##############################################################################
##############################################################################
###
### 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_1.23.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/scDblFinder.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 ‘scDblFinder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scDblFinder’ version ‘1.23.4’
* 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 ... WARNING
Missing or unexported object: ‘xgboost::xgb.params’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.xgbtrain: no visible global function definition for ‘packageVersion’
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:
  packageVersion threshold value variable
Consider adding
  importFrom("utils", "packageVersion")
to your NAMESPACE file.
* 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
clusterStickiness         41.461  0.194   6.369
scDblFinder               40.772  0.371   6.409
doubletThresholding       40.532  0.215   6.073
doubletPairwiseEnrichment 36.997  0.108   5.041
directDblClassification   14.597  0.029   2.006
* 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 ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 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
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘scDblFinder’ ...
** this is package ‘scDblFinder’ version ‘1.23.4’
** 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 4.5.1 Patched (2025-08-23 r88802) -- "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(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")
[1]	train-logloss:0.440600 
Will train until train_logloss hasn't improved in 2 rounds.

[2]	train-logloss:0.300078 
[3]	train-logloss:0.211246 
[4]	train-logloss:0.151689 
[5]	train-logloss:0.110405 
[6]	train-logloss:0.081185 
[7]	train-logloss:0.060214 
[8]	train-logloss:0.045017 
[9]	train-logloss:0.033927 
[10]	train-logloss:0.025788 
[11]	train-logloss:0.019788 
[12]	train-logloss:0.015345 
[13]	train-logloss:0.012039 
[14]	train-logloss:0.009565 
[15]	train-logloss:0.007703 
[1]	train-logloss:0.440600 
Will train until train_logloss hasn't improved in 2 rounds.

[2]	train-logloss:0.300078 
[3]	train-logloss:0.211246 
[4]	train-logloss:0.151689 
[5]	train-logloss:0.110405 
[6]	train-logloss:0.081185 
[7]	train-logloss:0.060214 
[8]	train-logloss:0.045017 
[9]	train-logloss:0.033927 
[10]	train-logloss:0.025788 
[11]	train-logloss:0.019788 
[12]	train-logloss:0.015345 
[13]	train-logloss:0.012039 
[14]	train-logloss:0.009565 
[1]	train-logloss:0.440600 
Will train until train_logloss hasn't improved in 2 rounds.

[2]	train-logloss:0.300078 
[3]	train-logloss:0.211246 
[4]	train-logloss:0.151689 
[5]	train-logloss:0.110405 
[6]	train-logloss:0.081185 
[7]	train-logloss:0.060214 
[8]	train-logloss:0.045017 
[9]	train-logloss:0.033927 
[10]	train-logloss:0.025788 
[11]	train-logloss:0.019788 
[12]	train-logloss:0.015345 
[13]	train-logloss:0.012039 
[14]	train-logloss:0.009565 
[15]	train-logloss:0.007703 
[1]	train-logloss:0.440589 
Will train until train_logloss hasn't improved in 2 rounds.

[2]	train-logloss:0.300064 
[3]	train-logloss:0.211231 
[4]	train-logloss:0.151674 
[5]	train-logloss:0.110391 
[6]	train-logloss:0.081172 
[7]	train-logloss:0.060201 
[8]	train-logloss:0.045005 
[9]	train-logloss:0.033915 
[10]	train-logloss:0.025777 
[11]	train-logloss:0.019777 
[12]	train-logloss:0.015334 
[13]	train-logloss:0.012029 
[14]	train-logloss:0.009556 
[15]	train-logloss:0.007694 
[16]	train-logloss:0.006282 
[1]	train-logloss:0.440589 
Will train until train_logloss hasn't improved in 2 rounds.

[2]	train-logloss:0.300064 
[3]	train-logloss:0.211231 
[4]	train-logloss:0.151674 
[5]	train-logloss:0.110391 
[6]	train-logloss:0.081172 
[7]	train-logloss:0.060201 
[8]	train-logloss:0.045005 
[9]	train-logloss:0.033915 
[10]	train-logloss:0.025777 
[11]	train-logloss:0.019777 
[12]	train-logloss:0.015334 
[13]	train-logloss:0.012029 
[14]	train-logloss:0.009556 
[15]	train-logloss:0.007694 
[1]	train-logloss:0.440589 
Will train until train_logloss hasn't improved in 2 rounds.

[2]	train-logloss:0.300064 
[3]	train-logloss:0.211231 
[4]	train-logloss:0.151674 
[5]	train-logloss:0.110391 
[6]	train-logloss:0.081172 
[7]	train-logloss:0.060201 
[8]	train-logloss:0.045005 
[9]	train-logloss:0.033915 
[10]	train-logloss:0.025777 
[11]	train-logloss:0.019777 
[12]	train-logloss:0.015334 
[13]	train-logloss:0.012029 
[14]	train-logloss:0.009556 
[1]	train-logloss:0.449158 
Will train until train_logloss hasn't improved in 2 rounds.

[2]	train-logloss:0.313813 
[3]	train-logloss:0.227885 
[4]	train-logloss:0.170290 
[5]	train-logloss:0.129553 
[6]	train-logloss:0.100109 
[7]	train-logloss:0.078563 
[8]	train-logloss:0.062003 
[9]	train-logloss:0.049638 
[10]	train-logloss:0.039590 
[11]	train-logloss:0.032235 
[12]	train-logloss:0.027060 
[13]	train-logloss:0.023087 
[14]	train-logloss:0.019677 
[1]	train-logloss:0.449584 
Will train until train_logloss hasn't improved in 2 rounds.

