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CHECK report for karyoploteR on malbec1

This page was generated on 2019-04-16 11:52:34 -0400 (Tue, 16 Apr 2019).

Package 813/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
karyoploteR 1.8.8
Bernat Gel
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/karyoploteR
Branch: RELEASE_3_8
Last Commit: be20832
Last Changed Date: 2019-04-02 08:11:59 -0400 (Tue, 02 Apr 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: karyoploteR
Version: 1.8.8
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:karyoploteR.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings karyoploteR_1.8.8.tar.gz
StartedAt: 2019-04-16 00:56:33 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 01:03:25 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 411.3 seconds
RetCode: 0
Status:  OK 
CheckDir: karyoploteR.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:karyoploteR.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings karyoploteR_1.8.8.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/karyoploteR.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘karyoploteR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘karyoploteR’ version ‘1.8.8’
* 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 ‘karyoploteR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘regioneR’ ‘GenomicRanges’
A package should be listed in only one of these fields.
* 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 R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
kpPlotDensity     28.812  3.356  37.913
kpPlotGenes       12.960  0.024  13.021
kpPlotRegions     10.416  0.000  10.511
kpPlotCoverage     8.252  0.004   8.285
kpPlotTranscripts  6.848  0.000   6.874
kpPlotBAMCoverage  6.020  0.132   6.156
getCytobands       4.744  0.048  31.785
* 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-3.8-bioc/meat/karyoploteR.Rcheck/00check.log’
for details.



Installation output

karyoploteR.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL karyoploteR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘karyoploteR’ ...
** R
** 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
* DONE (karyoploteR)

Tests output

karyoploteR.Rcheck/tests/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
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.

> library(testthat)
> library(karyoploteR)
Loading required package: regioneR
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
> 
> test_check("karyoploteR")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 128 SKIPPED: 3 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 15.120   0.424  15.569 

Example timings

karyoploteR.Rcheck/karyoploteR-Ex.timings

nameusersystemelapsed
autotrack0.0040.0000.002
colByChr0.6240.0040.630
darker0.0040.0000.002
filterParams0.0000.0000.001
getChromosomeNamesBoundingBox0.0560.0000.055
getCytobandColors0.0040.0000.002
getCytobands 4.744 0.04831.785
getDefaultPlotParams0.0560.0000.056
getMainTitleBoundingBox0.0240.0000.024
getVariantsColors0.0000.0000.001
kpAbline1.7480.0761.897
kpAddBaseNumbers0.3920.0000.389
kpAddChromosomeNames0.0400.0000.042
kpAddChromosomeSeparators0.4200.0000.422
kpAddCytobandLabels0.2320.0000.231
kpAddCytobands0.0200.0040.023
kpAddCytobandsAsLine0.0240.0000.024
kpAddLabels0.0560.0000.056
kpAddMainTitle0.0240.0000.024
kpArea0.2280.0000.227
kpArrows0.3600.0000.359
kpAxis0.1240.0000.124
kpBars0.0960.0000.097
kpDataBackground0.120.000.12
kpHeatmap0.0800.0000.081
kpLines0.160.000.16
kpPlotBAMCoverage6.0200.1326.156
kpPlotBAMDensity2.0800.0322.111
kpPlotBigWig0.9160.0000.937
kpPlotCoverage8.2520.0048.285
kpPlotDensity28.812 3.35637.913
kpPlotGenes12.960 0.02413.021
kpPlotLinks0.8400.0000.841
kpPlotLoess0.9040.0280.936
kpPlotMarkers1.2840.0001.284
kpPlotNames0.0520.0000.054
kpPlotRainfall0.6120.0000.612
kpPlotRegions10.416 0.00010.511
kpPlotRibbon0.0720.0080.079
kpPlotTranscripts6.8480.0006.874
kpPoints0.2240.0000.224
kpPolygon0.2040.0000.203
kpRect0.8320.0000.831
kpSegments0.5560.0000.554
kpText0.2560.0000.267
lighter0.0000.0000.002
makeGenesDataFromTxDb4.0400.0044.086
plotDefaultPlotParams0.1280.0000.130
plotKaryotype1.0600.0041.068
prepareParameters20.0440.0000.044
prepareParameters40.0240.0000.025