Back to Build/check report for BioC 3.19 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
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
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: 2024-07-02 07:30 -0400 (Tue, 02 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: 2024-07-02 12:02:22 -0400 (Tue, 02 Jul 2024)
EndedAt: 2024-07-02 12:22:52 -0400 (Tue, 02 Jul 2024)
EllapsedTime: 1230.0 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 (2024-04-24)
* 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      62.713 12.385  75.724
ZeiselNervousData        46.314  8.597  56.560
JessaBrainData           35.973  6.844  44.077
BacherTCellData          35.346  6.334  42.662
ErnstSpermatogenesisData 27.407  6.756  35.413
HeOrganAtlasData         24.221  8.054  32.864
ZhaoImmuneLiverData      18.806  3.909  23.431
GiladiHSCData            14.949  3.748  19.235
ZilionisLungData         14.611  2.087  17.146
StoeckiusHashingData     11.754  1.128  13.987
AztekinTailData           9.264  0.952  10.426
BachMammaryData           7.189  1.002   9.457
KotliarovPBMCData         6.802  1.197   8.279
NestorowaHSCData          6.533  1.028   8.061
LunSpikeInData            6.600  0.888   8.116
PaulHSCData               5.839  1.351   7.260
ShekharRetinaData         5.776  1.050   7.034
CampbellBrainData         5.447  1.322   7.007
MacoskoRetinaData         5.226  0.979   6.441
MessmerESCData            4.767  0.808   5.904
ChenBrainData             3.877  1.532   5.545
LedergorMyelomaData       3.951  0.889   5.020
* 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 (2024-04-24) -- "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 
354.367  46.316 424.153 

Example timings

scRNAseq.Rcheck/scRNAseq-Ex.timings

nameusersystemelapsed
AztekinTailData 9.264 0.95210.426
BachMammaryData7.1891.0029.457
BacherTCellData35.346 6.33442.662
BaronPancreasData2.6180.5363.316
BhaduriOrganoidData62.71312.38575.724
BuettnerESCData3.5830.6634.872
BunisHSPCData2.7000.6243.447
CampbellBrainData5.4471.3227.007
ChenBrainData3.8771.5325.545
DarmanisBrainData0.4470.0200.473
ERCCSpikeInConcentrations0.0190.0000.020
ErnstSpermatogenesisData27.407 6.75635.413
FletcherOlfactoryData1.1180.1771.306
GiladiHSCData14.949 3.74819.235
GrunHSCData0.4220.0370.463
GrunPancreasData1.0410.2001.253
HeOrganAtlasData24.221 8.05432.864
HermannSpermatogenesisData1.7200.2982.040
HuCortexData1.3960.2361.689
JessaBrainData35.973 6.84444.077
KolodziejczykESCData3.9850.5804.918
KotliarovPBMCData6.8021.1978.279
LaMannoBrainData3.1870.2503.487
LawlorPancreasData0.8190.0800.903
LedergorMyelomaData3.9510.8895.020
LengESCData0.5520.0440.598
LunSpikeInData6.6000.8888.116
MacoskoRetinaData5.2260.9796.441
MairPBMCData0.8930.1651.066
MarquesBrainData1.7890.2352.097
MessmerESCData4.7670.8085.904
MuraroPancreasData2.0580.1442.224
NestorowaHSCData6.5331.0288.061
NowakowskiCortexData3.1600.2483.432
PaulHSCData5.8391.3517.260
PollenGliaData0.3620.0130.379
ReprocessedData2.1790.0672.256
RichardTCellData3.3040.3904.015
RomanovBrainData1.2700.0511.340
SegerstolpePancreasData2.7010.4993.300
ShekharRetinaData5.7761.0507.034
StoeckiusHashingData11.754 1.12813.987
TasicBrainData1.9230.2672.194
UsoskinBrainData0.7580.0190.790
WuKidneyData0.8340.0450.895
XinPancreasData1.6730.2561.945
ZeiselBrainData2.0140.1522.190
ZeiselNervousData46.314 8.59756.560
ZhaoImmuneLiverData18.806 3.90923.431
ZhongPrefrontalData1.4980.1201.736
ZilionisLungData14.611 2.08717.146
countErccMolecules0.0430.0000.043
fetchDataset0.7520.0120.765
listDatasets0.010.000.01
listVersions0.0840.0030.627
polishDataset0.1930.0000.193
saveDataset0.9940.0520.992
searchDatasets1.1600.0121.390
surveyDatasets0.8510.0040.855