[2]	train-logloss:0.313727 
[3]	train-logloss:0.227324 
[4]	train-logloss:0.169328 
[5]	train-logloss:0.128216 
[6]	train-logloss:0.099005 
[7]	train-logloss:0.077684 
[8]	train-logloss:0.060846 
[9]	train-logloss:0.048352 
[10]	train-logloss:0.039617 
[11]	train-logloss:0.032679 
[12]	train-logloss:0.028292 
[1]	train-logloss:0.452688 
Will train until train_logloss hasn't improved in 2 rounds.

[2]	train-logloss:0.318154 
[3]	train-logloss:0.232756 
[4]	train-logloss:0.173681 
[5]	train-logloss:0.132427 
[6]	train-logloss:0.101868 
[7]	train-logloss:0.079012 
[8]	train-logloss:0.063157 
[9]	train-logloss:0.050077 
[10]	train-logloss:0.040462 
[11]	train-logloss:0.033822 
[12]	train-logloss:0.028594 
[13]	train-logloss:0.024852 
[14]	train-logloss:0.021757 
[15]	train-logloss:0.019060 
[16]	train-logloss:0.016949 
[1]	train-logloss:0.455094 
Will train until train_logloss hasn't improved in 2 rounds.

[2]	train-logloss:0.319546 
[3]	train-logloss:0.234671 
[4]	train-logloss:0.177233 
[5]	train-logloss:0.136376 
[6]	train-logloss:0.106647 
[7]	train-logloss:0.082335 
[8]	train-logloss:0.067515 
[9]	train-logloss:0.053841 
[10]	train-logloss:0.044397 
[11]	train-logloss:0.037282 
[12]	train-logloss:0.031340 
[13]	train-logloss:0.026841 
[14]	train-logloss:0.023606 
[1]	train-logloss:0.454219 
Will train until train_logloss hasn't improved in 2 rounds.

[2]	train-logloss:0.318805 
[3]	train-logloss:0.232689 
[4]	train-logloss:0.175413 
[5]	train-logloss:0.134283 
[6]	train-logloss:0.105106 
[7]	train-logloss:0.084055 
[8]	train-logloss:0.067470 
[9]	train-logloss:0.056171 
[10]	train-logloss:0.046074 
[11]	train-logloss:0.037976 
[12]	train-logloss:0.031842 
[13]	train-logloss:0.027292 
[14]	train-logloss:0.023804 
[15]	train-logloss:0.020586 
[1]	train-logloss:0.455563 
Will train until train_logloss hasn't improved in 2 rounds.

[2]	train-logloss:0.320917 
[3]	train-logloss:0.235315 
[4]	train-logloss:0.175218 
[5]	train-logloss:0.133877 
[6]	train-logloss:0.104099 
[7]	train-logloss:0.083106 
[8]	train-logloss:0.065957 
[9]	train-logloss:0.053588 
[10]	train-logloss:0.044815 
[11]	train-logloss:0.037935 
[12]	train-logloss:0.032378 
[13]	train-logloss:0.027686 
[14]	train-logloss:0.024314 
[15]	train-logloss:0.021484 
[1]	train-logloss:0.439549 
Will train until train_logloss hasn't improved in 2 rounds.

[2]	train-logloss:0.298794 
[3]	train-logloss:0.209914 
[4]	train-logloss:0.150369 
[5]	train-logloss:0.109118 
[6]	train-logloss:0.079937 
[7]	train-logloss:0.059007 
[8]	train-logloss:0.043851 
[9]	train-logloss:0.032800 
[10]	train-logloss:0.024702 
[11]	train-logloss:0.018742 
[12]	train-logloss:0.014341 
[13]	train-logloss:0.011080 
[14]	train-logloss:0.008653 
[15]	train-logloss:0.006840 
[16]	train-logloss:0.005477 
[1]	train-logloss:0.439549 
Will train until train_logloss hasn't improved in 2 rounds.

[2]	train-logloss:0.298794 
[3]	train-logloss:0.209914 
[4]	train-logloss:0.150369 
[5]	train-logloss:0.109118 
[6]	train-logloss:0.079937 
[7]	train-logloss:0.059007 
[8]	train-logloss:0.043851 
[9]	train-logloss:0.032800 
[10]	train-logloss:0.024702 
[11]	train-logloss:0.018742 
[12]	train-logloss:0.014341 
[13]	train-logloss:0.011080 
[14]	train-logloss:0.008653 
[1]	train-logloss:0.439549 
Will train until train_logloss hasn't improved in 2 rounds.

[2]	train-logloss:0.298794 
[3]	train-logloss:0.209914 
[4]	train-logloss:0.150369 
[5]	train-logloss:0.109118 
[6]	train-logloss:0.079937 
[7]	train-logloss:0.059007 
[8]	train-logloss:0.043851 
[9]	train-logloss:0.032800 
[10]	train-logloss:0.024702 
[11]	train-logloss:0.018742 
[12]	train-logloss:0.014341 
[13]	train-logloss:0.011080 
[14]	train-logloss:0.008653 
[ FAIL 0 | WARN 8 | SKIP 0 | PASS 104 ]

[ FAIL 0 | WARN 8 | SKIP 0 | PASS 104 ]
> 
> proc.time()
   user  system elapsed 
229.469   2.433  66.449