Package: seqsetvis

Version: 1.6.0

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_1.6.0.tar.gz

StartedAt: 2020-04-15 05:37:44 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 05:47:13 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 568.3 seconds

RetCode: 0

Status:  OK

CheckDir: seqsetvis.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running 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_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/seqsetvis.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.6.0’
* 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
ssvFetchBam              17.104 11.954   9.596
ssvFetchBamPE            11.781  9.718   3.488
ssvSignalBandedQuantiles 15.177  6.241   8.631
ssvSignalClustering       8.584  5.040   3.592
ssvFetchBigwig            5.192  4.149   2.186
ssvFetchGRanges           5.674  3.250   1.309
ssvFetchSignal            5.447  3.250   2.294
ssvSignalScatterplot      5.418  3.099   1.508
ssvSignalLineplotAgg      3.562  3.209   2.004
viewGRangesWinSummary_dt  3.522  2.895   1.945
ssvSignalHeatmap          4.210  1.828   1.483
fragLen_calcStranded      4.223  1.654   3.502
ssvSignalLineplot         4.329  0.990   3.932
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL seqsetvis
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/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 version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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: 1026 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
622.360 436.985 271.759 

name	user	system	elapsed
append_ynorm	0.281	0.365	0.096
applySpline	1.997	1.987	1.018
calc_norm_factors	0.083	0.110	0.028
centerAtMax	2.554	2.173	0.584
centerFixedSizeGRanges	1.519	0.071	0.246
clusteringKmeans	0.128	0.147	0.044
clusteringKmeansNestedHclust	0.152	0.177	0.049
col2hex	0.007	0.009	0.002
crossCorrByRle	1.194	0.709	0.791
easyLoad_bed	0.090	0.001	0.091
easyLoad_broadPeak	0.225	0.004	0.232
easyLoad_narrowPeak	0.057	0.004	0.061
fragLen_calcStranded	4.223	1.654	3.502
fragLen_fromMacs2Xls	0.002	0.000	0.003
ggellipse	0.951	0.010	0.984
harmonize_seqlengths	0.118	0.008	0.125
prepare_fetch_GRanges	0.055	0.001	0.056
quantileGRangesWidth	0.003	0.000	0.002
safeBrew	0.031	0.002	0.034
ssvFactorizeMembTable	0.037	0.001	0.038
ssvFeatureBars	1.240	0.005	1.258
ssvFeatureBinaryHeatmap	0.692	0.004	0.701
ssvFeatureEuler	0.828	0.005	0.841
ssvFeaturePie	0.797	0.003	0.805
ssvFeatureVenn	0.801	0.003	0.813
ssvFetchBam	17.104	11.954	9.596
ssvFetchBamPE	11.781	9.718	3.488
ssvFetchBigwig	5.192	4.149	2.186
ssvFetchGRanges	5.674	3.250	1.309
ssvFetchSignal	5.447	3.250	2.294
ssvMakeMembTable-methods	1.164	0.541	0.883
ssvOverlapIntervalSets	0.396	0.008	0.409
ssvSignalBandedQuantiles	15.177	6.241	8.631
ssvSignalClustering	8.584	5.040	3.592
ssvSignalHeatmap	4.210	1.828	1.483
ssvSignalLineplot	4.329	0.990	3.932
ssvSignalLineplotAgg	3.562	3.209	2.004
ssvSignalScatterplot	5.418	3.099	1.508
viewGRangesWinSample_dt	2.989	1.913	1.918
viewGRangesWinSummary_dt	3.522	2.895	1.945