Package: SummarizedBenchmark

Version: 2.2.3

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:SummarizedBenchmark.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings SummarizedBenchmark_2.2.3.tar.gz

StartedAt: 2019-10-16 05:19:21 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 05:22:48 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 207.7 seconds

RetCode: 0

Status:  OK

CheckDir: SummarizedBenchmark.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:SummarizedBenchmark.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings SummarizedBenchmark_2.2.3.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/SummarizedBenchmark.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘2.2.3’
* 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 11.4Mb
  sub-directories of 1Mb or more:
    data  10.6Mb
* 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
Package in Depends field not imported from: ‘BiocGenerics’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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 global function definition for
  ‘metadata’
.combineSummarizedBenchmarks: no visible binding for global variable
  ‘label’
.compare.meta: no visible binding for global variable ‘label’
.compare.meta : : no visible binding for global variable
  ‘label’
.compare.meta : : 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 ‘params’
.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 ‘.’
.show.BDData: no visible global function definition for ‘head’
.show.BDMethodList: no visible global function definition for ‘head’
.show.BenchDesign: no visible global function definition for ‘head’
.tidyForComparison: no visible binding for global variable ‘slot’
BDData: no visible global function definition for ‘.valueClassTest’
BDMethod: no visible global function definition for ‘.valueClassTest’
BDMethodList: no visible global function definition for
  ‘.valueClassTest’
BenchDesign: no visible global function definition for
  ‘.valueClassTest’
plotROC: no visible binding for global variable ‘FDR’
plotROC: no visible binding for global variable ‘TPR’
plotROC: no visible binding for global variable ‘method’
sb.correlation: no visible global function definition for ‘cor’
sb.sdad: no visible global function definition for ‘sd’
tidyUpMetrics: no visible binding for global variable ‘key’
tidyUpMetrics: no visible binding for global variable ‘value’
updateBench: no visible global function definition for ‘metadata’
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 ‘params’
updateBench: no visible binding for global variable ‘post’
show,BDData: no visible global function definition for ‘head’
show,BDMethodList: no visible global function definition for ‘head’
show,BenchDesign: no visible global function definition for ‘head’
Undefined global functions or variables:
  . .id .method .val .valueClassTest FDR TPR colid comparison cor f
  head key label meta metadata method overlap params post rerun sd slot
  value
Consider adding
  importFrom("methods", ".valueClassTest", "slot")
  importFrom("stats", "cor", "sd")
  importFrom("utils", "head")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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-3.9-bioc/meat/SummarizedBenchmark.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL SummarizedBenchmark
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* installing to library ‘/home/biocbuild/bbs-3.9-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
** 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)

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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: 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

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, 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: ggplot2
Loading required package: mclust
Package 'mclust' version 5.4.5
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: 6 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 24.750   0.992  25.755 

name	user	system	elapsed
BDMethodList	0.023	0.000	0.023
BenchDesign	0.014	0.000	0.014
SummarizedBenchmark-accessors	0.106	0.000	0.106
SummarizedBenchmark-class	1.243	0.015	1.394
SummarizedBenchmark	0.219	0.020	0.240
addMethod	0.04	0.00	0.04
addPerformanceMetric	0.038	0.000	0.038
allSB	0.001	0.000	0.002
availableMetrics	0.003	0.000	0.003
buildBench	1.720	0.377	2.384
dropMethod	0.035	0.004	0.039
estimateMetrics	0.609	0.032	0.640
expandMethod	0.052	0.008	0.060
modifyMethod	0.041	0.012	0.054
performanceMetrics	0.082	0.004	0.085
plotMethodsOverlap	0.002	0.000	0.002
plotROC	0.003	0.000	0.003
printMethod	0.049	0.004	0.053
sb	0.002	0.000	0.002
tdat	0.003	0.000	0.003
tidyUpMetrics	0.177	0.008	0.185