Back to Build/check report for BioC 3.19 experimental data
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This page was generated on 2024-07-11 14:51 -0400 (Thu, 11 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4741
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: 2024-07-11 07:30 -0400 (Thu, 11 Jul 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  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: 2.18.0
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: 2024-07-11 12:01:14 -0400 (Thu, 11 Jul 2024)
EndedAt: 2024-07-11 12:22:35 -0400 (Thu, 11 Jul 2024)
EllapsedTime: 1280.4 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 4.4.1 (2024-06-14)
* 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      62.295 12.322  75.034
ZeiselNervousData        48.784  9.588  60.036
JessaBrainData           38.152  6.316  45.731
BacherTCellData          35.328  8.451  44.766
ErnstSpermatogenesisData 26.885  5.874  34.414
HeOrganAtlasData         23.905  7.136  31.689
ZhaoImmuneLiverData      20.644  4.671  26.392
GiladiHSCData            15.178  3.903  19.593
ZilionisLungData         15.525  2.224  18.101
StoeckiusHashingData     12.734  1.609  24.825
AztekinTailData           9.475  1.676  11.394
KotliarovPBMCData         7.145  1.318   8.724
CampbellBrainData         6.332  2.101   8.673
BachMammaryData           7.165  1.029   9.397
NestorowaHSCData          7.039  0.980   8.491
LunSpikeInData            6.943  0.936   8.575
PaulHSCData               5.910  1.378   7.364
ShekharRetinaData         6.238  1.006   7.440
MacoskoRetinaData         5.551  1.042   6.826
MessmerESCData            4.915  0.872   6.087
LedergorMyelomaData       4.360  0.693   5.230
* 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 4.4.1 (2024-06-14) -- "Race for Your Life"
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 
365.616  68.058 450.844 

Example timings

scRNAseq.Rcheck/scRNAseq-Ex.timings

nameusersystemelapsed
AztekinTailData 9.475 1.67611.394
BachMammaryData7.1651.0299.397
BacherTCellData35.328 8.45144.766
BaronPancreasData2.770.663.77
BhaduriOrganoidData62.29512.32275.034
BuettnerESCData3.5170.6654.789
BunisHSPCData2.8700.4593.472
CampbellBrainData6.3322.1018.673
ChenBrainData2.9990.6183.762
DarmanisBrainData0.4680.0630.558
ERCCSpikeInConcentrations0.0210.0010.029
ErnstSpermatogenesisData26.885 5.87434.414
FletcherOlfactoryData1.2250.1071.355
GiladiHSCData15.178 3.90319.593
GrunHSCData0.4000.0170.422
GrunPancreasData1.0420.2211.383
HeOrganAtlasData23.905 7.13631.689
HermannSpermatogenesisData1.7000.2782.002
HuCortexData1.3860.3301.774
JessaBrainData38.152 6.31645.731
KolodziejczykESCData3.9490.7514.948
KotliarovPBMCData7.1451.3188.724
LaMannoBrainData3.2720.4513.823
LawlorPancreasData0.8280.0280.859
LedergorMyelomaData4.3600.6935.230
LengESCData0.5590.0670.629
LunSpikeInData6.9430.9368.575
MacoskoRetinaData5.5511.0426.826
MairPBMCData0.8340.1450.988
MarquesBrainData1.7340.2552.060
MessmerESCData4.9150.8726.087
MuraroPancreasData2.0070.2032.233
NestorowaHSCData7.0390.9808.491
NowakowskiCortexData3.1930.2413.456
PaulHSCData5.9101.3787.364
PollenGliaData0.3690.0340.410
ReprocessedData2.2180.2492.475
RichardTCellData3.8350.5874.750
RomanovBrainData1.3860.1071.549
SegerstolpePancreasData2.7820.1473.028
ShekharRetinaData6.2381.0067.440
StoeckiusHashingData12.734 1.60924.825
TasicBrainData1.9610.3602.324
UsoskinBrainData0.7770.0700.872
WuKidneyData0.8790.0860.978
XinPancreasData1.6540.2001.871
ZeiselBrainData2.0580.4122.505
ZeiselNervousData48.784 9.58860.036
ZhaoImmuneLiverData20.644 4.67126.392
ZhongPrefrontalData1.4750.2031.742
ZilionisLungData15.525 2.22418.101
countErccMolecules0.0350.0040.040
fetchDataset0.7530.0700.824
listDatasets0.0130.0010.013
listVersions0.0990.0000.498
polishDataset0.2190.0230.242
saveDataset1.0740.0591.081
searchDatasets1.1770.0401.475
surveyDatasets0.8530.0080.861