##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:scDblFinder.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings scDblFinder_1.23.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/scDblFinder.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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 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   5.987  0.126   6.165
doubletThresholding 5.508  0.097   5.635
scDblFinder         5.218  0.096   5.565
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/scDblFinder.Rcheck/00check.log’
for details.

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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 (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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:0.442237 
Will train until train_logloss hasn't improved in 2 rounds.

[2]	train-logloss:0.302439 
[3]	train-logloss:0.213908 
[4]	train-logloss:0.154604 
[5]	train-logloss:0.113460 
[6]	train-logloss:0.084337 
[7]	train-logloss:0.063431 
[8]	train-logloss:0.047922 
[9]	train-logloss:0.036842 
[10]	train-logloss:0.028686 
[11]	train-logloss:0.022669 
[12]	train-logloss:0.018148 
[13]	train-logloss:0.014760 
[14]	train-logloss:0.012206 
[15]	train-logloss:0.010226 
[16]	train-logloss:0.008645 
[1]	train-logloss:0.442237 
Will train until train_logloss hasn't improved in 2 rounds.

[2]	train-logloss:0.302439 
[3]	train-logloss:0.213908 
[4]	train-logloss:0.154604 
[5]	train-logloss:0.113460 
[6]	train-logloss:0.084337 
[7]	train-logloss:0.063431 
[8]	train-logloss:0.047922 
[9]	train-logloss:0.036842 
[10]	train-logloss:0.028686 
[11]	train-logloss:0.022669 
[12]	train-logloss:0.018148 
[13]	train-logloss:0.014760 
[14]	train-logloss:0.012206 
[15]	train-logloss:0.010226 
[1]	train-logloss:0.442237 
Will train until train_logloss hasn't improved in 2 rounds.

[2]	train-logloss:0.302439 
[3]	train-logloss:0.213908 
[4]	train-logloss:0.154604 
[5]	train-logloss:0.113460 
[6]	train-logloss:0.084337 
[7]	train-logloss:0.063431 
[8]	train-logloss:0.047922 
[9]	train-logloss:0.036842 
[10]	train-logloss:0.028686 
[11]	train-logloss:0.022669 
[12]	train-logloss:0.018148 
[13]	train-logloss:0.014760 
[14]	train-logloss:0.012206 
[15]	train-logloss:0.010226 
[1]	train-logloss:0.442211 
Will train until train_logloss hasn't improved in 2 rounds.

[2]	train-logloss:0.302265 
[3]	train-logloss:0.213550 
[4]	train-logloss:0.153976 
[5]	train-logloss:0.112617 
[6]	train-logloss:0.083303 
[7]	train-logloss:0.062165 
[8]	train-logloss:0.046820 
[9]	train-logloss:0.035586 
[10]	train-logloss:0.027316 
[11]	train-logloss:0.021198 
[12]	train-logloss:0.016642 
[13]	train-logloss:0.013232 
[14]	train-logloss:0.010665 
[1]	train-logloss:0.442211 
Will train until train_logloss hasn't improved in 2 rounds.

[2]	train-logloss:0.302265 
[3]	train-logloss:0.213550 
[4]	train-logloss:0.153976 
[5]	train-logloss:0.112617 
[6]	train-logloss:0.083303 
[7]	train-logloss:0.062165 
[8]	train-logloss:0.046820 
[9]	train-logloss:0.035586 
[10]	train-logloss:0.027316 
[11]	train-logloss:0.021198 
[12]	train-logloss:0.016642 
[1]	train-logloss:0.442211 
Will train until train_logloss hasn't improved in 2 rounds.

[2]	train-logloss:0.302265 
[3]	train-logloss:0.213550 
[4]	train-logloss:0.153976 
[5]	train-logloss:0.112617 
[6]	train-logloss:0.083303 
[7]	train-logloss:0.062165 
[8]	train-logloss:0.046820 
[9]	train-logloss:0.035586 
[10]	train-logloss:0.027316 
[11]	train-logloss:0.021198 
[12]	train-logloss:0.016642 
[13]	train-logloss:0.013232 
[14]	train-logloss:0.010665 
[1]	train-logloss:0.453884 
Will train until train_logloss hasn't improved in 2 rounds.

