Pierre-Luc Germain
| Snapshot Date: 2025-07-29 13:25 -0400 (Tue, 29 Jul 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) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-07-30 12:06 -0400 (Wed, 30 Jul 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4796 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4535 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4578 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4519 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4516 |
| 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 1877/2313 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| scDblFinder 1.23.3 (landing page) Pierre-Luc Germain
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 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: 1.23.3 |
| 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_1.23.3.tar.gz |
| StartedAt: 2025-07-30 02:20:34 -0400 (Wed, 30 Jul 2025) |
| EndedAt: 2025-07-30 02:29:26 -0400 (Wed, 30 Jul 2025) |
| EllapsedTime: 532.7 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: scDblFinder.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### 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_1.23.3.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/scDblFinder.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 24.04.2 LTS
* using session charset: UTF-8
* 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 5.772 0.156 5.822
doubletThresholding 5.187 0.039 5.066
scDblFinder 5.206 0.009 5.080
* 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.
scDblFinder.Rcheck/00install.out
############################################################################## ############################################################################## ### ### 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 ‘1.23.3’ ** 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)
scDblFinder.Rcheck/tests/testthat.Rout
R version 4.5.1 (2025-06-13) -- "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:0.442469
Will train until train_logloss hasn't improved in 2 rounds.
[2] train-logloss:0.303056
[3] train-logloss:0.214156
[4] train-logloss:0.154899
[5] train-logloss:0.113476
[6] train-logloss:0.084172
[7] train-logloss:0.063064
[8] train-logloss:0.047688
[9] train-logloss:0.036487
[10] train-logloss:0.028183
[11] train-logloss:0.022092
[12] train-logloss:0.017516
[13] train-logloss:0.014130
[14] train-logloss:0.011531
[15] train-logloss:0.009580
[1] train-logloss:0.442469
Will train until train_logloss hasn't improved in 2 rounds.
[2] train-logloss:0.303056
[3] train-logloss:0.214156
[4] train-logloss:0.154899
[5] train-logloss:0.113476
[6] train-logloss:0.084172
[7] train-logloss:0.063064
[8] train-logloss:0.047688
[9] train-logloss:0.036487
[10] train-logloss:0.028183
[11] train-logloss:0.022092
[12] train-logloss:0.017516
[13] train-logloss:0.014130
[14] train-logloss:0.011531
[15] train-logloss:0.009580
[16] train-logloss:0.008076
[1] train-logloss:0.442469
Will train until train_logloss hasn't improved in 2 rounds.
[2] train-logloss:0.303056
[3] train-logloss:0.214156
[4] train-logloss:0.154899
[5] train-logloss:0.113476
[6] train-logloss:0.084172
[7] train-logloss:0.063064
[8] train-logloss:0.047688
[9] train-logloss:0.036487
[10] train-logloss:0.028183
[11] train-logloss:0.022092
[12] train-logloss:0.017516
[13] train-logloss:0.014130
[14] train-logloss:0.011531
[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:0.440583
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
[18] train-logloss:0.004360
[19] train-logloss:0.003706
[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:0.447009
Will train until train_logloss hasn't improved in 2 rounds.
[2] train-logloss:0.309583
[3] train-logloss:0.221860
[4] train-logloss:0.163232
[5] train-logloss:0.121510
[6] train-logloss:0.092433
[7] train-logloss:0.070814
[8] train-logloss:0.054630
[9] train-logloss:0.043471
[10] train-logloss:0.034406
[11] train-logloss:0.027604
[12] train-logloss:0.023542
[13] train-logloss:0.019403
[14] train-logloss:0.016515
[15] train-logloss:0.014208
[1] train-logloss:0.447498
Will train until train_logloss hasn't improved in 2 rounds.
[2] train-logloss:0.309535
[3] train-logloss:0.221802
[4] train-logloss:0.163150
[5] train-logloss:0.121988
[6] train-logloss:0.092467
[7] train-logloss:0.070830
[8] train-logloss:0.054860
[9] train-logloss:0.042980
[10] train-logloss:0.034747
[11] train-logloss:0.027940
[12] train-logloss:0.023781
[13] train-logloss:0.019579
[14] train-logloss:0.016688
[15] train-logloss:0.014448
[1] train-logloss:0.447498
Will train until train_logloss hasn't improved in 2 rounds.
