Package: seqsetvis

Version: 1.7.1

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_1.7.1.tar.gz

StartedAt: 2020-01-16 08:48:45 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 09:01:38 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 773.1 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_1.7.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/seqsetvis.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.7.1’
* 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 (user + system) or elapsed time > 5s
                           user system elapsed
ssvFetchBam              19.388  6.603  13.271
ssvSignalBandedQuantiles 18.216  5.245  10.924
ssvFetchBamPE            14.205  6.651   4.724
ssvSignalClustering       5.807  2.535   3.294
ssvFetchBigwig            5.743  2.328   3.270
ssvFetchGRanges           5.640  2.252   1.745
ssvFetchSignal            5.382  2.269   3.206
ssvSignalScatterplot      5.184  1.896   1.678
fragLen_calcStranded      5.012  0.932   3.682
viewGRangesWinSummary_dt  4.115  1.678   2.477
ssvSignalLineplotAgg      4.075  1.541   2.375
centerAtMax               4.409  1.095   1.693
ssvSignalLineplot         4.734  0.417   4.368
* 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/4.0/Resources/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 Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 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: 1042 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
739.291 263.885 367.004 

name	user	system	elapsed
append_ynorm	0.327	0.234	0.121
applySpline	2.229	0.993	1.335
calc_norm_factors	0.074	0.041	0.031
centerAtMax	4.409	1.095	1.693
centerFixedSizeGRanges	0.316	0.012	0.328
clusteringKmeans	0.125	0.077	0.052
clusteringKmeansNestedHclust	0.157	0.102	0.064
col2hex	0.006	0.004	0.003
collapse_gr	1.834	0.400	1.673
convert_collapsed_coord	0.520	0.050	0.571
crossCorrByRle	0.776	0.006	0.785
easyLoad_bed	0.117	0.002	0.120
easyLoad_broadPeak	0.241	0.003	0.244
easyLoad_narrowPeak	0.075	0.001	0.076
expandCigar	0.439	0.178	0.254
fragLen_calcStranded	5.012	0.932	3.682
fragLen_fromMacs2Xls	0.003	0.000	0.005
ggellipse	1.226	0.023	1.250
harmonize_seqlengths	0.261	0.011	0.297
prepare_fetch_GRanges	0.067	0.001	0.067
quantileGRangesWidth	0.003	0.001	0.003
safeBrew	0.040	0.004	0.045
ssvFactorizeMembTable	0.050	0.004	0.053
ssvFeatureBars	1.394	0.011	1.405
ssvFeatureBinaryHeatmap	0.871	0.005	0.878
ssvFeatureEuler	1.153	0.009	1.168
ssvFeaturePie	1.069	0.007	1.084
ssvFeatureVenn	1.131	0.009	1.141
ssvFetchBam	19.388	6.603	13.271
ssvFetchBamPE	14.205	6.651	4.724
ssvFetchBigwig	5.743	2.328	3.270
ssvFetchGRanges	5.640	2.252	1.745
ssvFetchSignal	5.382	2.269	3.206
ssvMakeMembTable-methods	1.318	0.316	1.055
ssvOverlapIntervalSets	0.505	0.008	0.513
ssvSignalBandedQuantiles	18.216	5.245	10.924
ssvSignalClustering	5.807	2.535	3.294
ssvSignalHeatmap	3.180	1.123	2.129
ssvSignalLineplot	4.734	0.417	4.368
ssvSignalLineplotAgg	4.075	1.541	2.375
ssvSignalScatterplot	5.184	1.896	1.678
viewGRangesWinSample_dt	3.553	1.089	2.464
viewGRangesWinSummary_dt	4.115	1.678	2.477