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CHECK report for seqsetvis on machv2

This page was generated on 2020-10-17 11:59:34 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE seqsetvis PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1634/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
seqsetvis 1.8.0
Joseph R Boyd
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/seqsetvis
Branch: RELEASE_3_11
Last Commit: e646a13
Last Changed Date: 2020-04-27 15:15:20 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  NA 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: seqsetvis
Version: 1.8.0
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_1.8.0.tar.gz
StartedAt: 2020-10-17 05:15:01 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 05:25:59 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 658.1 seconds
RetCode: 0
Status:  OK 
CheckDir: seqsetvis.Rcheck
Warnings: 0

Command output

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### 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_1.8.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/seqsetvis.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.8.0’
* 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 (user + system) or elapsed time > 5s
                           user system elapsed
ssvFetchBam              11.324  0.184  11.519
ssvSignalBandedQuantiles  8.219  0.060   8.287
* 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


Installation output

seqsetvis.Rcheck/00install.out

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### Running command:
###
###   /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)

Tests output

seqsetvis.Rcheck/tests/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 
301.579   2.773 304.706 

Example timings

seqsetvis.Rcheck/seqsetvis-Ex.timings

nameusersystemelapsed
append_ynorm0.0780.0120.090
applySpline0.8250.0490.874
calc_norm_factors0.0210.0010.023
centerAtMax0.5370.0090.547
centerFixedSizeGRanges0.2370.0080.246
clusteringKmeans0.0320.0030.035
clusteringKmeansNestedHclust0.0430.0020.044
col2hex0.0020.0000.001
collapse_gr1.4210.0331.455
convert_collapsed_coord0.3320.0310.363
crossCorrByRle1.2300.0341.268
easyLoad_bed0.0880.0010.090
easyLoad_broadPeak0.1990.0020.202
easyLoad_narrowPeak0.0580.0010.059
expandCigar0.2000.0090.210
fragLen_calcStranded2.7910.0432.838
fragLen_fromMacs2Xls0.0020.0010.003
ggellipse0.7760.0080.786
harmonize_seqlengths0.1900.0090.199
prepare_fetch_GRanges0.0540.0010.056
quantileGRangesWidth0.0020.0000.003
safeBrew0.0330.0030.036
ssvFactorizeMembTable0.0400.0040.043
ssvFeatureBars0.8200.0050.825
ssvFeatureBinaryHeatmap0.6280.0090.641
ssvFeatureEuler0.6570.0060.665
ssvFeaturePie0.7360.0030.740
ssvFeatureVenn0.7680.0050.774
ssvFetchBam11.324 0.18411.519
ssvFetchBamPE3.6020.0593.665
ssvFetchBigwig2.4940.0122.507
ssvFetchGRanges1.3540.0031.357
ssvFetchSignal2.6050.0312.684
ssvMakeMembTable-methods1.0480.0101.059
ssvOverlapIntervalSets0.4430.0090.452
ssvSignalBandedQuantiles8.2190.0608.287
ssvSignalClustering3.3840.0393.424
ssvSignalHeatmap1.9270.0191.948
ssvSignalLineplot3.2660.0283.331
ssvSignalLineplotAgg1.5190.0061.525
ssvSignalScatterplot1.1480.0051.160
viewGRangesWinSample_dt2.1380.0212.163
viewGRangesWinSummary_dt1.9410.0391.982