Back to Build/check report for BioC 3.19 experimental data
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This page was generated on 2024-05-02 14:51:33 -0400 (Thu, 02 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
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 355/430HostnameOS / ArchINSTALLBUILDCHECK
scRNAseq 2.18.0  (landing page)
Aaron Lun
Snapshot Date: 2024-05-02 07:30:02 -0400 (Thu, 02 May 2024)
git_url: https://git.bioconductor.org/packages/scRNAseq
git_branch: RELEASE_3_19
git_last_commit: f2f5eb7
git_last_commit_date: 2024-04-30 10:47:50 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  YES

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: 2.18.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:scRNAseq.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings scRNAseq_2.18.0.tar.gz
StartedAt: 2024-05-02 12:33:42 -0400 (Thu, 02 May 2024)
EndedAt: 2024-05-02 12:55:13 -0400 (Thu, 02 May 2024)
EllapsedTime: 1291.4 seconds
RetCode: 0
Status:   OK  
CheckDir: scRNAseq.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:scRNAseq.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings scRNAseq_2.18.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-data-experiment/meat/scRNAseq.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* 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 ‘2.18.0’
* 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      62.283 12.874  76.279
ZeiselNervousData        45.560 10.244  57.547
JessaBrainData           36.117  7.213  44.531
BacherTCellData          34.720  7.686  43.328
ErnstSpermatogenesisData 27.930  7.307  36.585
HeOrganAtlasData         24.060  7.599  32.331
ZhaoImmuneLiverData      18.704  5.320  24.753
GiladiHSCData            15.055  5.157  20.719
ZilionisLungData         14.462  2.717  17.512
StoeckiusHashingData     13.051  2.074  16.037
AztekinTailData           9.440  1.068  10.719
BachMammaryData           8.303  1.454  11.225
CampbellBrainData         6.769  2.710   9.727
KotliarovPBMCData         6.815  1.496   8.584
LunSpikeInData            6.809  1.438   8.825
NestorowaHSCData          6.500  1.290   8.245
PaulHSCData               5.882  1.489   7.443
ShekharRetinaData         5.913  1.239   7.330
MacoskoRetinaData         5.221  1.319   6.771
MessmerESCData            4.792  1.121   6.398
LedergorMyelomaData       4.168  0.925   5.265
KolodziejczykESCData      4.153  0.806   5.200
* 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-3.19-data-experiment/meat/scRNAseq.Rcheck/00check.log’
for details.


Installation output

scRNAseq.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL scRNAseq
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-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 beta (2024-04-15 r86425) -- "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 
370.948  74.767 468.739 

Example timings

scRNAseq.Rcheck/scRNAseq-Ex.timings

nameusersystemelapsed
AztekinTailData 9.440 1.06810.719
BachMammaryData 8.303 1.45411.225
BacherTCellData34.720 7.68643.328
BaronPancreasData2.6510.6083.411
BhaduriOrganoidData62.28312.87476.279
BuettnerESCData3.4980.7854.898
BunisHSPCData2.7190.7443.577
CampbellBrainData6.7692.7109.727
ChenBrainData2.9580.8413.950
DarmanisBrainData0.4490.0790.537
ERCCSpikeInConcentrations0.0190.0040.022
ErnstSpermatogenesisData27.930 7.30736.585
FletcherOlfactoryData1.2460.1761.446
GiladiHSCData15.055 5.15720.719
GrunHSCData0.3890.0750.467
GrunPancreasData1.0030.2501.283
HeOrganAtlasData24.060 7.59932.331
HermannSpermatogenesisData1.7480.3592.129
HuCortexData1.3760.1781.609
JessaBrainData36.117 7.21344.531
KolodziejczykESCData4.1530.8065.200
KotliarovPBMCData6.8151.4968.584
LaMannoBrainData3.2130.4103.722
LawlorPancreasData0.8210.1280.950
LedergorMyelomaData4.1680.9255.265
LengESCData0.5710.0750.649
LunSpikeInData6.8091.4388.825
MacoskoRetinaData5.2211.3196.771
MairPBMCData0.8560.2091.074
MarquesBrainData1.7470.3982.216
MessmerESCData4.7921.1216.398
MuraroPancreasData2.0520.4682.543
NestorowaHSCData6.5001.2908.245
NowakowskiCortexData3.1630.5473.735
PaulHSCData5.8821.4897.443
PollenGliaData0.3660.0230.397
ReprocessedData2.1480.2612.418
RichardTCellData3.6420.7464.726
RomanovBrainData1.3650.2081.625
SegerstolpePancreasData2.7090.3483.156
ShekharRetinaData5.9131.2397.330
StoeckiusHashingData13.051 2.07416.037
TasicBrainData1.7430.2351.981
UsoskinBrainData0.8290.1380.992
WuKidneyData0.8440.0550.914
XinPancreasData1.5500.1761.742
ZeiselBrainData2.1180.4362.588
ZeiselNervousData45.56010.24457.547
ZhaoImmuneLiverData18.704 5.32024.753
ZhongPrefrontalData1.4410.2211.724
ZilionisLungData14.462 2.71717.512
countErccMolecules0.0420.0000.041
fetchDataset0.7110.1360.847
listDatasets0.0110.0000.011
listVersions0.1750.0140.511
polishDataset0.1960.0280.224
saveDataset0.9810.0660.973
searchDatasets1.2060.0281.534
surveyDatasets0.8720.0510.923