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CHECK report for SummarizedBenchmark on malbec2

This page was generated on 2018-10-17 08:31:23 -0400 (Wed, 17 Oct 2018).

Package 1445/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SummarizedBenchmark 1.0.4
Alejandro Reyes , Patrick Kimes
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/SummarizedBenchmark
Branch: RELEASE_3_7
Last Commit: 705ef69
Last Changed Date: 2018-07-23 10:25:46 -0400 (Mon, 23 Jul 2018)
malbec2 Linux (Ubuntu 16.04.1 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: SummarizedBenchmark
Version: 1.0.4
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:SummarizedBenchmark.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings SummarizedBenchmark_1.0.4.tar.gz
StartedAt: 2018-10-16 04:03:31 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 04:05:42 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 131.1 seconds
RetCode: 0
Status:  OK 
CheckDir: SummarizedBenchmark.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:SummarizedBenchmark.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings SummarizedBenchmark_1.0.4.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/SummarizedBenchmark.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.0.4’
* 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’
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  9.2Mb
  sub-directories of 1Mb or more:
    data   8.9Mb
* 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
.list2mat : <anonymous>: no visible binding for global variable
  ‘.method’
.list2mat : <anonymous>: no visible binding for global variable ‘.val’
.list2mat : <anonymous>: no visible binding for global variable ‘.id’
plotROC: no visible binding for global variable ‘FDR’
plotROC: no visible binding for global variable ‘TPR’
plotROC: no visible binding for global variable ‘method’
Undefined global functions or variables:
  .id .method .val FDR TPR method
* 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
  ‘/home/biocbuild/bbs-3.7-bioc/meat/SummarizedBenchmark.Rcheck/00check.log’
for details.



Installation output

SummarizedBenchmark.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL SummarizedBenchmark
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘SummarizedBenchmark’ ...
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (SummarizedBenchmark)

Tests output

SummarizedBenchmark.Rcheck/tests/testthat.Rout


R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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
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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, 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

Loading required package: BiocParallel

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

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: ggplot2
Loading required package: mclust
Package 'mclust' version 5.4.1
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

> 
> test_check("SummarizedBenchmark")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 134 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 10.580   1.320  12.043 

Example timings

SummarizedBenchmark.Rcheck/SummarizedBenchmark-Ex.timings

nameusersystemelapsed
Accessors0.0640.0120.074
BenchDesign0.0000.0000.001
SummarizedBenchmark-class0.4960.0360.620
SummarizedBenchmark0.1320.0040.136
addMethod0.0200.0000.019
addPerformanceMetric0.0360.0000.036
availableMetrics0.0040.0000.004
buildBench0.1880.0880.292
dropMethod0.0000.0000.001
estimateMetrics0.3880.0240.416
expandMethod0.0160.0040.020
is.BenchDesign0.0040.0000.002
modifyMethod0.0040.0000.006
performanceMetrics0.0640.0080.075
plotMethodsOverlap0.0000.0000.002
plotROC0.0040.0000.003
print.BenchDesign0.0040.0000.001
printMethod0.0000.0000.002
tdat0.0000.0000.002
tidyUpMetrics0.1200.0120.130