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This page was generated on 2021-10-16 15:51:46 -0400 (Sat, 16 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 336/404HostnameOS / ArchINSTALLBUILDCHECK
scRNAseq 2.7.2  (landing page)
Aaron Lun
Snapshot Date: 2021-10-16 09:30:02 -0400 (Sat, 16 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: 2021-10-16 12:34:32 -0400 (Sat, 16 Oct 2021)
EndedAt: 2021-10-16 12:58:05 -0400 (Sat, 16 Oct 2021)
EllapsedTime: 1413.1 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
###
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* 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           71.348 12.540  87.965
BhaduriOrganoidData        28.690  2.292  31.613
ZeiselNervousData          27.969  1.937  31.319
JessaBrainData             19.822  3.064  24.125
ErnstSpermatogenesisData   20.148  1.332  22.632
LunSpikeInData             20.738  0.733  24.546
BacherTCellData            18.910  2.469  21.948
GiladiHSCData              18.478  2.631  22.331
LaMannoBrainData           19.344  0.684  22.614
StoeckiusHashingData       14.183  0.891  16.897
BuettnerESCData            13.234  0.414  15.204
ZhaoImmuneLiverData        11.258  0.847  12.810
MessmerESCData             11.309  0.652  13.248
AztekinTailData            10.086  1.068  12.000
BachMammaryData            10.815  0.280  12.442
BunisHSPCData              10.512  0.448  11.906
ZilionisLungData           10.338  0.475  11.841
BaronPancreasData          10.107  0.415  11.640
ReprocessedData             9.934  0.531  11.513
KolodziejczykESCData        8.928  0.607  10.903
RichardTCellData            8.753  0.472  10.455
NestorowaHSCData            8.382  0.837  10.155
SegerstolpePancreasData     7.858  0.473   9.400
ZeiselBrainData             7.971  0.245   9.273
KotliarovPBMCData           7.776  0.405   8.815
MairPBMCData                7.813  0.228   8.874
FletcherOlfactoryData       7.577  0.236   8.474
CampbellBrainData           7.428  0.272   8.220
TasicBrainData              7.169  0.448   8.461
HermannSpermatogenesisData  6.490  0.692   7.810
GrunPancreasData            6.795  0.272   7.833
HuCortexData                6.083  0.552   7.406
ChenBrainData               6.304  0.188   7.032
NowakowskiCortexData        6.006  0.293   6.974
MacoskoRetinaData           5.564  0.304   6.382
LedergorMyelomaData         5.360  0.256   6.197
UsoskinBrainData            5.253  0.152   5.950
XinPancreasData             5.267  0.095   5.913
ShekharRetinaData           4.941  0.360   5.740
DarmanisBrainData           5.178  0.112   5.818
MuraroPancreasData          4.431  0.314   5.265
MarquesBrainData            4.248  0.204   5.044
* 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
###
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* 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 
502.268  37.077 604.585 

Example timings

scRNAseq.Rcheck/scRNAseq-Ex.timings

nameusersystemelapsed
AztekinTailData10.086 1.06812.000
BachMammaryData10.815 0.28012.442
BacherTCellData18.910 2.46921.948
BaronPancreasData10.107 0.41511.640
BhaduriOrganoidData28.690 2.29231.613
BuettnerESCData13.234 0.41415.204
BunisHSPCData10.512 0.44811.906
CampbellBrainData7.4280.2728.220
ChenBrainData6.3040.1887.032
DarmanisBrainData5.1780.1125.818
ERCCSpikeInConcentrations2.9270.0923.421
ErnstSpermatogenesisData20.148 1.33222.632
FletcherOlfactoryData7.5770.2368.474
GiladiHSCData18.478 2.63122.331
GrunHSCData2.9780.0203.400
GrunPancreasData6.7950.2727.833
HeOrganAtlasData71.34812.54087.965
HermannSpermatogenesisData6.4900.6927.810
HuCortexData6.0830.5527.406
JessaBrainData19.822 3.06424.125
KolodziejczykESCData 8.928 0.60710.903
KotliarovPBMCData7.7760.4058.815
LaMannoBrainData19.344 0.68422.614
LawlorPancreasData3.9630.1524.622
LedergorMyelomaData5.3600.2566.197
LengESCData3.9520.1014.592
LunSpikeInData20.738 0.73324.546
MacoskoRetinaData5.5640.3046.382
MairPBMCData7.8130.2288.874
MarquesBrainData4.2480.2045.044
MessmerESCData11.309 0.65213.248
MuraroPancreasData4.4310.3145.265
NestorowaHSCData 8.382 0.83710.155
NowakowskiCortexData6.0060.2936.974
PaulHSCData4.3410.1964.956
PollenGliaData3.6030.1374.265
ReprocessedData 9.934 0.53111.513
RichardTCellData 8.753 0.47210.455
RomanovBrainData3.7470.2134.467
SegerstolpePancreasData7.8580.4739.400
ShekharRetinaData4.9410.3605.740
StoeckiusHashingData14.183 0.89116.897
TasicBrainData7.1690.4488.461
UsoskinBrainData5.2530.1525.950
WuKidneyData2.4490.0402.903
XinPancreasData5.2670.0955.913
ZeiselBrainData7.9710.2459.273
ZeiselNervousData27.969 1.93731.319
ZhaoImmuneLiverData11.258 0.84712.810
ZhongPrefrontalData4.2110.1564.874
ZilionisLungData10.338 0.47511.841
listDatasets0.010.000.01