Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-30 12:08 -0400 (Sat, 30 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4824 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4615 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4562 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4541 |
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 1883/2320 | 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: 2025-08-29 21:31:02 -0400 (Fri, 29 Aug 2025) |
EndedAt: 2025-08-29 21:33:44 -0400 (Fri, 29 Aug 2025) |
EllapsedTime: 161.7 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 (2025-06-14 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 13.7.7 * 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 (2025-06-14 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 [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 [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 [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 [20] train-logloss:0.003262 [1] train-logloss:0.453316 Will train until train_logloss hasn't improved in 2 rounds. [2] train-logloss:0.315060 [3] train-logloss:0.226246 [4] train-logloss:0.165313 [5] train-logloss:0.123992 [6] train-logloss:0.093536 [7] train-logloss:0.071254 [8] train-logloss:0.055785 [9] train-logloss:0.043770 [10] train-logloss:0.034960 [11] train-logloss:0.028798 [12] train-logloss:0.023522 [13] train-logloss:0.019443 [14] train-logloss:0.016554 [15] train-logloss:0.014601 [16] train-logloss:0.012641 [17] train-logloss:0.011221 [1] train-logloss:0.450240 Will train until train_logloss hasn't improved in 2 rounds. [2] train-logloss:0.312365 [3] train-logloss:0.224543 [4] train-logloss:0.165165 [5] train-logloss:0.122521 [6] train-logloss:0.092849 [7] train-logloss:0.071107 [8] train-logloss:0.054934 [9] train-logloss:0.042785 [10] train-logloss:0.034261 [11] train-logloss:0.027825 [12] train-logloss:0.023060 [13] train-logloss:0.019657 [14] train-logloss:0.016219 [15] train-logloss:0.014293 [16] train-logloss:0.012588 [17] train-logloss:0.010775 [18] train-logloss:0.009927 [1] train-logloss:0.450494 Will train until train_logloss hasn't improved in 2 rounds. [2] train-logloss:0.312537 [3] train-logloss:0.224773 [4] train-logloss:0.165608 [5] train-logloss:0.124311 [6] train-logloss:0.095257 [7] train-logloss:0.073270 [8] train-logloss:0.057479 [9] train-logloss:0.045184 [10] train-logloss:0.036627 [11] train-logloss:0.029988 [12] train-logloss:0.025122 [13] train-logloss:0.020868 [14] train-logloss:0.017872 [15] train-logloss:0.015560 [16] train-logloss:0.013618 [17] train-logloss:0.012264 [1] train-logloss:0.458538 Will train until train_logloss hasn't improved in 2 rounds. [2] train-logloss:0.322812 [3] train-logloss:0.236237 [4] train-logloss:0.178614 [5] train-logloss:0.139200 [6] train-logloss:0.107515 [7] train-logloss:0.084660 [8] train-logloss:0.068052 [9] train-logloss:0.054416 [10] train-logloss:0.044431 [11] train-logloss:0.036760 [12] train-logloss:0.030661 [13] train-logloss:0.026975 [14] train-logloss:0.023238 [15] train-logloss:0.020486 [16] train-logloss:0.018323 [17] train-logloss:0.016260 [1] train-logloss:0.457018 Will train until train_logloss hasn't improved in 2 rounds. [2] train-logloss:0.325398 [3] train-logloss:0.242484 [4] train-logloss:0.180910 [5] train-logloss:0.142838 [6] train-logloss:0.110403 [7] train-logloss:0.084419 [8] train-logloss:0.066392 [9] train-logloss:0.055192 [10] train-logloss:0.045035 [11] train-logloss:0.037320 [12] train-logloss:0.031610 [13] train-logloss:0.027176 [14] train-logloss:0.024340 [15] train-logloss:0.021036 [16] train-logloss:0.018663 [17] train-logloss:0.016776 [18] train-logloss:0.015400 [19] train-logloss:0.014355 [1] train-logloss:0.459109 Will train until train_logloss hasn't improved in 2 rounds. [2] train-logloss:0.328713 [3] train-logloss:0.240326 [4] train-logloss:0.184046 [5] train-logloss:0.140903 [6] train-logloss:0.110400 [7] train-logloss:0.087368 [8] train-logloss:0.070320 [9] train-logloss:0.057060 [10] train-logloss:0.047270 [11] train-logloss:0.039943 [12] train-logloss:0.033401 [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 20.807 0.467 21.628
scDblFinder.Rcheck/scDblFinder-Ex.timings
name | user | system | elapsed | |
TFIDF | 0.015 | 0.001 | 0.015 | |
addDoublets | 0.109 | 0.008 | 0.118 | |
amulet | 0.604 | 0.003 | 0.610 | |
amuletFromCounts | 0.081 | 0.001 | 0.082 | |
clusterStickiness | 2.346 | 0.030 | 2.379 | |
computeDoubletDensity | 1.543 | 0.022 | 1.568 | |
createDoublets | 0.071 | 0.001 | 0.073 | |
cxds2 | 0.097 | 0.002 | 0.099 | |
directDblClassification | 0.677 | 0.022 | 0.699 | |
doubletPairwiseEnrichment | 1.672 | 0.017 | 1.689 | |
doubletThresholding | 2.222 | 0.031 | 2.252 | |
fastcluster | 0.167 | 0.003 | 0.170 | |
findDoubletClusters | 0.245 | 0.018 | 0.262 | |
getArtificialDoublets | 0.001 | 0.000 | 0.001 | |
getCellPairs | 0.003 | 0.000 | 0.002 | |
getExpectedDoublets | 0 | 0 | 0 | |
mockDoubletSCE | 0.066 | 0.001 | 0.066 | |
propHomotypic | 0 | 0 | 0 | |
recoverDoublets | 0.068 | 0.002 | 0.069 | |
scDblFinder | 2.223 | 0.035 | 2.258 | |
selFeatures | 0.078 | 0.001 | 0.079 | |