Back to Multiple platform build/check report for BioC 3.22:   simplified   long
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This page was generated on 2025-08-12 12:13 -0400 (Tue, 12 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4553
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4537
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4535
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 1880/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scDblFinder 1.23.3  (landing page)
Pierre-Luc Germain
Snapshot Date: 2025-08-11 13:45 -0400 (Mon, 11 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
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    WARNINGS  


CHECK results for scDblFinder on taishan

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: scDblFinder
Version: 1.23.3
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:scDblFinder.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings scDblFinder_1.23.3.tar.gz
StartedAt: 2025-08-12 10:41:14 -0000 (Tue, 12 Aug 2025)
EndedAt: 2025-08-12 10:48:27 -0000 (Tue, 12 Aug 2025)
EllapsedTime: 432.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: scDblFinder.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:scDblFinder.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings scDblFinder_1.23.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/scDblFinder.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* 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 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   6.135  0.200   6.321
scDblFinder         5.686  0.106   5.766
doubletThresholding 5.662  0.088   5.738
* 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
  ‘/home/biocbuild/bbs-3.22-bioc/meat/scDblFinder.Rcheck/00check.log’
for details.


Installation output

scDblFinder.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL scDblFinder
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 
[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 
[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 
[19]	train-logloss:0.003716 
[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 
[19]	train-logloss:0.003716 
[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 
[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 
[15]	train-logloss:0.007690 
[1]	train-logloss:0.450689 
Will train until train_logloss hasn't improved in 2 rounds.

[2]	train-logloss:0.314965 
[3]	train-logloss:0.229017 
[4]	train-logloss:0.171044 
[5]	train-logloss:0.130286 
[6]	train-logloss:0.100595 
[7]	train-logloss:0.077712 
[8]	train-logloss:0.061626 
[9]	train-logloss:0.049097 
[10]	train-logloss:0.040487 
[11]	train-logloss:0.033572 
[12]	train-logloss:0.028605 
[13]	train-logloss:0.024954 
[14]	train-logloss:0.021601 
[15]	train-logloss:0.019094 
[1]	train-logloss:0.450601 
Will train until train_logloss hasn't improved in 2 rounds.

[2]	train-logloss:0.314662 
[3]	train-logloss:0.228501 
[4]	train-logloss:0.170566 
[5]	train-logloss:0.129860 
[6]	train-logloss:0.101311 
[7]	train-logloss:0.080333 
[8]	train-logloss:0.064048 
[9]	train-logloss:0.051788 
[10]	train-logloss:0.042078 
[11]	train-logloss:0.035060 
[12]	train-logloss:0.029360 
[13]	train-logloss:0.025689 
[14]	train-logloss:0.022499 
[15]	train-logloss:0.020372 
[16]	train-logloss:0.018196 
[17]	train-logloss:0.016388 
[18]	train-logloss:0.015026 
[19]	train-logloss:0.013495 
[20]	train-logloss:0.012139 
[21]	train-logloss:0.011220 
[1]	train-logloss:0.451903 
Will train until train_logloss hasn't improved in 2 rounds.

[2]	train-logloss:0.316697 
[3]	train-logloss:0.230509 
[4]	train-logloss:0.172814 
[5]	train-logloss:0.132290 
[6]	train-logloss:0.103771 
[7]	train-logloss:0.081530 
[8]	train-logloss:0.065213 
[9]	train-logloss:0.052342 
[10]	train-logloss:0.042648 
[11]	train-logloss:0.035456 
[12]	train-logloss:0.029806 
[13]	train-logloss:0.026069 
[14]	train-logloss:0.022637 
[15]	train-logloss:0.019557 
[16]	train-logloss:0.017542 
[17]	train-logloss:0.015677 
[18]	train-logloss:0.014186 
[1]	train-logloss:0.446956 
Will train until train_logloss hasn't improved in 2 rounds.

[2]	train-logloss:0.309233 
[3]	train-logloss:0.221827 
[4]	train-logloss:0.163137 
[5]	train-logloss:0.121918 
[6]	train-logloss:0.092668 
[7]	train-logloss:0.071122 
[8]	train-logloss:0.055721 
[9]	train-logloss:0.044423 
[10]	train-logloss:0.035612 
[11]	train-logloss:0.029179 
[12]	train-logloss:0.024041 
[13]	train-logloss:0.019887 
[14]	train-logloss:0.017280 
[1]	train-logloss:0.447199 
Will train until train_logloss hasn't improved in 2 rounds.

[2]	train-logloss:0.309366 
[3]	train-logloss:0.221524 
[4]	train-logloss:0.162355 
[5]	train-logloss:0.121260 
[6]	train-logloss:0.091592 
[7]	train-logloss:0.070215 
[8]	train-logloss:0.054331 
[9]	train-logloss:0.043050 
[10]	train-logloss:0.034674 
[11]	train-logloss:0.028092 
[12]	train-logloss:0.023157 
[13]	train-logloss:0.019756 
[14]	train-logloss:0.016502 
[15]	train-logloss:0.014162 
[16]	train-logloss:0.012179 
[17]	train-logloss:0.011223 
[1]	train-logloss:0.447199 
Will train until train_logloss hasn't improved in 2 rounds.

[2]	train-logloss:0.309366 
[3]	train-logloss:0.221524 
[4]	train-logloss:0.162355 
[5]	train-logloss:0.121260 
[6]	train-logloss:0.091592 
[7]	train-logloss:0.070215 
[8]	train-logloss:0.054331 
[9]	train-logloss:0.043050 
[10]	train-logloss:0.034674 
[11]	train-logloss:0.028092 
[12]	train-logloss:0.023157 
[13]	train-logloss:0.019756 
[14]	train-logloss:0.016502 
[15]	train-logloss:0.014162 
[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 
 65.839   1.570  67.468 

Example timings

scDblFinder.Rcheck/scDblFinder-Ex.timings

nameusersystemelapsed
TFIDF0.0540.0050.058
addDoublets0.4870.0390.530
amulet1.6350.1321.773
amuletFromCounts0.3880.0040.392
clusterStickiness6.1350.2006.321
computeDoubletDensity3.0390.1873.233
createDoublets0.3360.0040.341
cxds20.4240.0200.445
directDblClassification2.0270.1242.151
doubletPairwiseEnrichment4.6230.0754.693
doubletThresholding5.6620.0885.738
fastcluster0.6610.0400.704
findDoubletClusters1.1210.0791.202
getArtificialDoublets0.0060.0000.005
getCellPairs0.0130.0000.014
getExpectedDoublets0.0030.0000.003
mockDoubletSCE0.3120.0040.316
propHomotypic0.0010.0000.001
recoverDoublets0.1620.0080.170
scDblFinder5.6860.1065.766
selFeatures0.3830.0040.388