Back to Build/check report for BioC 3.22 experimental data
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This page was generated on 2025-06-17 15:41 -0400 (Tue, 17 Jun 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4807
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 354/429HostnameOS / ArchINSTALLBUILDCHECK
scRNAseq 2.23.0  (landing page)
Aaron Lun
Snapshot Date: 2025-06-17 07:30 -0400 (Tue, 17 Jun 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 24.04.1 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: 2025-06-17 13:04:49 -0400 (Tue, 17 Jun 2025)
EndedAt: 2025-06-17 13:21:19 -0400 (Tue, 17 Jun 2025)
EllapsedTime: 989.8 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 4.5.0 (2025-04-11)
* 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 24.04.2 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      24.797  9.197  34.693
BacherTCellData          18.492  5.808  24.468
HeOrganAtlasData         12.508  7.640  20.340
ZeiselNervousData        14.609  5.375  20.432
JessaBrainData           11.019  4.395  15.761
ErnstSpermatogenesisData 10.385  4.182  14.904
StoeckiusHashingData      9.181  1.350  11.221
ZhaoImmuneLiverData       7.020  3.071  10.188
AztekinTailData           8.216  0.701   8.946
BachMammaryData           7.557  1.025   9.590
GiladiHSCData             5.151  3.375   8.923
LunSpikeInData            6.082  0.478   7.022
ZilionisLungData          4.147  1.216   5.394
NestorowaHSCData          4.296  0.497   5.090
* 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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
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 
312.062  55.469 384.494 

Example timings

scRNAseq.Rcheck/scRNAseq-Ex.timings

nameusersystemelapsed
AztekinTailData8.2160.7018.946
BachMammaryData7.5571.0259.590
BacherTCellData18.492 5.80824.468
BaronPancreasData1.0750.2381.321
BhaduriOrganoidData24.797 9.19734.693
BuettnerESCData3.3660.4334.061
BunisHSPCData1.0600.6631.741
CampbellBrainData1.9621.4773.790
ChenBrainData1.0100.5711.598
DarmanisBrainData0.2620.0430.311
ERCCSpikeInConcentrations0.0210.0000.021
ErnstSpermatogenesisData10.385 4.18214.904
FletcherOlfactoryData0.8460.4361.290
GiladiHSCData5.1513.3758.923
GrunHSCData0.2340.0350.273
GrunPancreasData0.6240.4351.063
HeOrganAtlasData12.508 7.64020.340
HermannSpermatogenesisData0.8000.2921.102
HuCortexData0.5240.1880.776
JessaBrainData11.019 4.39515.761
KolodziejczykESCData3.3090.8384.372
KotliarovPBMCData2.4460.5313.033
LaMannoBrainData1.6450.3181.984
LawlorPancreasData0.8020.1140.934
LedergorMyelomaData1.3850.2701.693
LengESCData0.4920.1010.625
LunSpikeInData6.0820.4787.022
MacoskoRetinaData1.6770.4242.134
MairPBMCData0.6300.1300.767
MarquesBrainData0.6810.1010.794
MessmerESCData3.7760.4614.521
MuraroPancreasData0.9270.2061.137
NestorowaHSCData4.2960.4975.090
NowakowskiCortexData1.5340.2791.827
PaulHSCData2.9310.5263.471
PollenGliaData0.3230.1250.461
ReprocessedData1.9720.2452.294
RichardTCellData3.2240.3013.809
RomanovBrainData0.4840.0830.575
SegerstolpePancreasData1.1920.2831.491
ShekharRetinaData2.0900.8713.037
StoeckiusHashingData 9.181 1.35011.221
TasicBrainData1.6770.3722.134
UsoskinBrainData0.6260.1040.738
WuKidneyData0.3640.0440.414
XinPancreasData0.8260.2371.072
ZeiselBrainData1.0790.3061.400
ZeiselNervousData14.609 5.37520.432
ZhaoImmuneLiverData 7.020 3.07110.188
ZhongPrefrontalData0.6010.1330.743
ZilionisLungData4.1471.2165.394
countErccMolecules0.0340.0020.035
fetchDataset0.6190.1360.755
listDatasets0.0090.0010.012
listPaths0.5700.0221.391
listVersions0.0100.0000.429
polishDataset0.1160.0070.124
saveDataset0.8820.0750.957
searchDatasets1.6970.0641.945
surveyDatasets0.9100.0630.973