Package: seqsetvis

Version: 1.0.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:seqsetvis.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings seqsetvis_1.0.2.tar.gz

StartedAt: 2018-10-17 00:01:39 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 00:07:53 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 374.5 seconds

RetCode: 0

Status:  OK

CheckDir: seqsetvis.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:seqsetvis.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings seqsetvis_1.0.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/seqsetvis.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘seqsetvis/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘seqsetvis’ version ‘1.0.2’
* package encoding: UTF-8
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘seqsetvis’ can be installed ... OK
* 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
* 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 ... OK
* 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 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
Examples with CPU or elapsed time > 5s
                           user system elapsed
ssvSignalBandedQuantiles 15.080  4.405  10.262
ssvFetchBam               8.302  0.086   8.451
ssvSignalClustering       5.094  2.780   3.071
ssvSignalScatterplot      4.867  2.115   1.583
ssvSignalLineplotAgg      5.819  0.585   1.960
ssvSignalLineplot         5.098  0.242   4.122
* 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: OK

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL seqsetvis
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘seqsetvis’ ...
** 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
* DONE (seqsetvis)

R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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.

> 
> ## load dependencies
> library(testthat)
> library(seqsetvis)
Loading required package: ggplot2
> library(data.table)
> 
> ## test package
> test_check(package = "seqsetvis")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 831 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
141.953  14.757 107.318 

name	user	system	elapsed
applySpline	1.776	0.401	1.186
centerAtMax	2.385	0.732	0.477
centerFixedSizeGRanges	0.581	0.170	0.180
clusteringKmeans	0.086	0.057	0.039
clusteringKmeansNestedHclust	1.074	0.735	0.624
col2hex	0.012	0.013	0.004
easyLoad_bed	0.285	0.305	0.085
easyLoad_broadPeak	0.440	0.348	0.225
easyLoad_narrowPeak	0.056	0.001	0.067
fetchBam	1.434	0.056	1.517
fragLen_calcStranded	2.399	0.042	2.461
fragLen_fromMacs2Xls	0.003	0.000	0.004
ggellipse	0.903	0.007	0.914
prepare_fetch_GRanges	0.025	0.000	0.024
quantileGRangesWidth	0.002	0.001	0.003
safeBrew	0.028	0.003	0.035
ssvFactorizeMembTable	0.021	0.001	0.022
ssvFeatureBars	0.879	0.003	0.886
ssvFeatureBinaryHeatmap	0.733	0.004	0.749
ssvFeatureEuler	0.835	0.004	0.851
ssvFeaturePie	0.919	0.004	0.933
ssvFeatureVenn	0.827	0.004	0.836
ssvFetchBam	8.302	0.086	8.451
ssvFetchBam.single	3.129	0.068	3.229
ssvFetchBigwig	1.371	0.028	1.410
ssvFetchBigwig.single	0.452	0.005	0.459
ssvFetchSignal	3.061	0.035	3.137
ssvMakeMembTable-methods	0.686	0.005	0.701
ssvOverlapIntervalSets	0.280	0.004	0.285
ssvSignalBandedQuantiles	15.080	4.405	10.262
ssvSignalClustering	5.094	2.780	3.071
ssvSignalHeatmap	3.234	1.169	1.663
ssvSignalLineplot	5.098	0.242	4.122
ssvSignalLineplotAgg	5.819	0.585	1.960
ssvSignalScatterplot	4.867	2.115	1.583
viewGRangesWinSample_dt	1.690	0.007	1.714
viewGRangesWinSummary_dt	1.713	0.011	1.600