Multiple platform build/check report for BioC 3.12 - CHECK report for minfi on tokay1

Package: minfi

Version: 1.36.0

Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:minfi.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings minfi_1.36.0.tar.gz

StartedAt: 2021-05-06 04:39:52 -0400 (Thu, 06 May 2021)

EndedAt: 2021-05-06 04:55:54 -0400 (Thu, 06 May 2021)

EllapsedTime: 961.6 seconds

RetCode: 0

Status: WARNINGS

CheckDir: minfi.Rcheck

Warnings: 1

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:minfi.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings minfi_1.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/minfi.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'minfi/DESCRIPTION' ... OK
* this is package 'minfi' version '1.36.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 'minfi' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEFkOrQ/R.INSTALL2018fd86966/minfi/man/GenomicMethylSet-class.Rd:129: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
  Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEFkOrQ/R.INSTALL2018fd86966/minfi/man/GenomicRatioSet-class.Rd:121: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.12-bioc/meat/minfi.Rcheck/00install.out' for details.
* checking installed package size ... OK
* 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
Unexported objects imported by ':::' calls:
  'DelayedArray:::get_verbose_block_processing'
  'DelayedArray:::normarg_grid' 'bumphunter:::.getEstimate'
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  '.guessArrayTypes'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
combineArrays      71.48   8.74   93.37
bumphunter         27.16   3.98   31.14
read.metharray.exp 15.89   0.08   15.97
read.metharray      7.50   0.08    7.58
compartments        5.82   1.65    7.48
preprocessFunnorm   4.04   2.31    6.36
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
combineArrays      73.35   3.62   77.06
bumphunter         39.23   6.18   45.42
read.metharray.exp 20.65   0.20   20.92
read.metharray     10.08   0.35   10.42
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.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, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.12-bioc/meat/minfi.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/minfi_1.36.0.tar.gz && rm -rf minfi.buildbin-libdir && mkdir minfi.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=minfi.buildbin-libdir minfi_1.36.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL minfi_1.36.0.zip && rm minfi_1.36.0.tar.gz minfi_1.36.0.zip
###
##############################################################################
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  % 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  174k  100  174k    0     0  7799k      0 --:--:-- --:--:-- --:--:-- 8313k

install for i386

* installing *source* package 'minfi' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'minfi'
    finding HTML links ... done
    DelayedArray_utils                      html  
    GenomicMethylSet-class                  html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEFkOrQ/R.INSTALL2018fd86966/minfi/man/GenomicMethylSet-class.Rd:129: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
    GenomicRatioSet-class                   html  
Rd warning: C:/Users/biocbuild/bbs-3.12-bioc/tmpdir/RtmpEFkOrQ/R.INSTALL2018fd86966/minfi/man/GenomicRatioSet-class.Rd:121: file link 'RangedSummarizedExperiment' in package 'SummarizedExperiment' does not exist and so has been treated as a topic
    IlluminaMethylationAnnotation-class     html  
    IlluminaMethylationManifest-class       html  
    MethylSet-class                         html  
    finding level-2 HTML links ... done

    RGChannelSet-class                      html  
    RatioSet-class                          html  
    blockFinder                             html  
    bumphunter                              html  
    combineArrays                           html  
    compartments                            html  
    controlStripPlot                        html  
    convertArray                            html  
    cpgCollapse                             html  
    densityBeanPlot                         html  
    densityPlot                             html  
    detectionP                              html  
    dmpFinder                               html  
    estimateCellCounts                      html  
    fixMethOutliers                         html  
    gaphunter                               html  
    getAnnotation                           html  
    getGenomicRatioSetFromGEO               html  
    getQC                                   html  
    getSex                                  html  
    logit2                                  html  
    makeGenomicRatioSetFromMatrix           html  
    mapToGenome-methods                     html  
    mdsPlot                                 html  
    minfi-defunct                           html  
    minfi-deprecated                        html  
    minfi-package                           html  
    minfiQC                                 html  
    plotBetasByType                         html  
    plotCpg                                 html  
    preprocessFunnorm                       html  
    preprocessIllumina                      html  
    preprocessNoob                          html  
    preprocessQuantile                      html  
    preprocessRaw                           html  
    preprocessSwan                          html  
    qcReport                                html  
    ratioConvert-methods                    html  
    read.metharray                          html  
    read.metharray.exp                      html  
    read.metharray.sheet                    html  
    readGEORawFile                          html  
    readTCGA                                html  
    subsetByLoci                            html  
    utils                                   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 'minfi' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'minfi' as minfi_1.36.0.zip
* DONE (minfi)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'minfi' successfully unpacked and MD5 sums checked


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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.

> require("minfi") || stop("unable to load minfi")
Loading required package: minfi
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.max, which.min

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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: 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: 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: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

Loading required package: bumphunter
Loading required package: foreach
Loading required package: iterators
Loading required package: locfit
locfit 1.5-9.4 	 2020-03-24
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
[1] TRUE
> BiocGenerics:::testPackage("minfi")
Loading required package: minfiData
Loading required package: IlluminaHumanMethylation450kmanifest
Loading required package: IlluminaHumanMethylation450kanno.ilmn12.hg19
Loading required package: digest
Loading required package: DelayedArray
Loading required package: Matrix

Attaching package: 'Matrix'

The following object is masked from 'package:S4Vectors':

    expand


Attaching package: 'DelayedArray'

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

    aperm, apply, rowsum



RUNIT TEST PROTOCOL -- Thu May 06 04:54:48 2021 
*********************************************** 
Number of test functions: 10 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
minfi RUnit Tests - 10 test functions, 0 errors, 0 failures
Number of test functions: 10 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: 'colGrid' is deprecated.
Use 'colAutoGrid' instead.
See help("Deprecated") 
2: 'colGrid' is deprecated.
Use 'colAutoGrid' instead.
See help("Deprecated") 
> 
> proc.time()
   user  system elapsed 
  55.92    3.48   60.98


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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.

