Back to Build/check report for BioC 3.21 experimental data
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This page was generated on 2025-10-07 15:01 -0400 (Tue, 07 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4832
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 356/432HostnameOS / ArchINSTALLBUILDCHECK
scRNAseq 2.22.0  (landing page)
Aaron Lun
Snapshot Date: 2025-10-07 07:30 -0400 (Tue, 07 Oct 2025)
git_url: https://git.bioconductor.org/packages/scRNAseq
git_branch: RELEASE_3_21
git_last_commit: 62a2b70
git_last_commit_date: 2025-04-15 10:08:35 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published


CHECK results for scRNAseq on nebbiolo1

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: 2.22.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:scRNAseq.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings scRNAseq_2.22.0.tar.gz
StartedAt: 2025-10-07 12:55:41 -0400 (Tue, 07 Oct 2025)
EndedAt: 2025-10-07 13:12:47 -0400 (Tue, 07 Oct 2025)
EllapsedTime: 1025.7 seconds
RetCode: 0
Status:   OK  
CheckDir: scRNAseq.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:scRNAseq.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings scRNAseq_2.22.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.21-data-experiment/meat/scRNAseq.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 ‘2.22.0’
* 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      24.894 10.172  36.016
BacherTCellData          19.034  5.848  26.158
ZeiselNervousData        14.440  5.869  21.892
HeOrganAtlasData         12.256  6.436  19.314
JessaBrainData           10.934  4.932  17.272
ErnstSpermatogenesisData 10.166  3.649  15.041
ZhaoImmuneLiverData       6.832  5.841  13.409
AztekinTailData           9.454  1.797  11.753
StoeckiusHashingData      9.252  1.532  11.937
BachMammaryData           7.456  1.290   9.594
LunSpikeInData            6.169  1.026   7.658
GiladiHSCData             4.899  1.747   7.220
ZilionisLungData          4.093  1.725   6.188
NestorowaHSCData          4.360  0.541   5.347
* 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-3.21-data-experiment/meat/scRNAseq.Rcheck/00check.log’
for details.


Installation output

scRNAseq.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL scRNAseq
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘scRNAseq’ ...
** this is package ‘scRNAseq’ version ‘2.22.0’
** 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 (2025-06-13) -- "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: 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("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 
341.781  69.706 436.559 

Example timings

scRNAseq.Rcheck/scRNAseq-Ex.timings

nameusersystemelapsed
AztekinTailData 9.454 1.79711.753
BachMammaryData7.4561.2909.594
BacherTCellData19.034 5.84826.158
BaronPancreasData1.0860.1491.367
BhaduriOrganoidData24.89410.17236.016
BuettnerESCData3.0640.6613.943
BunisHSPCData1.0390.5711.729
CampbellBrainData1.8040.9142.981
ChenBrainData0.9680.3581.465
DarmanisBrainData0.2570.0200.283
ERCCSpikeInConcentrations0.0180.0020.020
ErnstSpermatogenesisData10.166 3.64915.041
FletcherOlfactoryData0.8390.1901.048
GiladiHSCData4.8991.7477.220
GrunHSCData0.2260.0320.263
GrunPancreasData0.6060.2210.838
HeOrganAtlasData12.256 6.43619.314
HermannSpermatogenesisData0.8240.3101.161
HuCortexData0.4940.2460.796
JessaBrainData10.934 4.93217.272
KolodziejczykESCData3.2990.9214.519
KotliarovPBMCData2.3780.4913.155
LaMannoBrainData1.6510.2201.918
LawlorPancreasData0.7920.1250.919
LedergorMyelomaData1.3730.2301.788
LengESCData0.4940.0790.576
LunSpikeInData6.1691.0267.658
MacoskoRetinaData1.6010.1952.036
MairPBMCData0.5770.0540.641
MarquesBrainData0.6690.1240.870
MessmerESCData3.7070.6574.742
MuraroPancreasData0.8920.0390.953
NestorowaHSCData4.3600.5415.347
NowakowskiCortexData1.4470.1241.595
PaulHSCData3.0000.3463.416
PollenGliaData0.2290.0370.268
ReprocessedData2.0210.3512.380
RichardTCellData3.0510.5453.863
RomanovBrainData0.4840.1080.610
SegerstolpePancreasData1.1730.3921.665
ShekharRetinaData2.1590.7093.079
StoeckiusHashingData 9.252 1.53211.937
TasicBrainData1.6980.3282.028
UsoskinBrainData0.5290.0960.637
WuKidneyData0.3720.0700.458
XinPancreasData0.9570.2601.234
ZeiselBrainData0.8930.2621.177
ZeiselNervousData14.440 5.86921.892
ZhaoImmuneLiverData 6.832 5.84113.409
ZhongPrefrontalData0.6390.1700.877
ZilionisLungData4.0931.7256.188
countErccMolecules0.0350.0030.039
fetchDataset0.6700.2050.875
listDatasets0.0080.0040.012
listPaths0.5590.0441.551
listVersions0.0120.0020.580
polishDataset0.1670.0060.173
saveDataset0.8510.0590.866
searchDatasets1.8990.0852.151
surveyDatasets1.0080.0201.029