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### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:miQC.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings miQC_1.17.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/miQC.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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 ‘miQC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘miQC’ version ‘1.17.0’
* 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 ‘miQC’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 ... 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 ... NOTE
prepare_Rd: metrics.Rd:7-9: Dropping empty section \format
* 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 LazyData ... 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
filterCells 15.116  0.848  15.965
* 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 ‘miQC.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/miQC.Rcheck/vign_test/miQC/vignettes/miQC_files/figure-html/unnamed-chunk-6-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/miQC.Rcheck/vign_test/miQC/vignettes/miQC_files/figure-html/unnamed-chunk-9-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/miQC.Rcheck/vign_test/miQC/vignettes/miQC_files/figure-html/unnamed-chunk-10-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/miQC.Rcheck/vign_test/miQC/vignettes/miQC_files/figure-html/unnamed-chunk-12-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/miQC.Rcheck/vign_test/miQC/vignettes/miQC_files/figure-html/unnamed-chunk-12-2.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/miQC.Rcheck/vign_test/miQC/vignettes/miQC_files/figure-html/unnamed-chunk-12-3.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/miQC.Rcheck/vign_test/miQC/vignettes/miQC_files/figure-html/unnamed-chunk-12-4.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/miQC.Rcheck/vign_test/miQC/vignettes/miQC_files/figure-html/unnamed-chunk-13-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/miQC.Rcheck/vign_test/miQC/vignettes/miQC_files/figure-html/unnamed-chunk-13-2.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/miQC.Rcheck/vign_test/miQC/vignettes/miQC_files/figure-html/unnamed-chunk-14-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/miQC.Rcheck/vign_test/miQC/vignettes/miQC_files/figure-html/unnamed-chunk-15-1.png" but not available.
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/miQC.Rcheck/vign_test/miQC/vignettes/miQC_files/figure-html/unnamed-chunk-16-1.png" but not available.

Quitting from miQC.Rmd:251-254 [unnamed-chunk-17]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `$<-.data.frame`:
! replacement has 1 row, data has 0
---
Backtrace:
    ▆
 1. └─miQC::plotFiltering(...)
 2.   ├─base::`$<-`(`*tmp*`, "keep", value = `<lgl>`)
 3.   └─base::`$<-.data.frame`(`*tmp*`, "keep", value = `<lgl>`)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'miQC.Rmd' failed with diagnostics:
replacement has 1 row, data has 0
--- failed re-building ‘miQC.Rmd’

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

Error: Vignette re-building failed.
Execution halted

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

Status: 1 ERROR, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/miQC.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL miQC
###
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘miQC’ ...
** this is package ‘miQC’ version ‘1.17.0’
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (miQC)