> require("minfi") || stop("unable to load minfi")
Loading required package: minfi
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.max, which.min

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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: 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: 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: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

Loading required package: bumphunter
Loading required package: foreach
Loading required package: iterators
Loading required package: locfit
locfit 1.5-9.4 	 2020-03-24
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
[1] TRUE
> BiocGenerics:::testPackage("minfi")
Loading required package: minfiData
Loading required package: IlluminaHumanMethylation450kmanifest
Loading required package: IlluminaHumanMethylation450kanno.ilmn12.hg19
Loading required package: digest
Loading required package: DelayedArray
Loading required package: Matrix

Attaching package: 'Matrix'

The following object is masked from 'package:S4Vectors':

    expand


Attaching package: 'DelayedArray'

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

    aperm, apply, rowsum



RUNIT TEST PROTOCOL -- Thu May 06 04:55:46 2021 
*********************************************** 
Number of test functions: 10 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
minfi RUnit Tests - 10 test functions, 0 errors, 0 failures
Number of test functions: 10 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: 'colGrid' is deprecated.
Use 'colAutoGrid' instead.
See help("Deprecated") 
2: 'colGrid' is deprecated.
Use 'colAutoGrid' instead.
See help("Deprecated") 
> 
> proc.time()
   user  system elapsed 
  52.10    2.35   57.48

name	user	system	elapsed
GenomicMethylSet-class	0	0	0
GenomicRatioSet-class	0	0	0
IlluminaMethylationManifest-class	3.94	0.16	4.10
MethylSet-class	0	0	0
RGChannelSet-class	0	0	0
RatioSet-class	0	0	0
bumphunter	27.16	3.98	31.14
combineArrays	71.48	8.74	93.37
compartments	5.82	1.65	7.48
controlStripPlot	2.36	0.33	2.69
convertArray	1.82	0.35	2.15
densityBeanPlot	3.15	0.30	3.45
densityPlot	2.91	0.40	3.32
detectionP	0.19	0.04	0.21
dmpFinder	0.11	0.00	0.11
estimateCellCounts	0	0	0
fixMethOutliers	0.86	0.11	0.97
gaphunter	0.08	0.01	0.20
getAnnotation	0.84	0.06	0.91
getGenomicRatioSetFromGEO	0	0	0
getQC	0.22	0.02	0.23
getSex	1.10	0.12	1.22
logit2	0	0	0
makeGenomicRatioSetFromMatrix	1.37	0.18	1.55
mapToGenome-methods	0.19	0.01	0.20
mdsPlot	0.22	0.03	0.25
minfiQC	2.34	0.08	2.42
plotBetasByType	0	0	0
plotCpg	0.13	0.00	0.13
preprocessFunnorm	4.04	2.31	6.36
preprocessIllumina	2.46	0.14	2.59
preprocessNoob	0.64	0.11	0.75
preprocessQuantile	0.67	0.05	0.72
preprocessRaw	2.51	0.50	3.02
preprocessSwan	0.53	0.05	0.57
qcReport	0.04	0.01	0.05
ratioConvert-methods	0.06	0.00	0.06
read.metharray	7.50	0.08	7.58
read.metharray.exp	15.89	0.08	15.97
read.metharray.sheet	0.06	0.00	0.06
readGEORawFile	0	0	0
readTCGA	0	0	0
subsetByLoci	0.33	0.00	0.33
utils	0.12	0.03	0.16

name	user	system	elapsed
GenomicMethylSet-class	0	0	0
GenomicRatioSet-class	0	0	0
IlluminaMethylationManifest-class	4.59	0.15	4.75
MethylSet-class	0	0	0
RGChannelSet-class	0	0	0
RatioSet-class	0	0	0
bumphunter	39.23	6.18	45.42
combineArrays	73.35	3.62	77.06
compartments	2.76	0.31	3.08
controlStripPlot	3.27	0.25	3.52
convertArray	1.44	0.05	1.49
densityBeanPlot	2.02	0.23	2.25
densityPlot	3.22	0.49	3.70
detectionP	0.25	0.00	0.25
dmpFinder	0.09	0.01	0.11
estimateCellCounts	0	0	0
fixMethOutliers	0.97	0.10	1.06
gaphunter	0.09	0.00	0.10
getAnnotation	0.67	0.08	0.75
getGenomicRatioSetFromGEO	0	0	0
getQC	0.23	0.00	0.24
getSex	0.96	0.11	1.06
logit2	0	0	0
makeGenomicRatioSetFromMatrix	0.25	0.04	0.30
mapToGenome-methods	0.12	0.02	0.14
mdsPlot	0.86	0.25	1.11
minfiQC	1.81	0.19	2.00
plotBetasByType	0	0	0
plotCpg	0.09	0.00	0.09
preprocessFunnorm	3.01	0.26	3.28
preprocessIllumina	2.41	0.25	2.66
preprocessNoob	0.63	0.02	0.64
preprocessQuantile	0.73	0.04	0.78
preprocessRaw	2.16	0.27	2.42
preprocessSwan	0.51	0.01	0.53
qcReport	0.05	0.00	0.05
ratioConvert-methods	0.08	0.00	0.08
read.metharray	10.08	0.35	10.42
read.metharray.exp	20.65	0.20	20.92
read.metharray.sheet	0.09	0.00	0.09
readGEORawFile	0	0	0
readTCGA	0	0	0
subsetByLoci	0.54	0.00	0.54
utils	0.21	0.03	0.24

CHECK report for minfi on tokay1

Summary

Command output

Installation output

Tests output

Example timings