors::mergeROWS(x, i, value)
 29.                                 ├─BiocGenerics::do.call(`[<-`, args)
 30.                                 └─base::do.call(`[<-`, args)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'VplotR.Rmd' failed with diagnostics:
replacement has length zero
--- failed re-building ‘VplotR.Rmd’

SUMMARY: processing the following file failed:
  ‘VplotR.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.21-bioc/meat/VplotR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL VplotR
###
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘VplotR’ ...
** this is package ‘VplotR’ version ‘1.18.0’
** 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 (VplotR)

R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-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.

> library(testthat)
> library(VplotR)
Loading required package: GenomicRanges
Loading required package: stats4
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

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: ggplot2
> 
> test_check("VplotR")
[ FAIL 0 | WARN 20 | SKIP 0 | PASS 4 ]

[ FAIL 0 | WARN 20 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
 65.208   3.916  69.125