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This page was generated on 2024-06-25 17:43 -0400 (Tue, 25 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4760
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4494
merida1macOS 12.7.4 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4508
kjohnson1macOS 13.6.6 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4466
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 1086/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
karyoploteR 1.30.0  (landing page)
Bernat Gel
Snapshot Date: 2024-06-23 14:00 -0400 (Sun, 23 Jun 2024)
git_url: https://git.bioconductor.org/packages/karyoploteR
git_branch: RELEASE_3_19
git_last_commit: 064c446
git_last_commit_date: 2024-04-30 10:56:05 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for karyoploteR on kjohnson1

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: 1.30.0
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_1.30.0.tar.gz
StartedAt: 2024-06-24 23:43:06 -0400 (Mon, 24 Jun 2024)
EndedAt: 2024-06-24 23:52:16 -0400 (Mon, 24 Jun 2024)
EllapsedTime: 550.4 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_1.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/karyoploteR.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-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 Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘karyoploteR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘karyoploteR’ version ‘1.30.0’
* 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 ... 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     53.054  3.642  56.914
kpPlotGenes       21.340  0.446  21.790
mergeTranscripts  15.746  0.201  15.950
kpPlotHorizon     13.431  0.070  13.504
kpPlotRegions     10.709  0.067  10.776
kpPlotBAMCoverage  9.738  0.221   9.976
kpPlotManhattan    6.521  0.140   6.688
kpPlotTranscripts  5.527  0.039   5.587
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-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/4.4-arm64/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 version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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

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, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
    union, 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 
 20.300   0.852  21.165 

Example timings

karyoploteR.Rcheck/karyoploteR-Ex.timings

nameusersystemelapsed
addGeneNames3.8730.1003.975
autotrack0.0010.0000.002
colByCategory0.0030.0000.003
colByChr0.4810.0230.504
colByRegion1.0550.1041.160
colByValue0.2090.0070.215
darker0.0010.0000.001
filterParams0.0000.0000.001
findIntersections0.1150.0010.117
getChromosomeNamesBoundingBox0.0580.0020.060
getColorSchemas0.0010.0020.003
getCytobandColors0.0000.0010.002
getCytobands0.0020.0000.002
getDataPanelBoundingBox0.0450.0010.046
getDefaultPlotParams0.0690.0070.076
getMainTitleBoundingBox0.0350.0020.037
getTextSize0.0730.0020.075
getVariantsColors0.0000.0010.001
horizonColors0.0030.0010.003
is.color0.0010.0000.001
kpAbline2.4110.6233.039
kpAddBaseNumbers0.3060.0040.310
kpAddChromosomeNames0.0300.0010.032
kpAddChromosomeSeparators0.3840.0070.393
kpAddColorRect0.1840.0050.188
kpAddCytobandLabels0.3360.0050.342
kpAddCytobands0.0320.0010.034
kpAddCytobandsAsLine0.0680.0030.070
kpAddLabels0.3900.0060.396
kpAddMainTitle0.0320.0010.033
kpArea0.3000.0040.304
kpArrows0.5720.0070.579
kpAxis0.2780.0040.282
kpBars0.1690.0030.172
kpDataBackground0.2030.0030.205
kpHeatmap0.1310.0030.134
kpLines0.2930.0030.297
kpPlotBAMCoverage9.7380.2219.976
kpPlotBAMDensity2.3060.0552.393
kpPlotBigWig0.6170.0300.658
kpPlotCoverage0.4510.0190.488
kpPlotDensity53.054 3.64256.914
kpPlotGenes21.340 0.44621.790
kpPlotHorizon13.431 0.07013.504
kpPlotLinks1.1300.0381.171
kpPlotLoess0.0690.0020.071
kpPlotManhattan6.5210.1406.688
kpPlotMarkers1.6220.0181.641
kpPlotNames0.0990.0020.101
kpPlotRainfall0.7580.0080.766
kpPlotRegions10.709 0.06710.776
kpPlotRibbon0.0780.0020.081
kpPlotTranscripts5.5270.0395.587
kpPoints0.2420.0040.246
kpPolygon0.2000.0050.205
kpRect0.7190.0050.724
kpSegments0.4930.0050.499
kpText0.2580.0060.264
lighter0.0000.0000.001
makeGenesDataFromTxDb3.3730.0913.464
mergeTranscripts15.746 0.20115.950
plotDefaultPlotParams0.1570.0020.159
plotKaryotype1.1190.0521.172
plotPalettes0.0260.0030.028
prepareParameters20.0340.0020.035
prepareParameters40.0340.0020.036
processClipping0.0330.0020.035
transparent0.0010.0000.001