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CHECK report for SummarizedBenchmark on machv2

This page was generated on 2020-10-17 11:59:44 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE SummarizedBenchmark PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1757/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SummarizedBenchmark 2.6.0
Patrick Kimes
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/SummarizedBenchmark
Branch: RELEASE_3_11
Last Commit: 7d6f875
Last Changed Date: 2020-04-27 15:14:45 -0400 (Mon, 27 Apr 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  WARNINGS  NA 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: SummarizedBenchmark
Version: 2.6.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SummarizedBenchmark.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SummarizedBenchmark_2.6.0.tar.gz
StartedAt: 2020-10-17 05:44:04 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 05:48:56 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 292.7 seconds
RetCode: 0
Status:  OK 
CheckDir: SummarizedBenchmark.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:SummarizedBenchmark.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings SummarizedBenchmark_2.6.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/SummarizedBenchmark.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 ‘SummarizedBenchmark/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SummarizedBenchmark’ version ‘2.6.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'tidyr', 'SummarizedExperiment', 'S4Vectors', 'BiocGenerics',
  'UpSetR', 'rlang', 'stringr', 'BiocParallel', 'ggplot2', 'mclust',
  'dplyr', 'digest', 'sessioninfo', 'crayon', 'tibble'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘SummarizedBenchmark’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 12.1Mb
  sub-directories of 1Mb or more:
    data  11.2Mb
* 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
Unexported object imported by a ':::' call: ‘BiocGenerics:::replaceSlots’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.combineSummarizedBenchmarks: no visible binding for global variable
  ‘colid’
.combineSummarizedBenchmarks: no visible binding for global variable
  ‘label’
.compare.meta: no visible binding for global variable ‘label’
.compare.meta : <anonymous>: no visible binding for global variable
  ‘label’
.compare.meta : <anonymous>: no visible binding for global variable ‘.’
.compare.meta: no visible binding for global variable ‘value’
.compare.meta: no visible binding for global variable ‘comparison’
.list2mat: no visible binding for global variable ‘.method’
.list2mat: no visible binding for global variable ‘.val’
.list2mat: no visible binding for global variable ‘.id’
.printUpdateBench: no visible binding for global variable ‘f’
.printUpdateBench: no visible binding for global variable ‘meta’
.printUpdateBench: no visible binding for global variable ‘post’
.printUpdateBench: no visible binding for global variable ‘rerun’
.printUpdateBench: no visible binding for global variable ‘overlap’
.printUpdateBench: no visible binding for global variable ‘.’
plotROC: no visible binding for global variable ‘FDR’
plotROC: no visible binding for global variable ‘TPR’
plotROC: no visible binding for global variable ‘method’
tidyUpMetrics: no visible binding for global variable ‘key’
tidyUpMetrics: no visible binding for global variable ‘value’
updateBench: no visible binding for global variable ‘overlap’
updateBench: no visible binding for global variable ‘f’
updateBench: no visible binding for global variable ‘meta’
updateBench: no visible binding for global variable ‘post’
Undefined global functions or variables:
  . .id .method .val FDR TPR colid comparison f key label meta method
  overlap post rerun value
* 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
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/SummarizedBenchmark.Rcheck/00check.log’
for details.



Installation output

SummarizedBenchmark.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘SummarizedBenchmark’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (SummarizedBenchmark)

Tests output

SummarizedBenchmark.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("SummarizedBenchmark")
Loading required package: tidyr

Attaching package: 'tidyr'

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

    matches

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:tidyr':

    expand

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

Loading required package: UpSetR
Loading required package: rlang

Attaching package: 'rlang'

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

    exprs

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

    is_false, is_null, is_true

Loading required package: stringr
Loading required package: BiocParallel
Loading required package: ggplot2
Loading required package: mclust
Package 'mclust' version 5.4.6
Type 'citation("mclust")' for citing this R package in publications.
Loading required package: dplyr

Attaching package: 'dplyr'

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

    count

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

    combine

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

    intersect, setdiff, union

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

    intersect

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

    collapse, desc, intersect, setdiff, slice, union

The following objects are masked from 'package:S4Vectors':

    first, intersect, rename, setdiff, setequal, union

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

    combine, intersect, setdiff, union

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

    matches

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

    filter, lag

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

    intersect, setdiff, setequal, union

Loading required package: digest
Loading required package: sessioninfo
Loading required package: crayon

Attaching package: 'crayon'

The following object is masked from 'package:ggplot2':

    %+%

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

    chr

Loading required package: tibble
> 
> test_check("SummarizedBenchmark")

Option rerun is set to `FALSE`:
Rerunning performance metrics only for the following methods: BH2

══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 224 | SKIPPED: 0 | WARNINGS: 7 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 39.099   1.728  40.852 

Example timings

SummarizedBenchmark.Rcheck/SummarizedBenchmark-Ex.timings

nameusersystemelapsed
BDData-setter0.0470.0010.048
BDData0.0130.0010.015
BDMethod-setter0.0630.0010.064
BDMethod0.0130.0010.013
BDMethodList-setter0.0190.0000.020
BDMethodList0.0310.0010.031
BenchDesign0.0320.0010.033
SummarizedBenchmark-class1.1400.0481.193
SummarizedBenchmark0.3790.0110.391
addMethod0.0540.0080.062
addPerformanceMetric0.6210.0080.629
allSB0.0020.0020.003
assayNames-setter0.0980.0040.102
availableMetrics0.0030.0010.004
buildBench1.8000.1001.907
compareBDData0.0080.0010.009
compareBDMethod0.0590.0010.060
compareBenchDesigns0.4010.0360.438
dropMethod0.0550.0070.062
estimateMetrics0.8970.0560.953
expandMethod0.0460.0000.047
modifyMethod0.0610.0010.062
performanceMetrics-setter0.0810.0050.086
performanceMetrics0.0870.0040.091
plotMethodsOverlap0.0020.0040.006
plotROC0.0020.0030.005
printMethod0.0350.0010.037
sb0.0020.0030.005
tdat0.0020.0030.006
tidyUpMetrics0.3060.0020.309
updateBench1.5340.0521.590