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CHECK report for CATALYST on machv2

This page was generated on 2020-10-17 11:58:10 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE CATALYST PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 234/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CATALYST 1.12.2
Helena L. Crowell
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/CATALYST
Branch: RELEASE_3_11
Last Commit: 3846718
Last Changed Date: 2020-07-02 09:14:54 -0400 (Thu, 02 Jul 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: CATALYST
Version: 1.12.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CATALYST.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CATALYST_1.12.2.tar.gz
StartedAt: 2020-10-16 23:24:26 -0400 (Fri, 16 Oct 2020)
EndedAt: 2020-10-16 23:38:49 -0400 (Fri, 16 Oct 2020)
EllapsedTime: 862.6 seconds
RetCode: 0
Status:  OK 
CheckDir: CATALYST.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CATALYST.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CATALYST_1.12.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/CATALYST.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CATALYST/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CATALYST’ version ‘1.12.2’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘CATALYST’ 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 ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
plotPbExprs      18.669  0.602  19.291
plotMultiHeatmap 18.307  0.770  19.099
plotDiffHeatmap  17.053  0.886  17.990
plotDR           16.502  1.214  17.728
sce2fcs          16.120  1.097  17.266
plotExprHeatmap  13.755  0.593  14.366
plotAbundances   11.061  0.886  11.970
plotClusterExprs 10.517  0.721  11.247
plotCodes        10.268  0.873  11.154
clrDR             9.669  0.658  10.338
pbMDS             9.568  0.679  10.257
SCE-accessors     8.887  1.035   9.934
plotFreqHeatmap   8.731  0.757   9.502
mergeClusters     9.038  0.421   9.466
plotMahal         8.620  0.068   8.691
cluster           8.151  0.460   8.617
filterSCE         8.115  0.363   8.488
compCytof         7.939  0.239   8.185
extractClusters   7.480  0.520   8.006
plotSpillmat      7.356  0.178   7.547
computeSpillmat   6.487  0.204   6.693
plotScatter       6.537  0.086   6.669
plotYields        6.448  0.081   6.537
estCutoffs        6.171  0.112   6.286
plotExprs         5.873  0.073   5.952
adaptSpillmat     5.637  0.187   5.829
applyCutoffs      5.428  0.177   5.611
runDR             5.298  0.049   5.345
* 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: OK


Installation output

CATALYST.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CATALYST
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘CATALYST’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (CATALYST)

Tests output

CATALYST.Rcheck/tests/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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(CATALYST)
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
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, 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")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

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

    anyMissing, rowMedians


Attaching package: 'DelayedArray'

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

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    aperm, apply, rowsum

> 
> test_check("CATALYST")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 732 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
209.075   9.133 218.460 

Example timings

CATALYST.Rcheck/CATALYST-Ex.timings

nameusersystemelapsed
SCE-accessors8.8871.0359.934
adaptSpillmat5.6370.1875.829
applyCutoffs5.4280.1775.611
assignPrelim3.4710.0223.497
clrDR 9.669 0.65810.338
cluster8.1510.4608.617
compCytof7.9390.2398.185
computeSpillmat6.4870.2046.693
data0.0080.0110.019
estCutoffs6.1710.1126.286
extractClusters7.4800.5208.006
filterSCE8.1150.3638.488
guessPanel0.0540.0060.059
mergeClusters9.0380.4219.466
normCytof4.1320.0844.226
pbMDS 9.568 0.67910.257
plotAbundances11.061 0.88611.970
plotClusterExprs10.517 0.72111.247
plotCodes10.268 0.87311.154
plotCounts1.6230.0091.633
plotDR16.502 1.21417.728
plotDiffHeatmap17.053 0.88617.990
plotEvents3.9720.0193.995
plotExprHeatmap13.755 0.59314.366
plotExprs5.8730.0735.952
plotFreqHeatmap8.7310.7579.502
plotMahal8.6200.0688.691
plotMultiHeatmap18.307 0.77019.099
plotNRS1.8340.0121.849
plotPbExprs18.669 0.60219.291
plotScatter6.5370.0866.669
plotSpillmat7.3560.1787.547
plotYields6.4480.0816.537
prepData1.9930.0192.014
runDR5.2980.0495.345
sce2fcs16.120 1.09717.266