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This page was generated on 2024-06-15 12:33 -0400 (Sat, 15 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4685
lconwaymacOS 12.7.1 Montereyx86_644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4400
kjohnson3macOS 13.6.5 Venturaarm644.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" 4349
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 1832/2242HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scDblFinder 1.19.0  (landing page)
Pierre-Luc Germain
Snapshot Date: 2024-06-14 14:00 -0400 (Fri, 14 Jun 2024)
git_url: https://git.bioconductor.org/packages/scDblFinder
git_branch: devel
git_last_commit: 787bd83
git_last_commit_date: 2024-06-12 12:59:18 -0400 (Wed, 12 Jun 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.6.5 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


CHECK results for scDblFinder on nebbiolo2

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.

raw results


Summary

Package: scDblFinder
Version: 1.19.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:scDblFinder.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings scDblFinder_1.19.0.tar.gz
StartedAt: 2024-06-15 03:10:07 -0400 (Sat, 15 Jun 2024)
EndedAt: 2024-06-15 03:18:56 -0400 (Sat, 15 Jun 2024)
EllapsedTime: 528.9 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: scDblFinder.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:scDblFinder.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings scDblFinder_1.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/scDblFinder.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘scDblFinder/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scDblFinder’ version ‘1.19.0’
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
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:
  threshold value variable
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from Rd file 'scDblFinder.Rd':
scDblFinder
  Code: function(sce, clusters = NULL, samples = NULL, clustCor = NULL,
                 artificialDoublets = NULL, knownDoublets = NULL,
                 knownUse = c("discard", "positive"), dbr = NULL,
                 dbr.sd = NULL, nfeatures = 1352, dims = 20, k = NULL,
                 removeUnidentifiable = TRUE, includePCs = 19,
                 propRandom = 0, propMarkers = 0, aggregateFeatures =
                 FALSE, returnType = c("sce", "table", "full",
                 "counts"), score = c("xgb", "weighted", "ratio"),
                 processing = "default", metric = "logloss", nrounds =
                 0.25, max_depth = 4, iter = 3, trainingFeatures =
                 NULL, unident.th = NULL, multiSampleMode = c("split",
                 "singleModel", "singleModelSplitThres", "asOne"),
                 threshold = TRUE, verbose = TRUE, BPPARAM =
                 SerialParam(progressbar = verbose), ...)
  Docs: function(sce, clusters = NULL, samples = NULL, clustCor = NULL,
                 artificialDoublets = NULL, knownDoublets = NULL,
                 knownUse = c("discard", "positive"), dbr = NULL,
                 dbr.sd = NULL, nfeatures = 1352, dims = 20, k = NULL,
                 removeUnidentifiable = TRUE, includePCs = 19,
                 propRandom = 0, propMarkers = 0, aggregateFeatures =
                 FALSE, returnType = c("sce", "table", "full",
                 "counts"), score = c("xgb", "weighted", "ratio"),
                 processing = "default", metric = "logloss", nrounds =
                 0.25, max_depth = 4, iter = 3, trainingFeatures =
                 NULL, unident.th = NULL, multiSampleMode = c("split",
                 "singleModel", "singleModelSplitThres", "asOne"),
                 threshold = TRUE, verbose = is.null(samples), BPPARAM
                 = SerialParam(), ...)
  Mismatches in argument default values:
    Name: 'verbose' Code: TRUE Docs: is.null(samples)
    Name: 'BPPARAM' Code: SerialParam(progressbar = verbose) Docs: SerialParam()

* 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
doubletThresholding 5.507  0.084   5.592
scDblFinder         5.476  0.060   5.536
* 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, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/scDblFinder.Rcheck/00check.log’
for details.


Installation output

scDblFinder.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL scDblFinder
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘scDblFinder’ ...
** 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 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup"
Copyright (C) 2024 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

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, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
    union, 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: GenomeInfoDb
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")
[ FAIL 0 | WARN 8 | SKIP 0 | PASS 104 ]

[ FAIL 0 | WARN 8 | SKIP 0 | PASS 104 ]
> 
> proc.time()
   user  system elapsed 
 53.769   1.423  55.183 

Example timings

scDblFinder.Rcheck/scDblFinder-Ex.timings

nameusersystemelapsed
TFIDF0.0430.0000.044
addDoublets0.5710.0200.591
amulet1.5570.0961.654
amuletFromCounts0.4290.0000.429
clusterStickiness4.7960.1164.913
computeDoubletDensity4.4280.2124.640
createDoublets0.4140.0120.426
cxds20.5160.0080.525
directDblClassification2.6810.0442.725
doubletPairwiseEnrichment4.4330.0444.477
doubletThresholding5.5070.0845.592
fastcluster0.7730.0080.781
findDoubletClusters1.0510.0201.071
getArtificialDoublets0.0030.0000.004
getCellPairs0.0090.0000.009
getExpectedDoublets0.0020.0000.002
mockDoubletSCE0.4030.0000.403
propHomotypic000
recoverDoublets0.1260.0040.130
scDblFinder5.4760.0605.536
selFeatures0.4210.0110.433