Back to Build/check report for BioC 3.22 experimental data
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This page was generated on 2025-09-30 15:41 -0400 (Tue, 30 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4843
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 358/433HostnameOS / ArchINSTALLBUILDCHECK
scRNAseq 2.23.0  (landing page)
Aaron Lun
Snapshot Date: 2025-09-30 07:30 -0400 (Tue, 30 Sep 2025)
git_url: https://git.bioconductor.org/packages/scRNAseq
git_branch: devel
git_last_commit: efd05d7
git_last_commit_date: 2025-04-15 10:08:35 -0400 (Tue, 15 Apr 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: 2.23.0
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_2.23.0.tar.gz
StartedAt: 2025-09-30 13:02:26 -0400 (Tue, 30 Sep 2025)
EndedAt: 2025-09-30 13:18:44 -0400 (Tue, 30 Sep 2025)
EllapsedTime: 978.1 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_2.23.0.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 ‘2.23.0’
* 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 ... 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      24.709  9.838  34.891
BacherTCellData          19.542  5.907  25.611
ZeiselNervousData        15.079  5.329  20.909
HeOrganAtlasData         12.764  6.636  19.695
JessaBrainData           11.469  4.567  16.511
ErnstSpermatogenesisData 11.086  4.816  16.693
StoeckiusHashingData      9.652  1.520  12.033
ZhaoImmuneLiverData       7.027  3.120  10.238
BachMammaryData           8.449  0.862  10.499
AztekinTailData           7.979  0.762   8.770
GiladiHSCData             5.017  2.474   7.602
LunSpikeInData            6.674  0.592   7.894
ZilionisLungData          4.070  1.299   5.398
NestorowaHSCData          4.661  0.679   5.712
* 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 ‘2.23.0’
** 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 
298.910  33.676 365.168 

Example timings

scRNAseq.Rcheck/scRNAseq-Ex.timings

nameusersystemelapsed
AztekinTailData7.9790.7628.770
BachMammaryData 8.449 0.86210.499
BacherTCellData19.542 5.90725.611
BaronPancreasData1.0100.1701.195
BhaduriOrganoidData24.709 9.83834.891
BuettnerESCData3.3940.3194.135
BunisHSPCData1.0500.4261.497
CampbellBrainData1.8921.0582.981
ChenBrainData0.9990.4081.427
DarmanisBrainData0.2760.0520.332
ERCCSpikeInConcentrations0.0230.0020.025
ErnstSpermatogenesisData11.086 4.81616.693
FletcherOlfactoryData0.8570.2841.149
GiladiHSCData5.0172.4747.602
GrunHSCData0.2390.0440.287
GrunPancreasData0.6960.4351.139
HeOrganAtlasData12.764 6.63619.695
HermannSpermatogenesisData0.8200.2631.086
HuCortexData0.5290.1640.704
JessaBrainData11.469 4.56716.511
KolodziejczykESCData3.4690.4354.150
KotliarovPBMCData2.6560.9693.690
LaMannoBrainData1.6720.3802.075
LawlorPancreasData0.8040.1340.968
LedergorMyelomaData1.4470.3201.813
LengESCData0.5020.0610.602
LunSpikeInData6.6740.5927.894
MacoskoRetinaData1.6750.4562.174
MairPBMCData0.6540.0730.736
MarquesBrainData0.6890.0410.741
MessmerESCData3.9040.4164.654
MuraroPancreasData0.9300.2021.137
NestorowaHSCData4.6610.6795.712
NowakowskiCortexData1.5400.2671.840
PaulHSCData3.0900.4733.579
PollenGliaData0.3360.0940.433
ReprocessedData2.0140.2712.334
RichardTCellData3.1960.3033.787
RomanovBrainData0.5050.1240.637
SegerstolpePancreasData1.2470.3051.570
ShekharRetinaData2.2530.6893.018
StoeckiusHashingData 9.652 1.52012.033
TasicBrainData1.9670.3692.387
UsoskinBrainData0.5360.0610.604
WuKidneyData0.4080.0620.477
XinPancreasData0.8160.2861.111
ZeiselBrainData1.2180.3001.532
ZeiselNervousData15.079 5.32920.909
ZhaoImmuneLiverData 7.027 3.12010.238
ZhongPrefrontalData0.6180.1220.750
ZilionisLungData4.0701.2995.398
countErccMolecules0.0360.0000.038
fetchDataset0.6770.1720.849
listDatasets0.0110.0000.011
listPaths0.5890.0151.452
listVersions0.0160.0000.246
polishDataset0.1620.0020.164
saveDataset0.8250.0540.885
searchDatasets1.7340.0671.972
surveyDatasets0.9250.0510.976