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This page was generated on 2024-12-24 11:43 -0500 (Tue, 24 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" 4754
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 4472
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4426
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" 4381
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" 4373
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

Package 1069/2274HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
karyoploteR 1.33.0  (landing page)
Bernat Gel
Snapshot Date: 2024-12-23 13:40 -0500 (Mon, 23 Dec 2024)
git_url: https://git.bioconductor.org/packages/karyoploteR
git_branch: devel
git_last_commit: 4e6d89c
git_last_commit_date: 2024-10-29 10:16:53 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  NO, package depends on 'rtracklayer' which is only available as a source package that needs compilation
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  NO, package depends on 'rtracklayer' which is only available as a source package that needs compilation
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for karyoploteR on lconway

To the developers/maintainers of the karyoploteR package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: karyoploteR
Version: 1.33.0
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_1.33.0.tar.gz
StartedAt: 2024-12-23 21:13:03 -0500 (Mon, 23 Dec 2024)
EndedAt: 2024-12-23 21:22:18 -0500 (Mon, 23 Dec 2024)
EllapsedTime: 555.3 seconds
RetCode: 0
Status:   OK  
CheckDir: karyoploteR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.33.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/karyoploteR.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘karyoploteR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘karyoploteR’ version ‘1.33.0’
* 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 ‘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 ... NOTE
Problems with news in ‘NEWS’:
  Cannot process chunk/lines:
    NEW FEATURES
  Cannot process chunk/lines:
    SIGNIFICANT USER-VISIBLE CHANGES
  Cannot process chunk/lines:
    NEW FEATURES
  Cannot process chunk/lines:
    SIGNIFICANT USER-VISIBLE CHANGES
* checking code 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 whether startup messages can be suppressed ... 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 ... NOTE
checkRd: (-1) kpPlotBAMCoverage.Rd:48: Lost braces
    48 | There's more information at the \url{https://bernatgel.github.io/karyoploter_tutorial/}{karyoploteR tutorial}.
       |                                                                                        ^
checkRd: (-1) kpPlotBAMDensity.Rd:48: Lost braces
    48 | There's more information at the \url{https://bernatgel.github.io/karyoploter_tutorial/}{karyoploteR tutorial}.
       |                                                                                        ^
checkRd: (-1) kpPlotCoverage.Rd:46: Lost braces
    46 |  There's more information at the \url{https://bernatgel.github.io/karyoploter_tutorial/}{karyoploteR tutorial}.
       |                                                                                         ^
checkRd: (-1) kpPlotDensity.Rd:42: Lost braces
    42 | There's more information at the \url{https://bernatgel.github.io/karyoploter_tutorial/}{karyoploteR tutorial}.
       |                                                                                        ^
checkRd: (-1) kpPlotManhattan.Rd:80: Lost braces
    80 | There's more information at the \url{https://bernatgel.github.io/karyoploter_tutorial/}{karyoploteR tutorial}.
       |                                                                                        ^
checkRd: (-1) kpPlotMarkers.Rd:81: Lost braces
    81 | There's more information at the \url{https://bernatgel.github.io/karyoploter_tutorial/}{karyoploteR tutorial}.
       |                                                                                        ^
checkRd: (-1) kpPlotRainfall.Rd:47: Lost braces
    47 | There's more information at the \url{https://bernatgel.github.io/karyoploter_tutorial/}{karyoploteR tutorial}.
       |                                                                                        ^
checkRd: (-1) kpPoints.Rd:54: Lost braces
    54 | There's more information at the \url{https://bernatgel.github.io/karyoploter_tutorial/}{karyoploteR tutorial}.
       |                                                                                        ^
checkRd: (-1) kpRect.Rd:55: Lost braces
    55 | There's more information at the \url{https://bernatgel.github.io/karyoploter_tutorial/}{karyoploteR tutorial}.
       |                                                                                        ^
checkRd: (-1) plotKaryotype.Rd:61: Lost braces
    61 | There's more information at the \url{https://bernatgel.github.io/karyoploter_tutorial/}{karyoploteR tutorial}.
       |                                                                                        ^
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  getCytobands.Rd: GenomicRanges, memoise, forget
  kpPlotBAMCoverage.Rd: bamsignals
  kpPlotBAMDensity.Rd: Rsamtools
  kpPlotBigWig.Rd: BigWigFile
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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     41.776  3.435  45.632
kpPlotGenes       24.280  0.428  24.888
mergeTranscripts  18.359  0.189  18.673
kpPlotHorizon     17.354  0.135  17.626
kpPlotRegions     13.990  0.228  14.296
kpPlotBAMCoverage  8.957  0.313   9.426
kpPlotTranscripts  7.337  0.057   7.443
kpPlotManhattan    5.166  0.172   5.386
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-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/4.5-x86_64/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) (2024-11-20 r87352) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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: generics

