Bernat Gel
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/karyoploteR |
| Branch: RELEASE_3_9 |
| Last Commit: 3d1c8a2 |
| Last Changed Date: 2019-09-10 03:24:18 -0400 (Tue, 10 Sep 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:10:19 -0400 (Wed, 16 Oct 2019).
| Package 851/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| karyoploteR 1.10.5 Bernat Gel
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: karyoploteR |
| Version: 1.10.5 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:karyoploteR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings karyoploteR_1.10.5.tar.gz |
| StartedAt: 2019-10-16 02:39:42 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 02:47:44 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 482.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: karyoploteR.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:karyoploteR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings karyoploteR_1.10.5.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/karyoploteR.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (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 ‘1.10.5’
* 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 ... 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 or elapsed time > 5s
user system elapsed
kpPlotDensity 31.864 3.693 40.094
kpPlotGenes 26.455 0.052 27.332
mergeTranscripts 17.225 0.048 17.273
kpPlotCoverage 10.579 0.000 10.579
kpPlotRegions 9.228 0.000 9.277
kpPlotBAMCoverage 7.468 0.176 7.644
kpPlotTranscripts 5.579 0.003 5.585
getCytobands 3.944 0.080 37.853
* 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: 1 NOTE
See
‘/home/biocbuild/bbs-3.9-bioc/meat/karyoploteR.Rcheck/00check.log’
for details.
karyoploteR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL karyoploteR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-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
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
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, which.max, which.min
Loading required package: S4Vectors
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomeInfoDb
>
> test_check("karyoploteR")
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 132 | SKIPPED: 3 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
16.662 0.721 17.371
karyoploteR.Rcheck/karyoploteR-Ex.timings
| name | user | system | elapsed | |
| addGeneNames | 2.685 | 0.028 | 2.713 | |
| autotrack | 0.001 | 0.000 | 0.001 | |
| colByChr | 0.262 | 0.004 | 0.266 | |
| colByRegion | 0.770 | 0.072 | 0.841 | |
| darker | 0.000 | 0.002 | 0.002 | |
| filterParams | 0.000 | 0.000 | 0.001 | |
| getChromosomeNamesBoundingBox | 0.036 | 0.000 | 0.035 | |
| getCytobandColors | 0.002 | 0.000 | 0.002 | |
| getCytobands | 3.944 | 0.080 | 37.853 | |
| getDataPanelBoundingBox | 0.044 | 0.000 | 0.043 | |
| getDefaultPlotParams | 0.076 | 0.004 | 0.081 | |
| getMainTitleBoundingBox | 0.034 | 0.000 | 0.034 | |
| getTextSize | 0.064 | 0.003 | 0.067 | |
| getVariantsColors | 0.001 | 0.000 | 0.001 | |
| is.color | 0.001 | 0.000 | 0.001 | |
| kpAbline | 2.022 | 0.124 | 2.197 | |
| kpAddBaseNumbers | 0.316 | 0.000 | 0.316 | |
| kpAddChromosomeNames | 0.033 | 0.000 | 0.033 | |
| kpAddChromosomeSeparators | 0.457 | 0.000 | 0.457 | |
| kpAddCytobandLabels | 0.311 | 0.000 | 0.311 | |
| kpAddCytobands | 0.033 | 0.000 | 0.033 | |
| kpAddCytobandsAsLine | 0.071 | 0.000 | 0.071 | |
| kpAddLabels | 0.118 | 0.004 | 0.123 | |
| kpAddMainTitle | 0.034 | 0.000 | 0.033 | |
| kpArea | 0.331 | 0.000 | 0.332 | |
| kpArrows | 0.509 | 0.000 | 0.508 | |
| kpAxis | 0.312 | 0.000 | 0.312 | |
| kpBars | 0.147 | 0.000 | 0.147 | |
| kpDataBackground | 0.193 | 0.000 | 0.194 | |
| kpHeatmap | 0.115 | 0.000 | 0.114 | |
| kpLines | 0.221 | 0.000 | 0.222 | |
| kpPlotBAMCoverage | 7.468 | 0.176 | 7.644 | |
| kpPlotBAMDensity | 1.811 | 0.016 | 1.828 | |
| kpPlotBigWig | 0.567 | 0.000 | 0.579 | |
| kpPlotCoverage | 10.579 | 0.000 | 10.579 | |
| kpPlotDensity | 31.864 | 3.693 | 40.094 | |
| kpPlotGenes | 26.455 | 0.052 | 27.332 | |
| kpPlotLinks | 0.776 | 0.000 | 0.779 | |
| kpPlotLoess | 0.055 | 0.000 | 0.056 | |
| kpPlotMarkers | 1.286 | 0.003 | 1.297 | |
| kpPlotNames | 0.077 | 0.000 | 0.077 | |
| kpPlotRainfall | 0.531 | 0.004 | 0.536 | |
| kpPlotRegions | 9.228 | 0.000 | 9.277 | |
| kpPlotRibbon | 0.079 | 0.000 | 0.079 | |
| kpPlotTranscripts | 5.579 | 0.003 | 5.585 | |
| kpPoints | 0.152 | 0.000 | 0.151 | |
| kpPolygon | 0.120 | 0.000 | 0.121 | |
| kpRect | 0.468 | 0.000 | 0.468 | |
| kpSegments | 0.302 | 0.000 | 0.301 | |
| kpText | 0.143 | 0.000 | 0.143 | |
| lighter | 0.001 | 0.000 | 0.001 | |
| makeGenesDataFromTxDb | 3.264 | 0.000 | 3.263 | |
| mergeTranscripts | 17.225 | 0.048 | 17.273 | |
| plotDefaultPlotParams | 0.136 | 0.000 | 0.136 | |
| plotKaryotype | 1.270 | 0.004 | 1.274 | |
| prepareParameters2 | 0.058 | 0.000 | 0.058 | |
| prepareParameters4 | 0.038 | 0.000 | 0.038 | |
| processClipping | 0.037 | 0.000 | 0.037 | |
| transparent | 0.001 | 0.000 | 0.001 | |