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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:scDblFinder.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings scDblFinder_1.24.8.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/scDblFinder.Rcheck’
* using R version 4.5.2 (2025-10-31)
* 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 ‘scDblFinder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scDblFinder’ version ‘1.24.8’
* 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 ‘scDblFinder’ 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotThresholds: no visible binding for global variable ‘threshold’
plotThresholds: no visible binding for global variable ‘value’
plotThresholds: no visible binding for global variable ‘variable’
Undefined global functions or variables:
  threshold value variable
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  computeDoubletDensity.Rd: SummarizedExperiment-class,
    SingleCellExperiment-class, sizeFactors, scran-gene-selection,
    BiocNeighborParam-class, queryNeighbors, BiocSingularParam-class,
    BiocParallelParam-class, librarySizeFactors
  findDoubletClusters.Rd: SummarizedExperiment-class,
    SingleCellExperiment-class, findMarkers, colLabels,
    scran-gene-selection, librarySizeFactors, DataFrame-class,
    SimpleList-class
  recoverDoublets.Rd: SummarizedExperiment-class,
    SingleCellExperiment-class, assays, reducedDims,
    BiocNeighborParam-class, BiocParallelParam-class, DataFrame-class,
    metadata, doubletCells, doubletCluster
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
doubletThresholding 5.935  0.514   4.717
scDblFinder         5.914  0.379   4.699
clusterStickiness   5.994  0.168   5.231
* 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 ‘computeDoubletDensity.Rmd’ using rmarkdown
Warning: call dbDisconnect() when finished working with a connection
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/scDblFinder.Rcheck/vign_test/scDblFinder/vignettes/computeDoubletDensity_files/figure-html/unnamed-chunk-4-1.png" but not available.
--- finished re-building ‘computeDoubletDensity.Rmd’

--- re-building ‘findDoubletClusters.Rmd’ using rmarkdown
Warning: call dbDisconnect() when finished working with a connection
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/scDblFinder.Rcheck/vign_test/scDblFinder/vignettes/findDoubletClusters_files/figure-html/unnamed-chunk-3-1.png" but not available.
--- finished re-building ‘findDoubletClusters.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
--- finished re-building ‘introduction.Rmd’

--- re-building ‘recoverDoublets.Rmd’ using rmarkdown
--- finished re-building ‘recoverDoublets.Rmd’

--- re-building ‘scATAC.Rmd’ using rmarkdown

Quitting from scATAC.Rmd:100-103 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.coerce_matrix_build()`:
! NA values are not supported
---
Backtrace:
     ▆
  1. └─scDblFinder::clamulet(fragfile, k = 2, nfeatures = 3)
  2.   └─scDblFinder:::.evaluateKNN(...)
  3.     ├─base::suppressWarnings(findKNN(as.matrix(pca), max(k), BNPARAM = AnnoyParam()))
  4.     │ └─base::withCallingHandlers(...)
  5.     ├─BiocNeighbors::findKNN(as.matrix(pca), max(k), BNPARAM = AnnoyParam())
  6.     └─BiocNeighbors::findKNN(as.matrix(pca), max(k), BNPARAM = AnnoyParam())
  7.       └─BiocNeighbors (local) .local(...)
  8.         ├─BiocNeighbors::buildIndex(X, ..., BNPARAM = BNPARAM)
  9.         └─BiocNeighbors::buildIndex(X, ..., BNPARAM = BNPARAM)
 10.           ├─methods::callGeneric(X, transposed = transposed, ..., BNPARAM = defineBuilder(BNPARAM))
 11.           │ └─base::eval(call, parent.frame())
 12.           │   └─base::eval(call, parent.frame())
 13.           ├─BiocNeighbors::buildIndex(X, transposed = transposed, ..., BNPARAM = defineBuilder(BNPARAM))
 14.           └─BiocNeighbors::buildIndex(X, transposed = transposed, ..., BNPARAM = defineBuilder(BNPARAM))
 15.             └─BiocNeighbors:::.coerce_matrix_build(X, transposed)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'scATAC.Rmd' failed with diagnostics:
NA values are not supported
--- failed re-building ‘scATAC.Rmd’

--- re-building ‘scDblFinder.Rmd’ using rmarkdown
The magick package is required to crop "/home/biocbuild/bbs-3.22-bioc/meat/scDblFinder.Rcheck/vign_test/scDblFinder/vignettes/scDblFinder_files/figure-html/unnamed-chunk-5-1.png" but not available.
--- finished re-building ‘scDblFinder.Rmd’

SUMMARY: processing the following file failed:
  ‘scATAC.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/scDblFinder.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL scDblFinder
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘scDblFinder’ ...
** this is package ‘scDblFinder’ version ‘1.24.8’
** 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 (scDblFinder)

R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
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(scDblFinder)
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

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: Seqinfo
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")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

> test_check("scDblFinder")
[ FAIL 0 | WARN 8 | SKIP 0 | PASS 107 ]

[ FAIL 0 | WARN 8 | SKIP 0 | PASS 107 ]
> 
> proc.time()
   user  system elapsed 
 58.480   2.559  59.006