Attaching package: 'generics'

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

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    findMatches

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

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
> 
> test_check("karyoploteR")
[ FAIL 0 | WARN 0 | SKIP 3 | PASS 177 ]

══ Skipped tests (3) ═══════════════════════════════════════════════════════════
• empty test (3): 'test_plotKaryotype.R:27:1', 'test_plotKaryotype.R:34:1',
  'test_plotKaryotype.R:44:1'

[ FAIL 0 | WARN 0 | SKIP 3 | PASS 177 ]
> 
> proc.time()
   user  system elapsed 
 19.545   1.005  20.686 

Example timings

karyoploteR.Rcheck/karyoploteR-Ex.timings

nameusersystemelapsed
addGeneNames3.6930.0993.824
autotrack0.0010.0000.001
colByCategory0.0020.0000.002
colByChr0.5760.0110.594
colByRegion2.3230.1232.473
colByValue0.2210.0060.232
darker0.0010.0000.001
filterParams0.0010.0000.001
findIntersections0.1630.0020.166
getChromosomeNamesBoundingBox0.0610.0020.065
getColorSchemas0.0010.0020.003
getCytobandColors0.0010.0020.003
getCytobands0.0020.0000.002
getDataPanelBoundingBox0.0510.0020.055
getDefaultPlotParams0.0800.0080.089
getMainTitleBoundingBox0.0360.0020.040
getTextSize0.0980.0070.109
getVariantsColors0.0010.0010.001
horizonColors0.0030.0010.004
is.color0.0000.0000.001
kpAbline2.5911.0383.693
kpAddBaseNumbers0.4750.0090.491
kpAddChromosomeNames0.0380.0030.045
kpAddChromosomeSeparators0.5220.0090.537
kpAddColorRect0.1750.0040.182
kpAddCytobandLabels0.4670.0090.484
kpAddCytobands0.0430.0030.046
kpAddCytobandsAsLine0.0830.0040.093
kpAddLabels0.5160.0110.545
kpAddMainTitle0.0390.0020.046
kpArea0.4390.0070.452
kpArrows0.6980.0110.716
kpAxis0.3630.0060.374
kpBars0.2330.0040.241
kpDataBackground0.3030.0040.314
kpHeatmap0.1580.0040.176
kpLines0.3150.0060.329
kpPlotBAMCoverage8.9570.3139.426
kpPlotBAMDensity1.7290.0511.808
kpPlotBigWig1.0260.0331.070
kpPlotCoverage0.4700.0060.479
kpPlotDensity41.776 3.43545.632
kpPlotGenes24.280 0.42824.888
kpPlotHorizon17.354 0.13517.626
kpPlotLinks1.0950.0131.119
kpPlotLoess0.0730.0020.076
kpPlotManhattan5.1660.1725.386
kpPlotMarkers1.8490.0171.877
kpPlotNames0.1400.0020.143
kpPlotRainfall0.9020.0160.925
kpPlotRegions13.990 0.22814.296
kpPlotRibbon0.0970.0030.101
kpPlotTranscripts7.3370.0577.443
kpPoints0.3180.0040.324
kpPolygon0.2230.0050.230
kpRect0.8330.0100.846
kpSegments0.5960.0070.606
kpText0.2800.0040.285
lighter0.0010.0000.001
makeGenesDataFromTxDb3.5720.0713.676
mergeTranscripts18.359 0.18918.673
plotDefaultPlotParams0.1800.0020.183
plotKaryotype1.2040.0331.246
plotPalettes0.0180.0030.022
prepareParameters20.0410.0020.043
prepareParameters40.0420.0020.044
processClipping0.0380.0010.040
transparent0.0010.0000.001