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 12:06 -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 23:35:28 -0400 (Fri, 29 Aug 2025) |
EndedAt: 2025-08-29 23:41:57 -0400 (Fri, 29 Aug 2025) |
EllapsedTime: 388.9 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 (2025-06-13) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed clusterStickiness 5.751 0.112 5.900 doubletThresholding 5.172 0.088 5.293 scDblFinder 5.032 0.076 5.146 * 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-x86_64/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 (2025-06-13) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-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 [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 [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 [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 [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 [1] train-logloss:0.450870 Will train until train_logloss hasn't improved in 2 rounds. [2] train-logloss:0.315191 [3] train-logloss:0.229210 [4] train-logloss:0.171453 [5] train-logloss:0.130097 [6] train-logloss:0.099463 [7] train-logloss:0.075685 [8] train-logloss:0.059314 [9] train-logloss:0.046728 [10] train-logloss:0.037276 [11] train-logloss:0.029911 [12] train-logloss:0.024698 [13] train-logloss:0.020699 [1] train-logloss:0.450841 Will train until train_logloss hasn't improved in 2 rounds. [2] train-logloss:0.315280 [3] train-logloss:0.229102 [4] train-logloss:0.171231 [5] train-logloss:0.129871 [6] train-logloss:0.099738 [7] train-logloss:0.078586 [8] train-logloss:0.061802 [9] train-logloss:0.048945 [10] train-logloss:0.039985 [11] train-logloss:0.032086 [12] train-logloss:0.026771 [13] train-logloss:0.022829 [14] train-logloss:0.019776 [1] train-logloss:0.452230 Will train until train_logloss hasn't improved in 2 rounds. [2] train-logloss:0.317547 [3] train-logloss:0.232042 [4] train-logloss:0.173619 [5] train-logloss:0.131119 [6] train-logloss:0.101041 [7] train-logloss:0.078869 [8] train-logloss:0.062133 [9] train-logloss:0.049400 [10] train-logloss:0.040076 [11] train-logloss:0.033378 [12] train-logloss:0.027766 [13] train-logloss:0.023185 [14] train-logloss:0.020496 [15] train-logloss:0.017831 [16] train-logloss:0.015623 [1] train-logloss:0.452323 Will train until train_logloss hasn't improved in 2 rounds. [2] train-logloss:0.317268 [3] train-logloss:0.233291 [4] train-logloss:0.175743 [5] train-logloss:0.135864 [6] train-logloss:0.106167 [7] train-logloss:0.083734 [8] train-logloss:0.067900 [9] train-logloss:0.056194 [10] train-logloss:0.046301 [11] train-logloss:0.038490 [12] train-logloss:0.033365 [13] train-logloss:0.029288 [14] train-logloss:0.026171 [15] train-logloss:0.023168 [16] train-logloss:0.020335 [17] train-logloss:0.018521 [18] train-logloss:0.017177 [1] train-logloss:0.454743 Will train until train_logloss hasn't improved in 2 rounds. [2] train-logloss:0.321539 [3] train-logloss:0.234862 [4] train-logloss:0.176702 [5] train-logloss:0.134458 [6] train-logloss:0.105045 [7] train-logloss:0.082847 [8] train-logloss:0.067226 [9] train-logloss:0.055665 [10] train-logloss:0.045290 [11] train-logloss:0.037588 [1] train-logloss:0.453007 Will train until train_logloss hasn't improved in 2 rounds. [2] train-logloss:0.320435 [3] train-logloss:0.234115 [4] train-logloss:0.176252 [5] train-logloss:0.134242 [6] train-logloss:0.104849 [7] train-logloss:0.082679 [8] train-logloss:0.066983 [9] train-logloss:0.055117 [10] train-logloss:0.046138 [11] train-logloss:0.038748 [12] train-logloss:0.032915 [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 57.937 1.770 60.032
scDblFinder.Rcheck/scDblFinder-Ex.timings
name | user | system | elapsed | |
TFIDF | 0.047 | 0.004 | 0.050 | |
addDoublets | 0.400 | 0.041 | 0.444 | |
amulet | 1.576 | 0.012 | 1.598 | |
amuletFromCounts | 0.324 | 0.005 | 0.331 | |
clusterStickiness | 5.751 | 0.112 | 5.900 | |
computeDoubletDensity | 3.226 | 0.113 | 3.353 | |
createDoublets | 0.303 | 0.004 | 0.307 | |
cxds2 | 0.375 | 0.006 | 0.384 | |
directDblClassification | 1.980 | 0.071 | 2.065 | |
doubletPairwiseEnrichment | 4.564 | 0.051 | 4.634 | |
doubletThresholding | 5.172 | 0.088 | 5.293 | |
fastcluster | 0.566 | 0.010 | 0.580 | |
findDoubletClusters | 0.935 | 0.074 | 1.020 | |
getArtificialDoublets | 0.004 | 0.000 | 0.004 | |
getCellPairs | 0.008 | 0.001 | 0.008 | |
getExpectedDoublets | 0.002 | 0.000 | 0.003 | |
mockDoubletSCE | 0.282 | 0.005 | 0.298 | |
propHomotypic | 0.000 | 0.001 | 0.001 | |
recoverDoublets | 0.120 | 0.002 | 0.126 | |
scDblFinder | 5.032 | 0.076 | 5.146 | |
selFeatures | 0.295 | 0.005 | 0.303 | |