Back to Rapid builds (Linux only) of a subset of BioC 3.22 Report updated every 6 hours |
This page was generated on 2025-06-17 22:14 -0400 (Tue, 17 Jun 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 886 |
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 124/221 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | |||||||
karyoploteR 1.35.2 (landing page) Bernat Gel
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||
To the developers/maintainers of the karyoploteR package: - 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. |
Package: karyoploteR |
Version: 1.35.2 |
Command: /home/rapidbuild/bbs-3.22-bioc-rapid/R/bin/R CMD check --install=check:karyoploteR.install-out.txt --library=/home/rapidbuild/bbs-3.22-bioc-rapid/R/site-library --timings karyoploteR_1.35.2.tar.gz |
StartedAt: 2025-06-17 21:05:48 -0400 (Tue, 17 Jun 2025) |
EndedAt: 2025-06-17 21:13:22 -0400 (Tue, 17 Jun 2025) |
EllapsedTime: 454.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: karyoploteR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/rapidbuild/bbs-3.22-bioc-rapid/R/bin/R CMD check --install=check:karyoploteR.install-out.txt --library=/home/rapidbuild/bbs-3.22-bioc-rapid/R/site-library --timings karyoploteR_1.35.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/meat/karyoploteR.Rcheck’ * using R version 4.5.0 (2025-04-11) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.2 LTS * using session charset: UTF-8 * checking for file ‘karyoploteR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘karyoploteR’ version ‘1.35.2’ * 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 loading without being on the library search path ... 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 25.801 4.696 33.108 kpPlotGenes 14.188 0.102 15.731 kpPlotHorizon 10.997 0.089 12.649 mergeTranscripts 11.061 0.023 11.107 kpPlotRegions 7.764 0.002 7.773 kpPlotBAMCoverage 4.775 0.208 5.072 * 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 re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 4 NOTEs See ‘/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/meat/karyoploteR.Rcheck/00check.log’ for details.
karyoploteR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/rapidbuild/bbs-3.22-bioc-rapid/R/bin/R CMD INSTALL karyoploteR ### ############################################################################## ############################################################################## * installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library’ * installing *source* package ‘karyoploteR’ ... ** this is package ‘karyoploteR’ version ‘1.35.2’ ** 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)
karyoploteR.Rcheck/tests/testthat.Rout
R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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 17.585 1.134 18.747
karyoploteR.Rcheck/karyoploteR-Ex.timings
name | user | system | elapsed | |
addGeneNames | 2.540 | 0.076 | 2.891 | |
autotrack | 0.001 | 0.000 | 0.001 | |
colByCategory | 0.002 | 0.000 | 0.002 | |
colByChr | 0.348 | 0.001 | 0.357 | |
colByRegion | 0.711 | 0.077 | 0.798 | |
colByValue | 0.131 | 0.000 | 0.131 | |
darker | 0.001 | 0.000 | 0.001 | |
filterParams | 0.000 | 0.000 | 0.001 | |
findIntersections | 0.082 | 0.001 | 0.081 | |
getChromosomeNamesBoundingBox | 0.033 | 0.001 | 0.034 | |
getColorSchemas | 0.000 | 0.001 | 0.001 | |
getCytobandColors | 0.000 | 0.000 | 0.001 | |
getCytobands | 0.001 | 0.000 | 0.001 | |
getDataPanelBoundingBox | 0.030 | 0.000 | 0.031 | |
getDefaultPlotParams | 0.048 | 0.002 | 0.049 | |
getMainTitleBoundingBox | 0.025 | 0.000 | 0.025 | |
getTextSize | 0.052 | 0.000 | 0.052 | |
getVariantsColors | 0.000 | 0.000 | 0.001 | |
horizonColors | 0.003 | 0.000 | 0.003 | |
is.color | 0 | 0 | 0 | |
kpAbline | 0.667 | 0.029 | 0.732 | |
kpAddBaseNumbers | 0.272 | 0.003 | 0.277 | |
kpAddChromosomeNames | 0.025 | 0.000 | 0.024 | |
kpAddChromosomeSeparators | 0.307 | 0.000 | 0.323 | |
kpAddColorRect | 0.103 | 0.001 | 0.105 | |
kpAddCytobandLabels | 0.285 | 0.001 | 0.287 | |
kpAddCytobands | 0.026 | 0.000 | 0.026 | |
kpAddCytobandsAsLine | 0.051 | 0.000 | 0.055 | |
kpAddLabels | 0.307 | 0.001 | 0.348 | |
kpAddMainTitle | 0.027 | 0.000 | 0.026 | |
kpArea | 0.226 | 0.000 | 0.242 | |
kpArrows | 0.401 | 0.001 | 0.412 | |
kpAxis | 0.199 | 0.002 | 0.202 | |
kpBars | 0.120 | 0.000 | 0.121 | |
kpDataBackground | 1.361 | 0.000 | 1.421 | |
kpHeatmap | 0.092 | 0.000 | 0.093 | |
kpLines | 0.174 | 0.000 | 0.174 | |
kpPlotBAMCoverage | 4.775 | 0.208 | 5.072 | |
kpPlotBAMDensity | 1.199 | 0.020 | 1.274 | |
kpPlotBigWig | 1.788 | 0.037 | 2.005 | |
kpPlotCoverage | 0.277 | 0.001 | 0.278 | |
kpPlotDensity | 25.801 | 4.696 | 33.108 | |
kpPlotGenes | 14.188 | 0.102 | 15.731 | |
kpPlotHorizon | 10.997 | 0.089 | 12.649 | |
kpPlotLinks | 0.649 | 0.001 | 0.726 | |
kpPlotLoess | 0.074 | 0.002 | 0.076 | |
kpPlotManhattan | 3.376 | 0.044 | 3.507 | |
kpPlotMarkers | 1.166 | 0.002 | 1.173 | |
kpPlotNames | 0.075 | 0.000 | 0.076 | |
kpPlotRainfall | 0.516 | 0.000 | 0.518 | |
kpPlotRegions | 7.764 | 0.002 | 7.773 | |
kpPlotRibbon | 0.058 | 0.001 | 0.059 | |
kpPlotTranscripts | 4.430 | 0.001 | 4.433 | |
kpPoints | 0.211 | 0.000 | 0.216 | |
kpPolygon | 0.147 | 0.001 | 0.148 | |
kpRect | 0.518 | 0.002 | 0.520 | |
kpSegments | 0.358 | 0.001 | 0.359 | |
kpText | 0.175 | 0.000 | 0.175 | |
lighter | 0.000 | 0.000 | 0.001 | |
makeGenesDataFromTxDb | 1.929 | 0.008 | 1.938 | |
mergeTranscripts | 11.061 | 0.023 | 11.107 | |
plotDefaultPlotParams | 0.106 | 0.000 | 0.107 | |
plotKaryotype | 0.716 | 0.003 | 0.720 | |
plotPalettes | 0.013 | 0.001 | 0.014 | |
prepareParameters2 | 0.023 | 0.000 | 0.024 | |
prepareParameters4 | 0.024 | 0.000 | 0.024 | |
processClipping | 0.024 | 0.000 | 0.024 | |
transparent | 0.000 | 0.000 | 0.001 | |