Package: seqsetvis

Version: 1.3.6

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:seqsetvis.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings seqsetvis_1.3.6.tar.gz

StartedAt: 2019-04-09 03:35:35 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 03:43:31 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 475.7 seconds

RetCode: 0

Status:  OK

CheckDir: seqsetvis.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:seqsetvis.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings seqsetvis_1.3.6.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/seqsetvis.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.3.6’
* 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
ssvSignalBandedQuantiles 17.640  0.056   9.154
ssvFetchBam              15.946  0.035   8.094
ssvSignalClustering      11.255  0.032   3.726
ssvSignalScatterplot      7.092  0.007   2.283
ssvSignalHeatmap          6.272  0.036   2.463
ssvSignalLineplotAgg      5.421  0.016   2.273
ssvFetchSignal            5.308  0.024   2.535
* 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
  ‘/home/biocbuild/bbs-3.9-bioc/meat/seqsetvis.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL seqsetvis
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* installing to library ‘/home/biocbuild/bbs-3.9-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 Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 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: 988 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
617.303   2.748 209.926 

name	user	system	elapsed
applySpline	3.792	0.021	1.917
centerAtMax	4.781	0.032	0.950
centerFixedSizeGRanges	0.204	0.008	0.212
clusteringKmeans	2.576	0.013	0.459
clusteringKmeansNestedHclust	3.271	0.013	0.530
col2hex	0.001	0.000	0.002
crossCorrByRle	0.491	0.052	0.549
easyLoad_bed	0.087	0.000	0.087
easyLoad_broadPeak	0.187	0.000	0.187
easyLoad_narrowPeak	0.045	0.000	0.045
fragLen_calcStranded	3.156	0.064	2.579
fragLen_fromMacs2Xls	0.002	0.000	0.002
ggellipse	0.940	0.004	0.944
harmonize_seqlengths	0.148	0.000	0.148
prepare_fetch_GRanges	0.027	0.000	0.027
quantileGRangesWidth	0.001	0.000	0.001
safeBrew	0.028	0.000	0.028
ssvFactorizeMembTable	0.024	0.004	0.028
ssvFeatureBars	1.227	0.000	1.227
ssvFeatureBinaryHeatmap	0.619	0.000	0.627
ssvFeatureEuler	0.652	0.000	0.669
ssvFeaturePie	0.873	0.004	0.877
ssvFeatureVenn	0.555	0.000	0.555
ssvFetchBam	15.946	0.035	8.094
ssvFetchBigwig	2.457	0.004	1.335
ssvFetchGRanges	1.986	0.000	0.835
ssvFetchSignal	5.308	0.024	2.535
ssvMakeMembTable-methods	0.765	0.000	0.766
ssvOverlapIntervalSets	0.219	0.000	0.220
ssvSignalBandedQuantiles	17.640	0.056	9.154
ssvSignalClustering	11.255	0.032	3.726
ssvSignalHeatmap	6.272	0.036	2.463
ssvSignalLineplot	4.636	0.008	3.643
ssvSignalLineplotAgg	5.421	0.016	2.273
ssvSignalScatterplot	7.092	0.007	2.283
viewGRangesWinSample_dt	2.543	0.012	1.641
viewGRangesWinSummary_dt	4.240	0.008	1.886