[2]	train-logloss:0.321525 
[3]	train-logloss:0.231890 
[4]	train-logloss:0.171395 
[5]	train-logloss:0.129186 
[6]	train-logloss:0.097833 
[7]	train-logloss:0.075894 
[8]	train-logloss:0.059270 
[9]	train-logloss:0.048084 
[10]	train-logloss:0.038316 
[11]	train-logloss:0.031248 
[12]	train-logloss:0.025772 
[13]	train-logloss:0.022258 
[14]	train-logloss:0.019244 
[1]	train-logloss:0.454712 
Will train until train_logloss hasn't improved in 2 rounds.

[2]	train-logloss:0.322273 
[3]	train-logloss:0.232598 
[4]	train-logloss:0.172259 
[5]	train-logloss:0.130047 
[6]	train-logloss:0.099342 
[7]	train-logloss:0.076270 
[8]	train-logloss:0.059699 
[9]	train-logloss:0.048487 
[10]	train-logloss:0.038578 
[11]	train-logloss:0.031574 
[12]	train-logloss:0.027037 
[13]	train-logloss:0.023123 
[14]	train-logloss:0.020266 
[1]	train-logloss:0.454712 
Will train until train_logloss hasn't improved in 2 rounds.

[2]	train-logloss:0.322273 
[3]	train-logloss:0.232598 
[4]	train-logloss:0.172259 
[5]	train-logloss:0.130047 
[6]	train-logloss:0.099342 
[7]	train-logloss:0.076270 
[8]	train-logloss:0.059699 
[9]	train-logloss:0.048487 
[10]	train-logloss:0.038578 
[11]	train-logloss:0.031574 
[12]	train-logloss:0.027037 
[13]	train-logloss:0.023123 
[14]	train-logloss:0.020266 
[1]	train-logloss:0.445853 
Will train until train_logloss hasn't improved in 2 rounds.

[2]	train-logloss:0.307105 
[3]	train-logloss:0.218716 
[4]	train-logloss:0.159981 
[5]	train-logloss:0.119131 
[6]	train-logloss:0.089172 
[7]	train-logloss:0.068185 
[8]	train-logloss:0.052186 
[9]	train-logloss:0.040506 
[10]	train-logloss:0.032115 
[11]	train-logloss:0.025570 
[12]	train-logloss:0.020905 
[13]	train-logloss:0.017405 
[14]	train-logloss:0.014559 
[1]	train-logloss:0.445760 
Will train until train_logloss hasn't improved in 2 rounds.

[2]	train-logloss:0.307027 
[3]	train-logloss:0.218609 
[4]	train-logloss:0.159682 
[5]	train-logloss:0.118928 
[6]	train-logloss:0.089762 
[7]	train-logloss:0.068592 
[8]	train-logloss:0.052595 
[9]	train-logloss:0.041086 
[10]	train-logloss:0.032291 
[11]	train-logloss:0.026026 
[12]	train-logloss:0.021215 
[13]	train-logloss:0.017574 
[14]	train-logloss:0.014815 
[15]	train-logloss:0.012482 
[16]	train-logloss:0.011189 
[17]	train-logloss:0.010128 
[1]	train-logloss:0.445760 
Will train until train_logloss hasn't improved in 2 rounds.

[2]	train-logloss:0.307027 
[3]	train-logloss:0.218609 
[4]	train-logloss:0.159682 
[5]	train-logloss:0.118928 
[6]	train-logloss:0.089762 
[7]	train-logloss:0.068592 
[8]	train-logloss:0.052595 
[9]	train-logloss:0.041086 
[10]	train-logloss:0.032291 
[11]	train-logloss:0.026026 
[12]	train-logloss:0.021215 
[13]	train-logloss:0.017574 
[14]	train-logloss:0.014815 
[15]	train-logloss:0.012482 
[16]	train-logloss:0.011189 
[17]	train-logloss:0.010128 
[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 
 58.244   2.120  60.914