Back to Build/check report for BioC 3.21 experimental data
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This page was generated on 2025-06-19 15:19 -0400 (Thu, 19 Jun 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4838
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: 2025-06-19 07:30 -0400 (Thu, 19 Jun 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: 2025-06-19 12:54:22 -0400 (Thu, 19 Jun 2025)
EndedAt: 2025-06-19 13:09:39 -0400 (Thu, 19 Jun 2025)
EllapsedTime: 917.3 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 4.5.0 RC (2025-04-04 r88126)
* 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      23.681  8.173  32.194
BacherTCellData          16.686  4.491  22.207
ZeiselNervousData        14.001  5.556  21.110
HeOrganAtlasData         12.145  6.408  19.115
ErnstSpermatogenesisData 10.647  4.841  17.047
JessaBrainData           10.634  4.301  16.052
StoeckiusHashingData      8.704  1.051  10.486
AztekinTailData           7.644  1.859   9.713
ZhaoImmuneLiverData       6.409  2.565   9.722
BachMammaryData           6.853  1.285   8.885
GiladiHSCData             4.902  2.595   8.064
LunSpikeInData            5.918  0.957   7.521
NestorowaHSCData          4.504  1.108   5.990
MessmerESCData            3.892  1.375   5.525
ZilionisLungData          4.079  0.828   5.420
* 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
###
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* 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 4.5.0 RC (2025-04-04 r88126) -- "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 
284.432  49.699 352.601 

Example timings

scRNAseq.Rcheck/scRNAseq-Ex.timings

nameusersystemelapsed
AztekinTailData7.6441.8599.713
BachMammaryData6.8531.2858.885
BacherTCellData16.686 4.49122.207
BaronPancreasData0.9970.1351.168
BhaduriOrganoidData23.681 8.17332.194
BuettnerESCData2.9690.6693.884
BunisHSPCData0.9760.4191.517
CampbellBrainData1.8050.8802.952
ChenBrainData0.9950.3401.475
DarmanisBrainData0.2740.0260.305
ERCCSpikeInConcentrations0.0220.0000.022
ErnstSpermatogenesisData10.647 4.84117.047
FletcherOlfactoryData0.8240.2991.136
GiladiHSCData4.9022.5958.064
GrunHSCData0.2290.0410.275
GrunPancreasData0.6260.2630.910
HeOrganAtlasData12.145 6.40819.115
HermannSpermatogenesisData0.8170.2261.069
HuCortexData0.6140.1841.017
JessaBrainData10.634 4.30116.052
KolodziejczykESCData3.1550.8274.277
KotliarovPBMCData2.3130.2682.863
LaMannoBrainData1.5360.1821.764
LawlorPancreasData0.7720.0610.836
LedergorMyelomaData1.3560.1221.661
LengESCData0.4930.0690.565
LunSpikeInData5.9180.9577.521
MacoskoRetinaData1.7340.9192.891
MairPBMCData0.6630.1320.802
MarquesBrainData0.7160.2991.092
MessmerESCData3.8921.3755.525
MuraroPancreasData0.9900.4931.504
NestorowaHSCData4.5041.1085.990
NowakowskiCortexData1.4090.4321.865
PaulHSCData3.0070.4693.545
PollenGliaData0.2250.0190.247
ReprocessedData1.9690.2112.189
RichardTCellData2.9640.5933.766
RomanovBrainData0.4920.0840.595
SegerstolpePancreasData1.1290.2871.517
ShekharRetinaData2.1120.4842.806
StoeckiusHashingData 8.704 1.05110.486
TasicBrainData1.8510.3512.206
UsoskinBrainData0.4970.0300.540
WuKidneyData0.3650.0280.409
XinPancreasData0.9260.1871.129
ZeiselBrainData0.8950.1651.083
ZeiselNervousData14.001 5.55621.110
ZhaoImmuneLiverData6.4092.5659.722
ZhongPrefrontalData0.5840.1230.782
ZilionisLungData4.0790.8285.420
countErccMolecules0.0320.0010.033
fetchDataset0.5950.0400.634
listDatasets0.010.000.01
listPaths0.5160.0061.381
listVersions0.010.000.40
polishDataset0.1220.0110.133
saveDataset0.8960.0390.796
searchDatasets1.6340.0231.836
surveyDatasets0.8580.0140.872