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CHECK report for scater on malbec1

This page was generated on 2021-05-06 12:29:00 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the scater package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1629/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scater 1.18.6  (landing page)
Alan O'Callaghan
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/scater
Branch: RELEASE_3_12
Last Commit: 813ccd0
Last Changed Date: 2021-02-25 19:11:31 -0400 (Thu, 25 Feb 2021)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: scater
Version: 1.18.6
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:scater.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings scater_1.18.6.tar.gz
StartedAt: 2021-05-06 05:40:08 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 05:50:49 -0400 (Thu, 06 May 2021)
EllapsedTime: 640.8 seconds
RetCode: 0
Status:   OK  
CheckDir: scater.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:scater.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings scater_1.18.6.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/scater.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scater/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scater’ version ‘1.18.6’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘scater’ 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 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 ... NOTE
'library' or 'require' call to ‘NMF’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* 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
runNMF       16.896  0.320  17.374
plotRLE       8.844  0.528   9.602
runMultiUMAP  6.952  0.004   6.987
plot_reddim   5.896  0.028   6.140
runUMAP       5.044  0.000   5.255
* 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 NOTE
See
  ‘/home/biocbuild/bbs-3.12-bioc/meat/scater.Rcheck/00check.log’
for details.



Installation output

scater.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL scater
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘scater’ ...
** 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 (scater)

Tests output

scater.Rcheck/tests/testthat.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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.

> Sys.setenv("R_TESTS" = "")
> library(testthat)
> library(scater)
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
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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 object is masked from 'package:base':

    expand.grid

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

Loading required package: ggplot2
> 
> test_check("scater")
Loading required package: Matrix

Attaching package: 'Matrix'

The following object is masked from 'package:S4Vectors':

    expand


Attaching package: 'DelayedArray'

The following objects are masked from 'package:base':

    aperm, apply, rowsum

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 542 ]
> 
> proc.time()
   user  system elapsed 
340.864   3.304 346.809 

Example timings

scater.Rcheck/scater-Ex.timings

nameusersystemelapsed
accessors1.8840.0241.908
annotateBMFeatures000
batchCorrectedAverages0.1360.0040.278
bootstraps0.3480.0000.349
defunct000
getExplanatoryPCs1.0320.0081.042
getVarianceExplained0.4320.0000.434
ggsce2.6800.0562.742
multiplot0.0320.0000.032
nexprs0.4200.0120.430
plotColData2.6840.0322.732
plotDots1.2840.0121.298
plotExplanatoryPCs1.5960.0001.598
plotExplanatoryVariables0.8920.0040.899
plotExpression3.8360.0083.850
plotGroupedHeatmap0.8520.0080.860
plotHeatmap0.9480.0040.952
plotHighestExprs2.0040.0042.009
plotPlatePosition1.5960.0121.610
plotRLE8.8440.5289.602
plotReducedDim3.7400.0123.761
plotRowData0.6840.0000.683
plotScater4.1680.0204.213
plot_reddim5.8960.0286.140
retrieveCellInfo0.4040.0000.406
retrieveFeatureInfo0.4280.0000.428
runColDataPCA0.8800.0000.883
runDiffusionMap0.9720.0000.973
runMDS0.8760.0000.875
runMultiUMAP6.9520.0046.987
runNMF16.896 0.32017.374
runPCA1.140.001.17
runTSNE1.8480.0041.853
runUMAP5.0440.0005.255
toSingleCellExperiment0.0040.0000.001