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This page was generated on 2022-01-19 11:11:47 -0500 (Wed, 19 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4161
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4056
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 3998
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4115
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for karyoploteR on merida1


To the developers/maintainers of the karyoploteR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/karyoploteR.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 973/2074HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
karyoploteR 1.21.0  (landing page)
Bernat Gel
Snapshot Date: 2022-01-18 13:55:18 -0500 (Tue, 18 Jan 2022)
git_url: https://git.bioconductor.org/packages/karyoploteR
git_branch: master
git_last_commit: cb9ad80
git_last_commit_date: 2021-10-26 12:32:46 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'regioneR' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: karyoploteR
Version: 1.21.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:karyoploteR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings karyoploteR_1.21.0.tar.gz
StartedAt: 2022-01-19 02:09:21 -0500 (Wed, 19 Jan 2022)
EndedAt: 2022-01-19 02:21:52 -0500 (Wed, 19 Jan 2022)
EllapsedTime: 750.8 seconds
RetCode: 0
Status:   OK  
CheckDir: karyoploteR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:karyoploteR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings karyoploteR_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/karyoploteR.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.21.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 (user + system) or elapsed time > 5s
                        user system elapsed
kpPlotDensity         65.784  3.675  70.019
kpPlotGenes           39.864  0.515  40.519
mergeTranscripts      29.774  0.131  29.984
kpPlotHorizon         27.967  0.087  28.175
kpPlotRegions         22.397  0.135  22.641
kpPlotTranscripts     11.752  0.037  11.823
kpPlotBAMCoverage      8.126  0.394   8.546
kpPlotManhattan        8.141  0.174   8.388
makeGenesDataFromTxDb  5.731  0.054   5.805
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/karyoploteR.Rcheck/00check.log’
for details.



Installation output

karyoploteR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL karyoploteR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘karyoploteR’ ...
** using staged installation
** 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 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 (karyoploteR)

Tests output

karyoploteR.Rcheck/tests/testthat.Rout


R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences"
Copyright (C) 2022 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.

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

Attaching package: 'BiocGenerics'

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, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
> 
> test_check("karyoploteR")
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (3)

[ FAIL 0 | WARN 0 | SKIP 3 | PASS 181 ]
> 
> proc.time()
   user  system elapsed 
 27.705   1.228  28.986 

Example timings

karyoploteR.Rcheck/karyoploteR-Ex.timings

nameusersystemelapsed
addGeneNames3.2390.0853.330
autotrack0.0010.0000.002
colByCategory0.0030.0000.003
colByChr0.9350.0080.946
colByRegion2.0580.2232.285
colByValue0.3290.0040.334
darker0.0010.0000.001
filterParams0.0010.0010.001
findIntersections0.2370.0010.239
getChromosomeNamesBoundingBox0.0750.0020.077
getColorSchemas0.0020.0030.004
getCytobandColors0.0010.0010.002
getCytobands0.0020.0000.002
getDataPanelBoundingBox0.0740.0010.075
getDefaultPlotParams0.1090.0060.114
getMainTitleBoundingBox0.0570.0010.058
getTextSize0.1450.0020.146
getVariantsColors0.0010.0000.002
horizonColors0.0060.0000.006
is.color0.0010.0000.001
kpAbline3.8020.6274.440
kpAddBaseNumbers0.7310.0060.740
kpAddChromosomeNames0.0590.0010.060
kpAddChromosomeSeparators0.8710.0400.914
kpAddColorRect0.3380.0260.366
kpAddCytobandLabels0.7730.0060.780
kpAddCytobands0.0500.0010.051
kpAddCytobandsAsLine0.1220.0020.124
kpAddLabels0.2670.0020.269
kpAddMainTitle0.0550.0010.056
kpArea0.6550.0070.663
kpArrows1.0950.0141.110
kpAxis0.5610.0030.565
kpBars0.3490.0020.351
kpDataBackground0.4200.0020.423
kpHeatmap0.2550.0020.257
kpLines0.4970.0050.504
kpPlotBAMCoverage8.1260.3948.546
kpPlotBAMDensity2.5680.0592.637
kpPlotBigWig1.7090.0561.771
kpPlotCoverage0.8480.0120.862
kpPlotDensity65.784 3.67570.019
kpPlotGenes39.864 0.51540.519
kpPlotHorizon27.967 0.08728.175
kpPlotLinks1.9520.0121.977
kpPlotLoess0.1180.0020.119
kpPlotManhattan8.1410.1748.388
kpPlotMarkers3.3090.0173.350
kpPlotNames0.2150.0020.218
kpPlotRainfall1.4080.0081.433
kpPlotRegions22.397 0.13522.641
kpPlotRibbon0.1620.0020.166
kpPlotTranscripts11.752 0.03711.823
kpPoints0.4910.0030.497
kpPolygon0.4560.0040.462
kpRect1.3270.0051.335
kpSegments0.9700.0030.977
kpText0.4790.0020.484
lighter0.0020.0000.001
makeGenesDataFromTxDb5.7310.0545.805
mergeTranscripts29.774 0.13129.984
plotDefaultPlotParams0.3040.0040.310
plotKaryotype1.9280.0251.961
plotPalettes0.0280.0030.032
prepareParameters20.0560.0010.057
prepareParameters40.0570.0020.058
processClipping0.0500.0010.052
transparent0.0010.0000.001