Pierre-Luc Germain
| Snapshot Date: 2025-10-03 13:45 -0400 (Fri, 03 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/scDblFinder |
| git_branch: devel |
| git_last_commit: 4088b78 |
| git_last_commit_date: 2025-08-11 07:14:13 -0400 (Mon, 11 Aug 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-04 12:06 -0400 (Sat, 04 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4853 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4640 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4585 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4576 |
| 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 1898/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| scDblFinder 1.23.4 (landing page) Pierre-Luc Germain
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
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. |
| Package: scDblFinder |
| Version: 1.23.4 |
| 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 |
| StartedAt: 2025-10-03 21:32:43 -0400 (Fri, 03 Oct 2025) |
| EndedAt: 2025-10-03 21:35:05 -0400 (Fri, 03 Oct 2025) |
| EllapsedTime: 141.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: scDblFinder.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### 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: 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 13.7.7
* 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
* 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.
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 ‘1.23.4’ ** 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)
scDblFinder.Rcheck/tests/testthat.Rout
R version 4.5.1 Patched (2025-09-10 r88807) -- "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
[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
[15] train-logloss:0.007703
[16] train-logloss:0.006290
[17] train-logloss:0.005208
[18] train-logloss:0.004371
[1] train-logloss:0.442220
Will train until train_logloss hasn't improved in 2 rounds.
[2] train-logloss:0.302417
[3] train-logloss:0.213883
[4] train-logloss:0.154538
[5] train-logloss:0.113400
[6] train-logloss:0.084280
[7] train-logloss:0.063381
[8] train-logloss:0.048231
[9] train-logloss:0.036942
[10] train-logloss:0.028656
[11] train-logloss:0.022590
[12] train-logloss:0.017918
[13] train-logloss:0.014446
[14] train-logloss:0.011909
[15] train-logloss:0.009920
[1] train-logloss:0.442220
Will train until train_logloss hasn't improved in 2 rounds.
[2] train-logloss:0.302417
[3] train-logloss:0.213883
[4] train-logloss:0.154538
[5] train-logloss:0.113400
[6] train-logloss:0.084280
[7] train-logloss:0.063381
[8] train-logloss:0.048231
[9] train-logloss:0.036942
[10] train-logloss:0.028656
[11] train-logloss:0.022590
[12] train-logloss:0.017918
[13] train-logloss:0.014446
[14] train-logloss:0.011909
[15] train-logloss:0.009920
[1] train-logloss:0.442220
Will train until train_logloss hasn't improved in 2 rounds.
[2] train-logloss:0.302417
[3] train-logloss:0.213883
[4] train-logloss:0.154538
[5] train-logloss:0.113400
[6] train-logloss:0.084280
[7] train-logloss:0.063381
[8] train-logloss:0.048231
[9] train-logloss:0.036942
[10] train-logloss:0.028656
[11] train-logloss:0.022590
[12] train-logloss:0.017918
[13] train-logloss:0.014446
[1] train-logloss:0.449971
Will train until train_logloss hasn't improved in 2 rounds.
[2] train-logloss:0.314062
[3] train-logloss:0.226730
[4] train-logloss:0.167580
[5] train-logloss:0.125818
[6] train-logloss:0.096902
[7] train-logloss:0.074574
[8] train-logloss:0.059569
[9] train-logloss:0.047972
[10] train-logloss:0.039316
[11] train-logloss:0.032484
[12] train-logloss:0.027407
[13] train-logloss:0.023253
[14] train-logloss:0.020303
[1] train-logloss:0.449923
Will train until train_logloss hasn't improved in 2 rounds.
[2] train-logloss:0.313993
[3] train-logloss:0.226654
[4] train-logloss:0.167503
[5] train-logloss:0.125362
[6] train-logloss:0.096540
[7] train-logloss:0.074548
[8] train-logloss:0.059517
[9] train-logloss:0.048169
[10] train-logloss:0.039349
[11] train-logloss:0.032948
[12] train-logloss:0.027898
[13] train-logloss:0.023179
[14] train-logloss:0.019826
[15] train-logloss:0.017374
[1] train-logloss:0.449923
Will train until train_logloss hasn't improved in 2 rounds.
