Back to Build/check report for BioC 3.21 experimental data
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This page was generated on 2025-07-31 15:01 -0400 (Thu, 31 Jul 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4823
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: 2025-07-31 07:30 -0400 (Thu, 31 Jul 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 24.04.1 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: 2025-07-31 12:54:36 -0400 (Thu, 31 Jul 2025)
EndedAt: 2025-07-31 13:10:33 -0400 (Thu, 31 Jul 2025)
EllapsedTime: 956.6 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 24.04.2 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      23.819  8.729  32.913
BacherTCellData          17.441  5.810  24.390
ZeiselNervousData        14.450  6.247  22.253
HeOrganAtlasData         12.185  6.421  19.270
JessaBrainData           10.662  4.407  16.169
ErnstSpermatogenesisData 10.202  4.245  15.795
StoeckiusHashingData      9.021  1.523  11.382
ZhaoImmuneLiverData       6.627  2.772  10.132
BachMammaryData           7.350  1.873  10.089
AztekinTailData           7.209  0.707   8.120
GiladiHSCData             4.934  2.506   8.009
LunSpikeInData            6.172  1.227   7.981
NestorowaHSCData          4.323  0.814   5.553
ZilionisLungData          4.016  1.058   5.493
* 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 
290.868  66.663 384.109 

Example timings

scRNAseq.Rcheck/scRNAseq-Ex.timings

nameusersystemelapsed
AztekinTailData7.2090.7078.120
BachMammaryData 7.350 1.87310.089
BacherTCellData17.441 5.81024.390
BaronPancreasData1.0150.1401.193
BhaduriOrganoidData23.819 8.72932.913
BuettnerESCData3.0430.8144.171
BunisHSPCData1.0230.4741.617
CampbellBrainData1.7951.0903.152
ChenBrainData0.9550.4191.515
DarmanisBrainData0.2430.0400.289
ERCCSpikeInConcentrations0.0190.0010.020
ErnstSpermatogenesisData10.202 4.24515.795
FletcherOlfactoryData0.8280.3381.180
GiladiHSCData4.9342.5068.009
GrunHSCData0.2380.0390.283
GrunPancreasData0.6110.3200.942
HeOrganAtlasData12.185 6.42119.270
HermannSpermatogenesisData0.7670.2501.043
HuCortexData0.4970.1960.751
JessaBrainData10.662 4.40716.169
KolodziejczykESCData3.4661.0174.827
KotliarovPBMCData2.4260.5263.234
LaMannoBrainData1.5820.2871.915
LawlorPancreasData0.7860.1280.917
LedergorMyelomaData1.3320.1861.702
LengESCData0.4960.0760.574
LunSpikeInData6.1721.2277.981
MacoskoRetinaData1.6530.4512.341
MairPBMCData0.6050.1020.715
MarquesBrainData0.6800.1230.877
MessmerESCData3.7160.8374.800
MuraroPancreasData0.9000.2271.147
NestorowaHSCData4.3230.8145.553
NowakowskiCortexData1.4200.2531.695
PaulHSCData2.9270.2333.230
PollenGliaData0.2190.0210.243
ReprocessedData1.9710.2282.207
RichardTCellData2.9260.4883.662
RomanovBrainData0.4970.0740.590
SegerstolpePancreasData1.1520.3181.570
ShekharRetinaData2.1780.5693.006
StoeckiusHashingData 9.021 1.52311.382
TasicBrainData1.8610.4032.267
UsoskinBrainData0.5340.1000.647
WuKidneyData0.3700.0680.454
XinPancreasData0.9610.1821.160
ZeiselBrainData0.9090.2331.165
ZeiselNervousData14.450 6.24722.253
ZhaoImmuneLiverData 6.627 2.77210.132
ZhongPrefrontalData0.6140.1040.811
ZilionisLungData4.0161.0585.493
countErccMolecules0.0340.0030.037
fetchDataset0.6250.1470.771
listDatasets0.010.000.01
listPaths0.5380.0301.480
listVersions0.0100.0010.263
polishDataset0.1130.0010.114
saveDataset0.8520.0540.824
searchDatasets1.6330.0541.841
surveyDatasets0.8640.0280.892