[2] train-logloss:0.309535
[3] train-logloss:0.221802
[4] train-logloss:0.163150
[5] train-logloss:0.121988
[6] train-logloss:0.092467
[7] train-logloss:0.070830
[8] train-logloss:0.054860
[9] train-logloss:0.042980
[10] train-logloss:0.034747
[11] train-logloss:0.027940
[12] train-logloss:0.023781
[13] train-logloss:0.019579
[14] train-logloss:0.016688
[15] train-logloss:0.014448
[16] train-logloss:0.013146
[17] train-logloss:0.011585
[1] train-logloss:0.448653
Will train until train_logloss hasn't improved in 2 rounds.
[2] train-logloss:0.312238
[3] train-logloss:0.225695
[4] train-logloss:0.167307
[5] train-logloss:0.126828
[6] train-logloss:0.096417
[7] train-logloss:0.075663
[8] train-logloss:0.059408
[9] train-logloss:0.046418
[10] train-logloss:0.037440
[11] train-logloss:0.031197
[12] train-logloss:0.026168
[13] train-logloss:0.022194
[14] train-logloss:0.018867
[15] train-logloss:0.016418
[16] train-logloss:0.014735
[1] train-logloss:0.448631
Will train until train_logloss hasn't improved in 2 rounds.
[2] train-logloss:0.312438
[3] train-logloss:0.225705
[4] train-logloss:0.167525
[5] train-logloss:0.126707
[6] train-logloss:0.095895
[7] train-logloss:0.074112
[8] train-logloss:0.058862
[9] train-logloss:0.047203
[10] train-logloss:0.038394
[11] train-logloss:0.031704
[12] train-logloss:0.026448
[13] train-logloss:0.022221
[1] train-logloss:0.448631
Will train until train_logloss hasn't improved in 2 rounds.
[2] train-logloss:0.312438
[3] train-logloss:0.225705
[4] train-logloss:0.167525
[5] train-logloss:0.126707
[6] train-logloss:0.095895
[7] train-logloss:0.074112
[8] train-logloss:0.058862
[9] train-logloss:0.047203
[10] train-logloss:0.038394
[11] train-logloss:0.031704
[12] train-logloss:0.026448
[13] train-logloss:0.022221
[14] train-logloss:0.018963
[15] train-logloss:0.016741
[16] train-logloss:0.014642
[17] train-logloss:0.013369
[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
55.763 2.713 58.183
scDblFinder.Rcheck/scDblFinder-Ex.timings
| name | user | system | elapsed | |
| TFIDF | 0.042 | 0.005 | 0.047 | |
| addDoublets | 0.361 | 0.050 | 0.411 | |
| amulet | 1.657 | 0.063 | 1.721 | |
| amuletFromCounts | 0.272 | 0.000 | 0.273 | |
| clusterStickiness | 5.772 | 0.156 | 5.822 | |
| computeDoubletDensity | 3.501 | 0.227 | 3.728 | |
| createDoublets | 0.23 | 0.00 | 0.23 | |
| cxds2 | 0.313 | 0.000 | 0.313 | |
| directDblClassification | 1.960 | 0.038 | 1.964 | |
| doubletPairwiseEnrichment | 4.349 | 0.017 | 4.284 | |
| doubletThresholding | 5.187 | 0.039 | 5.066 | |
| fastcluster | 0.488 | 0.006 | 0.494 | |
| findDoubletClusters | 0.782 | 0.051 | 0.833 | |
| getArtificialDoublets | 0.004 | 0.000 | 0.004 | |
| getCellPairs | 0.009 | 0.000 | 0.008 | |
| getExpectedDoublets | 0.001 | 0.000 | 0.002 | |
| mockDoubletSCE | 0.213 | 0.000 | 0.213 | |
| propHomotypic | 0.000 | 0.000 | 0.001 | |
| recoverDoublets | 0.13 | 0.00 | 0.13 | |
| scDblFinder | 5.206 | 0.009 | 5.080 | |
| selFeatures | 0.279 | 0.000 | 0.278 | |