Back to Build/check report for BioC 3.21 experimental data
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This page was generated on 2025-07-22 15:01 -0400 (Tue, 22 Jul 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4821
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: 2025-07-22 07:30 -0400 (Tue, 22 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: 2025-07-22 12:54:39 -0400 (Tue, 22 Jul 2025)
EndedAt: 2025-07-22 13:11:18 -0400 (Tue, 22 Jul 2025)
EllapsedTime: 998.7 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
###
##############################################################################
##############################################################################


* 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      24.687 10.021  35.315
BacherTCellData          17.422  6.416  24.862
ZeiselNervousData        14.179  5.514  21.181
HeOrganAtlasData         12.878  6.813  20.412
JessaBrainData           10.752  5.001  16.861
ErnstSpermatogenesisData 10.915  4.560  16.775
StoeckiusHashingData      8.937  1.486  11.197
ZhaoImmuneLiverData       6.519  2.568   9.839
BachMammaryData           7.032  1.359   9.215
AztekinTailData           7.151  0.677   8.037
GiladiHSCData             5.156  2.416   8.152
LunSpikeInData            6.190  1.372   8.008
NestorowaHSCData          4.334  0.823   5.541
ZilionisLungData          4.011  1.041   5.418
* 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 
323.427  76.629 420.341 

Example timings

scRNAseq.Rcheck/scRNAseq-Ex.timings

nameusersystemelapsed
AztekinTailData7.1510.6778.037
BachMammaryData7.0321.3599.215
BacherTCellData17.422 6.41624.862
BaronPancreasData1.0150.2461.307
BhaduriOrganoidData24.68710.02135.315
BuettnerESCData3.2060.8134.278
BunisHSPCData1.0610.4751.661
CampbellBrainData1.8481.0353.151
ChenBrainData1.0100.4251.716
DarmanisBrainData0.2630.0490.318
ERCCSpikeInConcentrations0.0180.0020.020
ErnstSpermatogenesisData10.915 4.56016.775
FletcherOlfactoryData0.8930.3111.216
GiladiHSCData5.1562.4168.152
GrunHSCData0.2810.0450.331
GrunPancreasData0.6930.3731.077
HeOrganAtlasData12.878 6.81320.412
HermannSpermatogenesisData0.7920.2631.083
HuCortexData0.5150.1880.762
JessaBrainData10.752 5.00116.861
KolodziejczykESCData3.2870.9864.584
KotliarovPBMCData2.4370.6333.355
LaMannoBrainData1.5850.3151.948
LawlorPancreasData0.7840.1310.916
LedergorMyelomaData1.3670.1921.755
LengESCData0.4960.0810.579
LunSpikeInData6.1901.3728.008
MacoskoRetinaData1.5950.5492.379
MairPBMCData0.5900.1390.736
MarquesBrainData0.6770.1290.882
MessmerESCData3.6930.8844.811
MuraroPancreasData0.8890.2371.148
NestorowaHSCData4.3340.8235.541
NowakowskiCortexData1.4510.2881.773
PaulHSCData2.9540.3853.442
PollenGliaData0.2220.0310.256
ReprocessedData1.9760.2052.191
RichardTCellData3.0000.6603.902
RomanovBrainData0.4930.1030.614
SegerstolpePancreasData1.1690.3631.630
ShekharRetinaData2.1380.6753.024
StoeckiusHashingData 8.937 1.48611.197
TasicBrainData1.8670.4132.283
UsoskinBrainData0.5090.0740.595
WuKidneyData0.3730.0580.448
XinPancreasData0.9290.2141.157
ZeiselBrainData0.8960.2091.127
ZeiselNervousData14.179 5.51421.181
ZhaoImmuneLiverData6.5192.5689.839
ZhongPrefrontalData0.5910.1160.772
ZilionisLungData4.0111.0415.418
countErccMolecules0.0340.0000.034
fetchDataset0.6060.1330.740
listDatasets0.0080.0020.010
listPaths0.4820.0071.239
listVersions0.0110.0000.454
polishDataset0.1220.0020.124
saveDataset0.9060.0490.815
searchDatasets1.7470.0461.942
surveyDatasets0.8660.0140.880