Package: seqsetvis

Version: 1.3.6

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_1.3.6.tar.gz

StartedAt: 2019-04-09 03:41:51 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 03:49:10 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 439.7 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_1.3.6.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/seqsetvis.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘1.3.6’
* 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 ... NOTE
ssvFetchBam.single: no visible binding for global variable ‘x’
ssvFetchBam.single: no visible binding for global variable ‘id’
Undefined global functions or variables:
  id x
* 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
ssvFetchBam              16.055 10.086   8.459
ssvSignalBandedQuantiles 13.439  6.300   8.595
ssvSignalClustering       5.833  4.495   2.628
ssvSignalScatterplot      4.767  3.945   1.400
ssvFetchBigwig            4.867  3.326   1.425
ssvSignalLineplotAgg      4.136  3.446   1.759
ssvFetchSignal            4.359  2.656   1.946
viewGRangesWinSummary_dt  3.508  2.384   1.513
ssvFetchGRanges           3.491  2.111   0.794
applySpline               3.354  1.985   1.690
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/seqsetvis.Rcheck/00check.log’
for details.

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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/3.6/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 Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
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: 988 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
426.824 296.452 158.580 

name	user	system	elapsed
applySpline	3.354	1.985	1.690
centerAtMax	1.640	1.317	0.455
centerFixedSizeGRanges	0.610	0.439	0.231
clusteringKmeans	0.191	0.136	0.051
clusteringKmeansNestedHclust	0.224	0.155	0.055
col2hex	0.012	0.006	0.003
crossCorrByRle	1.167	0.586	0.645
easyLoad_bed	0.088	0.001	0.095
easyLoad_broadPeak	0.179	0.001	0.186
easyLoad_narrowPeak	0.048	0.001	0.050
fragLen_calcStranded	3.611	1.339	2.625
fragLen_fromMacs2Xls	0.002	0.000	0.002
ggellipse	0.898	0.011	0.921
harmonize_seqlengths	0.133	0.004	0.139
prepare_fetch_GRanges	0.023	0.001	0.023
quantileGRangesWidth	0.001	0.000	0.002
safeBrew	0.024	0.003	0.026
ssvFactorizeMembTable	0.037	0.002	0.038
ssvFeatureBars	1.222	0.011	1.250
ssvFeatureBinaryHeatmap	0.595	0.004	0.605
ssvFeatureEuler	0.855	0.007	0.874
ssvFeaturePie	0.888	0.003	0.901
ssvFeatureVenn	0.861	0.004	0.883
ssvFetchBam	16.055	10.086	8.459
ssvFetchBigwig	4.867	3.326	1.425
ssvFetchGRanges	3.491	2.111	0.794
ssvFetchSignal	4.359	2.656	1.946
ssvMakeMembTable-methods	1.153	0.504	0.741
ssvOverlapIntervalSets	0.274	0.005	0.286
ssvSignalBandedQuantiles	13.439	6.300	8.595
ssvSignalClustering	5.833	4.495	2.628
ssvSignalHeatmap	2.600	1.929	1.374
ssvSignalLineplot	3.871	0.830	3.333
ssvSignalLineplotAgg	4.136	3.446	1.759
ssvSignalScatterplot	4.767	3.945	1.400
viewGRangesWinSample_dt	2.832	1.841	1.466
viewGRangesWinSummary_dt	3.508	2.384	1.513