Back to Multiple platform build/check report for BioC 3.22:   simplified   long
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This page was generated on 2025-08-06 13:57 -0400 (Wed, 06 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4813
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4550
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4592
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4534
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1878/2315HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scDblFinder 1.23.3  (landing page)
Pierre-Luc Germain
Snapshot Date: 2025-08-05 13:25 -0400 (Tue, 05 Aug 2025)
git_url: https://git.bioconductor.org/packages/scDblFinder
git_branch: devel
git_last_commit: c4e3ebc
git_last_commit_date: 2025-07-17 09:22:00 -0400 (Thu, 17 Jul 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


CHECK results for scDblFinder on kjohnson3

To the developers/maintainers of the scDblFinder package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scDblFinder.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: scDblFinder
Version: 1.23.3
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_1.23.3.tar.gz
StartedAt: 2025-08-05 21:25:41 -0400 (Tue, 05 Aug 2025)
EndedAt: 2025-08-05 21:28:01 -0400 (Tue, 05 Aug 2025)
EllapsedTime: 140.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: scDblFinder.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### 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_1.23.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/scDblFinder.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scDblFinder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scDblFinder’ version ‘1.23.3’
* 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
* 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.


Installation output

scDblFinder.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘scDblFinder’ ...
** this is package ‘scDblFinder’ version ‘1.23.3’
** 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)

Tests output

scDblFinder.Rcheck/tests/testthat.Rout


R version 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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:0.440600 
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 
[16]	train-logloss:0.006290 
[17]	train-logloss:0.005208 
[18]	train-logloss:0.004371 
[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 
[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 
[16]	train-logloss:0.006290 
[17]	train-logloss:0.005208 
[18]	train-logloss:0.004371 
[1]	train-logloss:0.440583 
Will train until train_logloss hasn't improved in 2 rounds.

[2]	train-logloss:0.300057 
[3]	train-logloss:0.211224 
[4]	train-logloss:0.151667 
[5]	train-logloss:0.110384 
[6]	train-logloss:0.081165 
[7]	train-logloss:0.060195 
[8]	train-logloss:0.044999 
[9]	train-logloss:0.033909 
[10]	train-logloss:0.025771 
[11]	train-logloss:0.019771 
[12]	train-logloss:0.015329 
[13]	train-logloss:0.012024 
[14]	train-logloss:0.009551 
[15]	train-logloss:0.007690 
[16]	train-logloss:0.006277 
[17]	train-logloss:0.005196 
[1]	train-logloss:0.440583 
Will train until train_logloss hasn't improved in 2 rounds.

[2]	train-logloss:0.300057 
[3]	train-logloss:0.211224 
[4]	train-logloss:0.151667 
[5]	train-logloss:0.110384 
[6]	train-logloss:0.081165 
[7]	train-logloss:0.060195 
[8]	train-logloss:0.044999 
[9]	train-logloss:0.033909 
[10]	train-logloss:0.025771 
[11]	train-logloss:0.019771 
[12]	train-logloss:0.015329 
[13]	train-logloss:0.012024 
[14]	train-logloss:0.009551 
[15]	train-logloss:0.007690 
[16]	train-logloss:0.006277 
[1]	train-logloss:0.440583 
Will train until train_logloss hasn't improved in 2 rounds.

[2]	train-logloss:0.300057 
[3]	train-logloss:0.211224 
[4]	train-logloss:0.151667 
[5]	train-logloss:0.110384 
[6]	train-logloss:0.081165 
[7]	train-logloss:0.060195 
[8]	train-logloss:0.044999 
[9]	train-logloss:0.033909 
[10]	train-logloss:0.025771 
[11]	train-logloss:0.019771 
[12]	train-logloss:0.015329 
[13]	train-logloss:0.012024 
[14]	train-logloss:0.009551 
[1]	train-logloss:0.451308 
Will train until train_logloss hasn't improved in 2 rounds.

[2]	train-logloss:0.315941 
[3]	train-logloss:0.229817 
[4]	train-logloss:0.170171 
[5]	train-logloss:0.129371 
[6]	train-logloss:0.100297 
[7]	train-logloss:0.079839 
[8]	train-logloss:0.063744 
[9]	train-logloss:0.051450 
[10]	train-logloss:0.041852 
[1]	train-logloss:0.456086 
Will train until train_logloss hasn't improved in 2 rounds.

