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This page was generated on 2022-06-24 12:05:27 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4156
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4221
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for SummarizedBenchmark on nebbiolo1


To the developers/maintainers of the SummarizedBenchmark package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SummarizedBenchmark.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1951/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SummarizedBenchmark 2.14.0  (landing page)
Patrick Kimes
Snapshot Date: 2022-06-23 13:55:15 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/SummarizedBenchmark
git_branch: RELEASE_3_15
git_last_commit: aac0d7a
git_last_commit_date: 2022-04-26 11:47:56 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    NA  

Summary

Package: SummarizedBenchmark
Version: 2.14.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:SummarizedBenchmark.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings SummarizedBenchmark_2.14.0.tar.gz
StartedAt: 2022-06-23 22:16:24 -0400 (Thu, 23 Jun 2022)
EndedAt: 2022-06-23 22:19:36 -0400 (Thu, 23 Jun 2022)
EllapsedTime: 192.3 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: SummarizedBenchmark.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:SummarizedBenchmark.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings SummarizedBenchmark_2.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/SummarizedBenchmark.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-pc-linux-gnu (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 ‘2.14.0’
* 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  7.3Mb
  sub-directories of 1Mb or more:
    data   6.4Mb
* 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: no visible binding for global variable ‘value’
.compare.meta: no visible binding for global variable ‘comparison’
.list2mat: no visible binding for global variable ‘.id’
.list2mat: no visible binding for global variable ‘.val’
.list2mat: no visible binding for global variable ‘.method’
.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’
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 LazyData ... WARNING
  LazyData DB of 6.4 MB without LazyDataCompression set
  See §1.1.6 of 'Writing R Extensions'
* 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: 1 WARNING, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/SummarizedBenchmark.Rcheck/00check.log’
for details.



Installation output

SummarizedBenchmark.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL SummarizedBenchmark
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/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 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"
Copyright (C) 2022 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("SummarizedBenchmark")
Loading required package: tidyr

Attaching package: 'tidyr'

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

    matches

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 object is masked from 'package:tidyr':

    expand

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

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 5.4.10
Type 'citation("mclust")' for citing this R package in publications.
Loading required package: dplyr

Attaching package: 'dplyr'

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:matrixStats':

    count

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")

Attaching package: 'iCOBRA'

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

    score, score<-

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

    score, score<-


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

Found already estimated performance metrics, replacing these
Found already estimated performance metrics, replacing these
Found already estimated performance metrics, replacing these
Found already estimated performance metrics, replacing these
[ FAIL 0 | WARN 39 | SKIP 0 | PASS 224 ]

[ FAIL 0 | WARN 39 | SKIP 0 | PASS 224 ]
> 
> proc.time()
   user  system elapsed 
 27.086   1.467  28.769 

Example timings

SummarizedBenchmark.Rcheck/SummarizedBenchmark-Ex.timings

nameusersystemelapsed
BDData-setter0.0230.0010.023
BDData0.0080.0000.008
BDMethod-setter0.0340.0000.034
BDMethod0.0070.0000.007
BDMethodList-setter0.010.000.01
BDMethodList0.0160.0000.016
BenchDesign0.0120.0020.015
SummarizedBenchmark-class0.6420.0490.692
SummarizedBenchmark0.1890.0000.190
addMethod0.0290.0000.030
addPerformanceMetric0.0470.0040.051
allSB0.0010.0000.002
assayNames-setter0.0650.0000.065
availableMetrics0.0020.0000.002
buildBench1.6500.0791.764
compareBDData0.0040.0000.004
compareBDMethod0.0320.0000.032
compareBenchDesigns0.3490.0320.382
dropMethod0.0240.0110.034
estimateMetrics0.5350.0560.591
expandMethod0.0340.0000.035
modifyMethod0.0310.0000.031
performanceMetrics-setter0.0420.0000.043
performanceMetrics0.0430.0000.043
plotMethodsOverlap0.0020.0000.002
plotROC0.0000.0010.002
printMethod0.0150.0050.021
sb0.0020.0000.001
tdat0.0020.0000.001
tidyUpMetrics0.1740.0000.174
updateBench1.2460.0481.295