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This page was generated on 2021-10-21 15:52:03 -0400 (Thu, 21 Oct 2021).

CHECK results for scRNAseq on nebbiolo2

To the developers/maintainers of the scRNAseq package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 338/406HostnameOS / ArchINSTALLBUILDCHECK
scRNAseq 2.7.2  (landing page)
Aaron Lun
Snapshot Date: 2021-10-21 09:30:01 -0400 (Thu, 21 Oct 2021)
git_url: https://git.bioconductor.org/packages/scRNAseq
git_branch: master
git_last_commit: c02d586
git_last_commit_date: 2021-07-28 02:21:13 -0400 (Wed, 28 Jul 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published

Summary

Package: scRNAseq
Version: 2.7.2
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:scRNAseq.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings scRNAseq_2.7.2.tar.gz
StartedAt: 2021-10-21 12:38:31 -0400 (Thu, 21 Oct 2021)
EndedAt: 2021-10-21 13:02:48 -0400 (Thu, 21 Oct 2021)
EllapsedTime: 1456.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: scRNAseq.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:scRNAseq.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings scRNAseq_2.7.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-data-experiment/meat/scRNAseq.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scRNAseq/DESCRIPTION’ ... OK
* this is package ‘scRNAseq’ version ‘2.7.2’
* 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 ... WARNING
Problems with news in ‘inst/NEWS.Rd’:
  inst/NEWS.Rd:35: unexpected section header '\section'
  inst/NEWS.Rd:51: unexpected section header '\section'
  inst/NEWS.Rd:59: unexpected section header '\section'
  inst/NEWS.Rd:67: unexpected section header '\section'
  inst/NEWS.Rd:70: unexpected END_OF_INPUT '
  '
* checking R 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 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
HeOrganAtlasData           74.028 10.622  89.716
BhaduriOrganoidData        30.213  2.532  33.679
ZeiselNervousData          29.504  2.097  33.077
BacherTCellData            20.259  2.611  23.438
JessaBrainData             20.013  2.596  24.202
LunSpikeInData             21.799  0.466  25.198
ErnstSpermatogenesisData   20.725  1.324  23.177
GiladiHSCData              19.219  2.243  22.711
LaMannoBrainData           20.107  0.527  23.399
StoeckiusHashingData       15.033  0.768  17.679
BuettnerESCData            13.728  0.664  15.975
ZhaoImmuneLiverData        11.939  0.841  13.582
MessmerESCData             11.824  0.429  14.042
BachMammaryData            11.655  0.320  13.390
ReprocessedData            11.001  0.696  12.730
AztekinTailData            10.500  1.138  12.447
ZilionisLungData           11.056  0.443  12.557
BaronPancreasData          10.748  0.435  12.230
BunisHSPCData              10.668  0.511  12.127
NestorowaHSCData            9.199  0.696  10.987
RichardTCellData            9.268  0.388  11.140
KolodziejczykESCData        8.950  0.455  10.730
KotliarovPBMCData           8.526  0.304   9.568
ZeiselBrainData             8.434  0.300   9.703
SegerstolpePancreasData     8.278  0.411   9.683
MairPBMCData                8.313  0.093   9.321
TasicBrainData              7.612  0.373   8.812
FletcherOlfactoryData       7.736  0.225   8.638
CampbellBrainData           7.625  0.312   8.501
GrunPancreasData            7.252  0.272   8.344
ChenBrainData               6.319  0.200   7.150
NowakowskiCortexData        6.250  0.236   7.235
HuCortexData                6.195  0.245   7.401
HermannSpermatogenesisData  6.074  0.124   6.862
LedergorMyelomaData         5.675  0.325   6.662
MacoskoRetinaData           5.528  0.256   6.292
XinPancreasData             5.632  0.096   6.432
DarmanisBrainData           5.448  0.112   6.152
UsoskinBrainData            5.439  0.120   6.235
ShekharRetinaData           5.242  0.268   6.129
PaulHSCData                 4.973  0.264   5.910
MuraroPancreasData          4.998  0.228   5.805
LengESCData                 4.377  0.384   5.318
ZhongPrefrontalData         4.497  0.136   5.302
MarquesBrainData            4.389  0.155   5.090
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.14-data-experiment/meat/scRNAseq.Rcheck/00check.log’
for details.



Installation output

scRNAseq.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL scRNAseq
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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, 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, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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 37 | SKIP 0 | PASS 120 ]
Warning message:
call dbDisconnect() when finished working with a connection 
> 
> proc.time()
   user  system elapsed 
526.406  28.734 622.171 

Example timings

scRNAseq.Rcheck/scRNAseq-Ex.timings

nameusersystemelapsed
AztekinTailData10.500 1.13812.447
BachMammaryData11.655 0.32013.390
BacherTCellData20.259 2.61123.438
BaronPancreasData10.748 0.43512.230
BhaduriOrganoidData30.213 2.53233.679
BuettnerESCData13.728 0.66415.975
BunisHSPCData10.668 0.51112.127
CampbellBrainData7.6250.3128.501
ChenBrainData6.3190.2007.150
DarmanisBrainData5.4480.1126.152
ERCCSpikeInConcentrations3.0590.0923.537
ErnstSpermatogenesisData20.725 1.32423.177
FletcherOlfactoryData7.7360.2258.638
GiladiHSCData19.219 2.24322.711
GrunHSCData3.1810.0443.769
GrunPancreasData7.2520.2728.344
HeOrganAtlasData74.02810.62289.716
HermannSpermatogenesisData6.0740.1246.862
HuCortexData6.1950.2457.401
JessaBrainData20.013 2.59624.202
KolodziejczykESCData 8.950 0.45510.730
KotliarovPBMCData8.5260.3049.568
LaMannoBrainData20.107 0.52723.399
LawlorPancreasData4.1430.0964.770
LedergorMyelomaData5.6750.3256.662
LengESCData4.3770.3845.318
LunSpikeInData21.799 0.46625.198
MacoskoRetinaData5.5280.2566.292
MairPBMCData8.3130.0939.321
MarquesBrainData4.3890.1555.090
MessmerESCData11.824 0.42914.042
MuraroPancreasData4.9980.2285.805
NestorowaHSCData 9.199 0.69610.987
NowakowskiCortexData6.2500.2367.235
PaulHSCData4.9730.2645.910
PollenGliaData4.0360.0924.707
ReprocessedData11.001 0.69612.730
RichardTCellData 9.268 0.38811.140
RomanovBrainData3.9270.1764.620
SegerstolpePancreasData8.2780.4119.683
ShekharRetinaData5.2420.2686.129
StoeckiusHashingData15.033 0.76817.679
TasicBrainData7.6120.3738.812
UsoskinBrainData5.4390.1206.235
WuKidneyData2.6390.0403.038
XinPancreasData5.6320.0966.432
ZeiselBrainData8.4340.3009.703
ZeiselNervousData29.504 2.09733.077
ZhaoImmuneLiverData11.939 0.84113.582
ZhongPrefrontalData4.4970.1365.302
ZilionisLungData11.056 0.44312.557
listDatasets0.0100.0010.011