Package: seqsetvis

Version: 1.6.0

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:seqsetvis.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings seqsetvis_1.6.0.tar.gz

StartedAt: 2020-04-15 05:37:47 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 05:48:29 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 641.8 seconds

RetCode: 0

Status:  OK

CheckDir: seqsetvis.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:seqsetvis.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings seqsetvis_1.6.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/seqsetvis.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (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 ‘1.6.0’
* 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 18.736  0.108  10.296
ssvFetchBam              17.580  0.080  10.079
ssvFetchBamPE            16.140  0.096   4.974
ssvSignalClustering      13.964  0.052   5.429
ssvSignalScatterplot      7.228  0.032   2.363
viewGRangesWinSummary_dt  6.372  0.028   2.569
ssvSignalHeatmap          6.352  0.040   2.223
ssvSignalLineplotAgg      6.116  0.036   2.571
ssvFetchSignal            5.588  0.040   2.952
append_ynorm              5.104  0.056   1.183
centerAtMax               5.080  0.048   1.369
* 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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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL seqsetvis
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘seqsetvis’ ...
** 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 (seqsetvis)

R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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.

> 
> ## load dependencies
> library(testthat)
> library(seqsetvis)
Loading required package: ggplot2
> library(data.table)
> 
> ## test package
> test_check(package = "seqsetvis")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 1026 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
930.076   4.212 363.532 

name	user	system	elapsed
append_ynorm	5.104	0.056	1.183
applySpline	3.468	0.016	1.324
calc_norm_factors	1.144	0.012	0.229
centerAtMax	5.080	0.048	1.369
centerFixedSizeGRanges	0.232	0.000	0.233
clusteringKmeans	2.832	0.020	0.573
clusteringKmeansNestedHclust	3.576	0.008	0.684
col2hex	0.000	0.000	0.001
crossCorrByRle	0.624	0.004	0.639
easyLoad_bed	0.060	0.000	0.062
easyLoad_broadPeak	0.128	0.000	0.128
easyLoad_narrowPeak	0.036	0.000	0.036
fragLen_calcStranded	2.808	0.016	2.274
fragLen_fromMacs2Xls	0.004	0.000	0.002
ggellipse	0.920	0.004	0.923
harmonize_seqlengths	0.168	0.004	0.175
prepare_fetch_GRanges	0.052	0.000	0.050
quantileGRangesWidth	0.000	0.004	0.003
safeBrew	0.032	0.000	0.031
ssvFactorizeMembTable	0.028	0.004	0.033
ssvFeatureBars	2.104	0.000	2.108
ssvFeatureBinaryHeatmap	0.656	0.076	0.736
ssvFeatureEuler	0.852	0.004	0.863
ssvFeaturePie	0.748	0.000	0.749
ssvFeatureVenn	0.580	0.000	0.582
ssvFetchBam	17.580	0.080	10.079
ssvFetchBamPE	16.140	0.096	4.974
ssvFetchBigwig	3.284	0.020	2.051
ssvFetchGRanges	2.412	0.008	1.291
ssvFetchSignal	5.588	0.040	2.952
ssvMakeMembTable-methods	0.692	0.000	0.696
ssvOverlapIntervalSets	0.336	0.004	0.339
ssvSignalBandedQuantiles	18.736	0.108	10.296
ssvSignalClustering	13.964	0.052	5.429
ssvSignalHeatmap	6.352	0.040	2.223
ssvSignalLineplot	4.832	0.004	3.542
ssvSignalLineplotAgg	6.116	0.036	2.571
ssvSignalScatterplot	7.228	0.032	2.363
viewGRangesWinSample_dt	2.692	0.016	1.829
viewGRangesWinSummary_dt	6.372	0.028	2.569