[2]	train-logloss:0.321162 
[3]	train-logloss:0.235027 
[4]	train-logloss:0.177050 
[5]	train-logloss:0.134315 
[6]	train-logloss:0.104248 
[7]	train-logloss:0.081535 
[8]	train-logloss:0.065578 
[9]	train-logloss:0.053591 
[10]	train-logloss:0.044807 
[11]	train-logloss:0.036564 
[12]	train-logloss:0.031126 
[13]	train-logloss:0.027161 
[14]	train-logloss:0.023490 
[15]	train-logloss:0.021125 
[16]	train-logloss:0.018551 
[17]	train-logloss:0.016798 
[1]	train-logloss:0.456086 
Will train until train_logloss hasn't improved in 2 rounds.

[2]	train-logloss:0.321162 
[3]	train-logloss:0.235027 
[4]	train-logloss:0.177050 
[5]	train-logloss:0.134315 
[6]	train-logloss:0.104248 
[7]	train-logloss:0.081535 
[8]	train-logloss:0.065578 
[9]	train-logloss:0.053591 
[10]	train-logloss:0.044807 
[11]	train-logloss:0.036564 
[12]	train-logloss:0.031126 
[13]	train-logloss:0.027161 
[14]	train-logloss:0.023490 
[15]	train-logloss:0.021125 
[16]	train-logloss:0.018551 
[17]	train-logloss:0.016798 
[18]	train-logloss:0.015258 
[19]	train-logloss:0.013656 
[1]	train-logloss:0.454702 
Will train until train_logloss hasn't improved in 2 rounds.

[2]	train-logloss:0.321469 
[3]	train-logloss:0.235850 
[4]	train-logloss:0.177725 
[5]	train-logloss:0.134380 
[6]	train-logloss:0.103626 
[7]	train-logloss:0.081274 
[8]	train-logloss:0.064311 
[9]	train-logloss:0.051952 
[10]	train-logloss:0.042354 
[11]	train-logloss:0.035754 
[12]	train-logloss:0.030386 
[1]	train-logloss:0.457192 
Will train until train_logloss hasn't improved in 2 rounds.

[2]	train-logloss:0.324924 
[3]	train-logloss:0.235745 
[4]	train-logloss:0.178223 
[5]	train-logloss:0.137639 
[6]	train-logloss:0.107382 
[7]	train-logloss:0.084632 
[8]	train-logloss:0.066259 
[9]	train-logloss:0.053465 
[10]	train-logloss:0.043511 
[11]	train-logloss:0.035717 
[12]	train-logloss:0.030361 
[13]	train-logloss:0.026710 
[14]	train-logloss:0.023216 
[15]	train-logloss:0.020581 
[16]	train-logloss:0.017986 
[17]	train-logloss:0.016042 
[1]	train-logloss:0.458155 
Will train until train_logloss hasn't improved in 2 rounds.

[2]	train-logloss:0.326157 
[3]	train-logloss:0.236626 
[4]	train-logloss:0.177893 
[5]	train-logloss:0.136047 
[6]	train-logloss:0.107623 
[7]	train-logloss:0.085014 
[8]	train-logloss:0.068266 
[9]	train-logloss:0.055531 
[10]	train-logloss:0.045779 
[11]	train-logloss:0.038365 
[12]	train-logloss:0.031994 
[13]	train-logloss:0.027771 
[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 
 21.431   0.563  22.603 

Example timings

scDblFinder.Rcheck/scDblFinder-Ex.timings

nameusersystemelapsed
TFIDF0.0160.0010.017
addDoublets0.1140.0100.125
amulet0.6000.0050.641
amuletFromCounts0.1000.0010.121
clusterStickiness2.5910.0372.721
computeDoubletDensity1.6570.0231.717
createDoublets0.0860.0010.096
cxds20.1070.0020.111
directDblClassification0.7650.0180.810
doubletPairwiseEnrichment1.8650.0201.979
doubletThresholding2.6320.0322.694
fastcluster0.1970.0030.200
findDoubletClusters0.2450.0170.261
getArtificialDoublets0.0010.0000.001
getCellPairs0.0030.0000.002
getExpectedDoublets0.0010.0000.000
mockDoubletSCE0.0670.0020.069
propHomotypic000
recoverDoublets0.0680.0020.070
scDblFinder2.5630.0332.627
selFeatures0.0960.0010.097