| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-06-06 11:00:34 -0000 (Tue, 06 Jun 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4366 |
| 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 | ||||
|
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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 1029/2199 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| karyoploteR 1.27.0 (landing page) Bernat Gel
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | |||||||||
| Package: karyoploteR |
| Version: 1.27.0 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:karyoploteR.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings karyoploteR_1.27.0.tar.gz |
| StartedAt: 2023-06-06 00:50:00 -0000 (Tue, 06 Jun 2023) |
| EndedAt: 2023-06-06 01:01:18 -0000 (Tue, 06 Jun 2023) |
| EllapsedTime: 678.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: karyoploteR.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:karyoploteR.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings karyoploteR_1.27.0.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/karyoploteR.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘karyoploteR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘karyoploteR’ version ‘1.27.0’
* 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 ... 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 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 loading without being on the library search path ... OK
* checking 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 ... 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 46.446 3.614 50.354
kpPlotGenes 29.849 0.847 30.752
mergeTranscripts 24.210 0.204 24.455
kpPlotHorizon 19.663 0.155 19.857
kpPlotRegions 16.279 0.048 16.359
kpPlotTranscripts 9.501 0.104 9.623
kpPlotBAMCoverage 7.302 0.155 7.471
kpPlotManhattan 5.332 0.080 5.423
* 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 ...
‘karyoploteR.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.18-bioc/meat/karyoploteR.Rcheck/00check.log’
for details.
karyoploteR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL karyoploteR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/site-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)
karyoploteR.Rcheck/tests/testthat.Rout
R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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
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, sort, 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 181 ]
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (3)
[ FAIL 0 | WARN 0 | SKIP 3 | PASS 181 ]
>
> proc.time()
user system elapsed
22.566 1.580 24.179
karyoploteR.Rcheck/karyoploteR-Ex.timings
| name | user | system | elapsed | |
| addGeneNames | 2.726 | 0.060 | 2.791 | |
| autotrack | 0.001 | 0.000 | 0.001 | |
| colByCategory | 0.003 | 0.000 | 0.003 | |
| colByChr | 0.725 | 0.000 | 0.726 | |
| colByRegion | 1.466 | 0.036 | 1.504 | |
| colByValue | 0.251 | 0.004 | 0.256 | |
| darker | 0.001 | 0.000 | 0.002 | |
| filterParams | 0.001 | 0.000 | 0.001 | |
| findIntersections | 0.171 | 0.000 | 0.172 | |
| getChromosomeNamesBoundingBox | 0.052 | 0.000 | 0.053 | |
| getColorSchemas | 0.002 | 0.000 | 0.001 | |
| getCytobandColors | 0.000 | 0.001 | 0.001 | |
| getCytobands | 0.000 | 0.001 | 0.002 | |
| getDataPanelBoundingBox | 0.057 | 0.000 | 0.058 | |
| getDefaultPlotParams | 0.091 | 0.004 | 0.096 | |
| getMainTitleBoundingBox | 0.043 | 0.000 | 0.043 | |
| getTextSize | 0.114 | 0.000 | 0.114 | |
| getVariantsColors | 0.000 | 0.001 | 0.001 | |
| horizonColors | 0.003 | 0.001 | 0.005 | |
| is.color | 0.001 | 0.000 | 0.001 | |
| kpAbline | 2.721 | 0.068 | 2.796 | |
| kpAddBaseNumbers | 0.516 | 0.000 | 0.517 | |
| kpAddChromosomeNames | 0.043 | 0.000 | 0.043 | |
| kpAddChromosomeSeparators | 0.630 | 0.056 | 0.688 | |
| kpAddColorRect | 0.229 | 0.008 | 0.238 | |
| kpAddCytobandLabels | 0.520 | 0.000 | 0.521 | |
| kpAddCytobands | 0.04 | 0.00 | 0.04 | |
| kpAddCytobandsAsLine | 0.082 | 0.000 | 0.083 | |
| kpAddLabels | 0.611 | 0.000 | 0.613 | |
| kpAddMainTitle | 0.040 | 0.000 | 0.041 | |
| kpArea | 0.462 | 0.000 | 0.464 | |
| kpArrows | 0.750 | 0.000 | 0.752 | |
| kpAxis | 0.399 | 0.004 | 0.404 | |
| kpBars | 0.232 | 0.008 | 0.241 | |
| kpDataBackground | 0.298 | 0.000 | 0.298 | |
| kpHeatmap | 0.191 | 0.000 | 0.191 | |
| kpLines | 0.387 | 0.024 | 0.412 | |
| kpPlotBAMCoverage | 7.302 | 0.155 | 7.471 | |
| kpPlotBAMDensity | 1.728 | 0.024 | 1.756 | |
| kpPlotBigWig | 1.122 | 0.004 | 1.131 | |
| kpPlotCoverage | 0.565 | 0.012 | 0.578 | |
| kpPlotDensity | 46.446 | 3.614 | 50.354 | |
| kpPlotGenes | 29.849 | 0.847 | 30.752 | |
| kpPlotHorizon | 19.663 | 0.155 | 19.857 | |
| kpPlotLinks | 1.288 | 0.012 | 1.303 | |
| kpPlotLoess | 0.080 | 0.004 | 0.083 | |
| kpPlotManhattan | 5.332 | 0.080 | 5.423 | |
| kpPlotMarkers | 2.342 | 0.004 | 2.350 | |
| kpPlotNames | 0.157 | 0.000 | 0.157 | |
| kpPlotRainfall | 1.130 | 0.000 | 1.132 | |
| kpPlotRegions | 16.279 | 0.048 | 16.359 | |
| kpPlotRibbon | 0.122 | 0.000 | 0.121 | |
| kpPlotTranscripts | 9.501 | 0.104 | 9.623 | |
| kpPoints | 0.404 | 0.004 | 0.408 | |
| kpPolygon | 0.314 | 0.000 | 0.314 | |
| kpRect | 1.196 | 0.000 | 1.199 | |
| kpSegments | 0.766 | 0.000 | 0.767 | |
| kpText | 0.368 | 0.004 | 0.373 | |
| lighter | 0.001 | 0.000 | 0.001 | |
| makeGenesDataFromTxDb | 4.406 | 0.052 | 4.466 | |
| mergeTranscripts | 24.210 | 0.204 | 24.455 | |
| plotDefaultPlotParams | 0.225 | 0.000 | 0.225 | |
| plotKaryotype | 1.304 | 0.012 | 1.318 | |
| plotPalettes | 0.013 | 0.004 | 0.017 | |
| prepareParameters2 | 0.038 | 0.004 | 0.042 | |
| prepareParameters4 | 0.045 | 0.000 | 0.045 | |
| processClipping | 0.044 | 0.000 | 0.043 | |
| transparent | 0.001 | 0.000 | 0.001 | |