Back to Build/check report for BioC 3.20 experimental data
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This page was generated on 2024-07-02 14:51 -0400 (Tue, 02 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4693
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 350/425HostnameOS / ArchINSTALLBUILDCHECK
scRNAseq 2.19.1  (landing page)
Aaron Lun
Snapshot Date: 2024-07-02 07:30 -0400 (Tue, 02 Jul 2024)
git_url: https://git.bioconductor.org/packages/scRNAseq
git_branch: devel
git_last_commit: b80f408
git_last_commit_date: 2024-06-20 15:47:45 -0400 (Thu, 20 Jun 2024)
nebbiolo2Linux (Ubuntu 22.04.3 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: 2.19.1
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:scRNAseq.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings scRNAseq_2.19.1.tar.gz
StartedAt: 2024-07-02 12:02:33 -0400 (Tue, 02 Jul 2024)
EndedAt: 2024-07-02 12:23:58 -0400 (Tue, 02 Jul 2024)
EllapsedTime: 1285.0 seconds
RetCode: 0
Status:   OK  
CheckDir: scRNAseq.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:scRNAseq.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings scRNAseq_2.19.1.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.20-data-experiment/meat/scRNAseq.Rcheck’
* using R version 4.4.0 RC (2024-04-16 r86468)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘scRNAseq/DESCRIPTION’ ... OK
* this is package ‘scRNAseq’ version ‘2.19.1’
* 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      66.700 12.305  80.859
ZeiselNervousData        60.141  9.756  70.487
JessaBrainData           38.856  6.400  45.801
BacherTCellData          35.422  7.722  43.264
ErnstSpermatogenesisData 29.424  6.117  36.190
HeOrganAtlasData         23.947  7.497  31.595
ZhaoImmuneLiverData      22.557  5.210  27.855
ZilionisLungData         16.552  2.595  19.247
GiladiHSCData            14.948  3.342  18.364
StoeckiusHashingData     12.696  1.488  24.232
AztekinTailData           9.321  0.965  10.312
KotliarovPBMCData         8.513  1.438  10.023
BachMammaryData           7.572  0.751   9.442
CampbellBrainData         6.192  1.857   8.078
ShekharRetinaData         6.705  1.324   8.105
NestorowaHSCData          6.688  0.740   7.789
PaulHSCData               5.964  1.434   7.413
LunSpikeInData            6.768  0.414   7.822
MacoskoRetinaData         5.547  0.958   6.544
ChenBrainData             3.917  1.815   5.752
LedergorMyelomaData       4.907  0.771   5.731
MessmerESCData            4.988  0.474   5.772
* 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-3.20-data-experiment/meat/scRNAseq.Rcheck/00check.log’
for details.


Installation output

scRNAseq.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL scRNAseq
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘scRNAseq’ ...
** 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 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup"
Copyright (C) 2024 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

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, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
    union, 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 176 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• is.null(gh_token) is TRUE (1): 'test-uploadDirectory.R:59:5'

[ FAIL 0 | WARN 35 | SKIP 1 | PASS 176 ]
Warning message:
call dbDisconnect() when finished working with a connection 
> 
> proc.time()
   user  system elapsed 
373.449  44.753 438.490 

Example timings

scRNAseq.Rcheck/scRNAseq-Ex.timings

nameusersystemelapsed
AztekinTailData 9.321 0.96510.312
BachMammaryData7.5720.7519.442
BacherTCellData35.422 7.72243.264
BaronPancreasData2.6200.5123.138
BhaduriOrganoidData66.70012.30580.859
BuettnerESCData3.4280.2954.264
BunisHSPCData2.8960.7053.621
CampbellBrainData6.1921.8578.078
ChenBrainData3.9171.8155.752
DarmanisBrainData0.4310.0520.489
ERCCSpikeInConcentrations0.0190.0000.020
ErnstSpermatogenesisData29.424 6.11736.190
FletcherOlfactoryData1.1430.1191.270
GiladiHSCData14.948 3.34218.364
GrunHSCData0.4030.0280.435
GrunPancreasData1.0310.1351.177
HeOrganAtlasData23.947 7.49731.595
HermannSpermatogenesisData1.6850.0801.775
HuCortexData1.4870.2771.774
JessaBrainData38.856 6.40045.801
KolodziejczykESCData3.9950.1744.446
KotliarovPBMCData 8.513 1.43810.023
LaMannoBrainData3.2470.1123.381
LawlorPancreasData0.8300.0920.950
LedergorMyelomaData4.9070.7715.731
LengESCData0.5600.0910.690
LunSpikeInData6.7680.4147.822
MacoskoRetinaData5.5470.9586.544
MairPBMCData0.8710.1191.003
MarquesBrainData1.7400.3202.072
MessmerESCData4.9880.4745.772
MuraroPancreasData2.1090.2132.334
NestorowaHSCData6.6880.7407.789
NowakowskiCortexData3.2180.2103.438
PaulHSCData5.9641.4347.413
PollenGliaData0.3840.0080.394
ReprocessedData2.2690.0372.400
RichardTCellData3.5190.1673.989
RomanovBrainData1.3170.0271.353
SegerstolpePancreasData2.7630.4203.200
ShekharRetinaData6.7051.3248.105
StoeckiusHashingData12.696 1.48824.232
TasicBrainData2.0220.2352.354
UsoskinBrainData0.7700.0440.821
WuKidneyData0.8780.0520.937
XinPancreasData1.6900.2991.996
ZeiselBrainData2.0760.1592.239
ZeiselNervousData60.141 9.75670.487
ZhaoImmuneLiverData22.557 5.21027.855
ZhongPrefrontalData1.4680.2281.704
ZilionisLungData16.552 2.59519.247
countErccMolecules0.0360.0000.036
fetchDataset0.7510.0320.783
listDatasets0.0100.0000.011
listVersions0.0850.0040.547
polishDataset0.2040.0010.204
saveDataset1.1640.0351.128
searchDatasets1.2690.0041.556
surveyDatasets0.8880.0040.892