Back to Build/check report for BioC 3.22 experimental data
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This page was generated on 2025-10-23 15:41 -0400 (Thu, 23 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4894
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 360/435HostnameOS / ArchINSTALLBUILDCHECK
scRNAseq 2.23.1  (landing page)
Aaron Lun
Snapshot Date: 2025-10-23 07:30 -0400 (Thu, 23 Oct 2025)
git_url: https://git.bioconductor.org/packages/scRNAseq
git_branch: devel
git_last_commit: c47ea39
git_last_commit_date: 2025-10-10 14:11:42 -0400 (Fri, 10 Oct 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published


CHECK results for scRNAseq on nebbiolo2

To the developers/maintainers of the scRNAseq package:
- 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: scRNAseq
Version: 2.23.1
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:scRNAseq.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings scRNAseq_2.23.1.tar.gz
StartedAt: 2025-10-23 13:02:02 -0400 (Thu, 23 Oct 2025)
EndedAt: 2025-10-23 13:17:17 -0400 (Thu, 23 Oct 2025)
EllapsedTime: 914.3 seconds
RetCode: 0
Status:   OK  
CheckDir: scRNAseq.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:scRNAseq.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings scRNAseq_2.23.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-data-experiment/meat/scRNAseq.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘scRNAseq/DESCRIPTION’ ... OK
* this is package ‘scRNAseq’ version ‘2.23.1’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘scRNAseq’ 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* 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
BhaduriOrganoidData      23.721  7.848  32.306
BacherTCellData          16.933  4.332  21.448
ZeiselNervousData        14.307  5.018  19.793
HeOrganAtlasData         12.062  6.297  18.509
JessaBrainData           10.674  3.698  14.796
ErnstSpermatogenesisData 10.128  3.940  14.442
StoeckiusHashingData      9.084  1.245  11.234
ZhaoImmuneLiverData       6.415  2.802   9.310
AztekinTailData           7.180  0.690   7.902
BachMammaryData           6.958  0.572   8.950
GiladiHSCData             4.898  2.443   7.510
LunSpikeInData            6.093  0.703   7.306
ZilionisLungData          4.143  1.066   5.398
NestorowaHSCData          4.366  0.538   5.261
* 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 NOTE
See
  ‘/home/biocbuild/bbs-3.22-data-experiment/meat/scRNAseq.Rcheck/00check.log’
for details.


Installation output

scRNAseq.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL scRNAseq
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘scRNAseq’ ...
** this is package ‘scRNAseq’ version ‘2.23.1’
** 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 (scRNAseq)

Tests output

scRNAseq.Rcheck/tests/testthat.Rout


R version 4.5.1 Patched (2025-08-23 r88802) -- "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(scRNAseq)
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("scRNAseq")
[ FAIL 0 | WARN 35 | SKIP 1 | PASS 186 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• is.null(gh_token) is TRUE (1): 'test-uploadDirectory.R:59:5'

[ FAIL 0 | WARN 35 | SKIP 1 | PASS 186 ]
Warning message:
call dbDisconnect() when finished working with a connection 
> 
> proc.time()
   user  system elapsed 
289.163  49.793 360.622 

Example timings

scRNAseq.Rcheck/scRNAseq-Ex.timings

nameusersystemelapsed
AztekinTailData7.1800.6907.902
BachMammaryData6.9580.5728.950
BacherTCellData16.933 4.33221.448
BaronPancreasData0.9840.1241.119
BhaduriOrganoidData23.721 7.84832.306
BuettnerESCData3.0470.2653.598
BunisHSPCData0.9900.4321.446
CampbellBrainData1.7340.9162.684
ChenBrainData0.9330.3531.304
DarmanisBrainData0.2440.0240.273
ERCCSpikeInConcentrations0.0210.0000.021
ErnstSpermatogenesisData10.128 3.94014.442
FletcherOlfactoryData0.8410.3101.406
GiladiHSCData4.8982.4437.510
GrunHSCData0.2330.0390.276
GrunPancreasData0.6260.3210.956
HeOrganAtlasData12.062 6.29718.509
HermannSpermatogenesisData0.8060.2151.025
HuCortexData0.5180.1920.720
JessaBrainData10.674 3.69814.796
KolodziejczykESCData3.1760.4273.918
KotliarovPBMCData2.5240.7443.324
LaMannoBrainData1.6540.3592.072
LawlorPancreasData0.7900.1340.954
LedergorMyelomaData1.4570.2871.819
LengESCData0.5090.0670.619
LunSpikeInData6.0930.7037.306
MacoskoRetinaData1.6170.4602.115
MairPBMCData0.5920.0760.676
MarquesBrainData0.6720.0740.756
MessmerESCData3.7650.4064.456
MuraroPancreasData0.8870.2191.117
NestorowaHSCData4.3660.5385.261
NowakowskiCortexData1.4610.1661.644
PaulHSCData2.9640.4463.423
PollenGliaData0.3320.0600.395
ReprocessedData2.0030.2062.307
RichardTCellData3.0350.2993.637
RomanovBrainData0.4990.0800.587
SegerstolpePancreasData1.1780.2771.462
ShekharRetinaData2.1950.5112.774
StoeckiusHashingData 9.084 1.24511.234
TasicBrainData1.8910.3612.304
UsoskinBrainData0.5050.0500.561
WuKidneyData0.3720.0540.432
XinPancreasData0.8010.2391.049
ZeiselBrainData1.0760.2401.324
ZeiselNervousData14.307 5.01819.793
ZhaoImmuneLiverData6.4152.8029.310
ZhongPrefrontalData0.5960.1170.723
ZilionisLungData4.1431.0665.398
countErccMolecules0.0330.0000.034
fetchDataset0.6420.1550.798
listDatasets0.0090.0010.010
listPaths0.5080.0251.558
listVersions0.0110.0000.469
polishDataset0.1130.0030.116
saveDataset0.8090.0600.756
searchDatasets1.7030.0631.986
surveyDatasets0.8900.0850.975