[2] train-logloss:0.313993
[3] train-logloss:0.226654
[4] train-logloss:0.167503
[5] train-logloss:0.125362
[6] train-logloss:0.096540
[7] train-logloss:0.074548
[8] train-logloss:0.059517
[9] train-logloss:0.048169
[10] train-logloss:0.039349
[11] train-logloss:0.032948
[12] train-logloss:0.027898
[13] train-logloss:0.023179
[14] train-logloss:0.019826
[15] train-logloss:0.017374
[1] train-logloss:0.457597
Will train until train_logloss hasn't improved in 2 rounds.
[2] train-logloss:0.326443
[3] train-logloss:0.240703
[4] train-logloss:0.182230
[5] train-logloss:0.140655
[6] train-logloss:0.111754
[7] train-logloss:0.089470
[8] train-logloss:0.072307
[9] train-logloss:0.059866
[10] train-logloss:0.049292
[11] train-logloss:0.041917
[12] train-logloss:0.036029
[13] train-logloss:0.030896
[14] train-logloss:0.027735
[15] train-logloss:0.024091
[16] train-logloss:0.021555
[17] train-logloss:0.019680
[18] train-logloss:0.017882
[19] train-logloss:0.016503
[1] train-logloss:0.458423
Will train until train_logloss hasn't improved in 2 rounds.
[2] train-logloss:0.324735
[3] train-logloss:0.239895
[4] train-logloss:0.182157
[5] train-logloss:0.139828
[6] train-logloss:0.110474
[7] train-logloss:0.088757
[8] train-logloss:0.071367
[9] train-logloss:0.058703
[10] train-logloss:0.048750
[11] train-logloss:0.040917
[12] train-logloss:0.035548
[13] train-logloss:0.030823
[14] train-logloss:0.027142
[1] train-logloss:0.458652
Will train until train_logloss hasn't improved in 2 rounds.
[2] train-logloss:0.326969
[3] train-logloss:0.242131
[4] train-logloss:0.184501
[5] train-logloss:0.141879
[6] train-logloss:0.111731
[7] train-logloss:0.089813
[8] train-logloss:0.073424
[9] train-logloss:0.060502
[10] train-logloss:0.050720
[11] train-logloss:0.042625
[12] train-logloss:0.037017
[13] train-logloss:0.031953
[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
21.344 0.505 22.202
scDblFinder.Rcheck/scDblFinder-Ex.timings
| name | user | system | elapsed | |
| TFIDF | 0.026 | 0.001 | 0.028 | |
| addDoublets | 0.116 | 0.002 | 0.121 | |
| amulet | 0.630 | 0.003 | 0.659 | |
| amuletFromCounts | 0.093 | 0.001 | 0.106 | |
| clusterStickiness | 2.812 | 0.039 | 3.015 | |
| computeDoubletDensity | 1.715 | 0.025 | 1.833 | |
| createDoublets | 0.084 | 0.001 | 0.088 | |
| cxds2 | 0.123 | 0.003 | 0.129 | |
| directDblClassification | 0.850 | 0.018 | 0.926 | |
| doubletPairwiseEnrichment | 1.841 | 0.021 | 1.950 | |
| doubletThresholding | 2.317 | 0.029 | 2.374 | |
| fastcluster | 0.168 | 0.003 | 0.177 | |
| findDoubletClusters | 0.245 | 0.011 | 0.263 | |
| getArtificialDoublets | 0.002 | 0.000 | 0.001 | |
| getCellPairs | 0.002 | 0.000 | 0.003 | |
| getExpectedDoublets | 0.000 | 0.000 | 0.001 | |
| mockDoubletSCE | 0.069 | 0.001 | 0.073 | |
| propHomotypic | 0 | 0 | 0 | |
| recoverDoublets | 0.068 | 0.001 | 0.076 | |
| scDblFinder | 2.704 | 0.037 | 2.804 | |
| selFeatures | 0.079 | 0.002 | 0.079 | |