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CHECK report for SummarizedBenchmark on tokay2

This page was generated on 2019-04-09 12:37:10 -0400 (Tue, 09 Apr 2019).

Package 1573/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SummarizedBenchmark 2.1.1
Alejandro Reyes , Patrick Kimes
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/SummarizedBenchmark
Branch: master
Last Commit: 3765755
Last Changed Date: 2019-01-20 12:34:07 -0400 (Sun, 20 Jan 2019)
malbec2 Linux (Ubuntu 18.04.2 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
celaya2 OS X 10.11.6 El Capitan / x86_64  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 

Summary

Package: SummarizedBenchmark
Version: 2.1.1
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SummarizedBenchmark.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings SummarizedBenchmark_2.1.1.tar.gz
StartedAt: 2019-04-09 06:14:13 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 06:19:17 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 303.7 seconds
RetCode: 0
Status:  OK  
CheckDir: SummarizedBenchmark.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:SummarizedBenchmark.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings SummarizedBenchmark_2.1.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/SummarizedBenchmark.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'SummarizedBenchmark/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'SummarizedBenchmark' version '2.1.1'
* 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 whether package 'SummarizedBenchmark' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 11.5Mb
  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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 : <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 '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'
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 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/SummarizedBenchmark.Rcheck/00check.log'
for details.



Installation output

SummarizedBenchmark.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/SummarizedBenchmark_2.1.1.tar.gz && rm -rf SummarizedBenchmark.buildbin-libdir && mkdir SummarizedBenchmark.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SummarizedBenchmark.buildbin-libdir SummarizedBenchmark_2.1.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL SummarizedBenchmark_2.1.1.zip && rm SummarizedBenchmark_2.1.1.tar.gz SummarizedBenchmark_2.1.1.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 4404k  100 4404k    0     0  41.5M      0 --:--:-- --:--:-- --:--:-- 44.7M

install for i386

* installing *source* package 'SummarizedBenchmark' ...
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'SummarizedBenchmark'
    finding HTML links ... done
    BDData-class                            html  
    BDData                                  html  
    BDMethod-class                          html  
    BDMethod                                html  
    BDMethodList-accessors                  html  
    BDMethodList-class                      html  
    BDMethodList                            html  
    BenchDesign-accessors                   html  
    BenchDesign-class                       html  
    BenchDesign                             html  
    SummarizedBenchmark-accessors           html  
    SummarizedBenchmark-class               html  
    finding level-2 HTML links ... done

    SummarizedBenchmark                     html  
    addMethod                               html  
    addPerformanceMetric                    html  
    allSB                                   html  
    availableMetrics                        html  
    buildBench                              html  
    compareBDData                           html  
    compareBDMethod                         html  
    compareBenchDesigns                     html  
    dropMethod                              html  
    estimateMetrics                         html  
    expandMethod                            html  
    hashBDData                              html  
    modifyMethod                            html  
    modmethod                               html  
    performanceMetrics                      html  
    plotMethodsOverlap                      html  
    plotROC                                 html  
    printMethod                             html  
    sb                                      html  
    tdat                                    html  
    tidyBDMethod                            html  
    tidyUpMetrics                           html  
    updateBench                             html  
** 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

install for x64

* installing *source* package 'SummarizedBenchmark' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SummarizedBenchmark' as SummarizedBenchmark_2.1.1.zip
* DONE (SummarizedBenchmark)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'SummarizedBenchmark' successfully unpacked and MD5 sums checked

Tests output

SummarizedBenchmark.Rcheck/tests_i386/testthat.Rout


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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, 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

Attaching package: 'IRanges'

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

    windows

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 5.4.3
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 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  26.34    3.31   30.42 

SummarizedBenchmark.Rcheck/tests_x64/testthat.Rout


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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, 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

Attaching package: 'IRanges'

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

    windows

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 5.4.3
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 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  28.28    2.93   31.73 

Example timings

SummarizedBenchmark.Rcheck/examples_i386/SummarizedBenchmark-Ex.timings

nameusersystemelapsed
BDMethodList0.010.010.03
BenchDesign0.000.020.01
SummarizedBenchmark-accessors0.100.030.12
SummarizedBenchmark-class0.530.070.61
SummarizedBenchmark0.150.020.17
addMethod0.030.020.05
addPerformanceMetric0.050.010.06
allSB000
availableMetrics000
buildBench1.030.221.76
dropMethod0.030.000.03
estimateMetrics0.340.020.36
expandMethod0.050.000.05
modifyMethod0.030.000.03
performanceMetrics0.050.000.05
plotMethodsOverlap0.000.010.01
plotROC0.000.020.02
printMethod0.010.000.01
sb0.000.010.02
tdat000
tidyUpMetrics0.110.000.11

SummarizedBenchmark.Rcheck/examples_x64/SummarizedBenchmark-Ex.timings

nameusersystemelapsed
BDMethodList0.030.000.03
BenchDesign0.030.000.03
SummarizedBenchmark-accessors0.110.010.13
SummarizedBenchmark-class0.980.031.01
SummarizedBenchmark0.180.020.20
addMethod0.020.020.03
addPerformanceMetric0.030.010.05
allSB0.000.020.02
availableMetrics000
buildBench0.690.150.84
dropMethod0.050.000.05
estimateMetrics0.610.000.61
expandMethod0.040.020.06
modifyMethod0.050.000.05
performanceMetrics0.080.010.09
plotMethodsOverlap0.000.020.02
plotROC0.000.020.01
printMethod0.030.000.03
sb0.000.010.02
tdat0.010.000.01
tidyUpMetrics0.160.000.16