Bernat Gel
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/karyoploteR |
| Branch: RELEASE_3_7 |
| Last Commit: 8dfb702 |
| Last Changed Date: 2018-09-21 06:36:38 -0400 (Fri, 21 Sep 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:57:41 -0400 (Wed, 17 Oct 2018).
| Package 769/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| karyoploteR 1.6.3 Bernat Gel
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: karyoploteR |
| Version: 1.6.3 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:karyoploteR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings karyoploteR_1.6.3.tar.gz |
| StartedAt: 2018-10-16 22:12:26 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 22:19:45 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 439.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: karyoploteR.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:karyoploteR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings karyoploteR_1.6.3.tar.gz
###
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##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/karyoploteR.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.6.3’
* 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 58.701 4.660 63.787
kpPlotGenes 18.110 0.306 18.504
kpPlotTranscripts 6.862 0.031 6.936
makeGenesDataFromTxDb 5.320 0.096 5.453
getCytobands 3.756 0.131 37.710
* 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
‘/Users/biocbuild/bbs-3.7-bioc/meat/karyoploteR.Rcheck/00check.log’
for details.
karyoploteR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL karyoploteR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘karyoploteR’ ... ** 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 * DONE (karyoploteR)
karyoploteR.Rcheck/tests/testthat.Rout
R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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: memoise
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, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, 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
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: rtracklayer
>
> test_check("karyoploteR")
══ testthat results ═══════════════════════════════════════════════════════════
OK: 128 SKIPPED: 1 FAILED: 0
>
> proc.time()
user system elapsed
14.845 0.696 15.637
karyoploteR.Rcheck/karyoploteR-Ex.timings
| name | user | system | elapsed | |
| darker | 0.001 | 0.000 | 0.002 | |
| filterParams | 0.002 | 0.000 | 0.002 | |
| getChromosomeNamesBoundingBox | 0.140 | 0.003 | 0.143 | |
| getCytobandColors | 0.004 | 0.001 | 0.005 | |
| getCytobands | 3.756 | 0.131 | 37.710 | |
| getDefaultPlotParams | 0.072 | 0.004 | 0.076 | |
| getMainTitleBoundingBox | 0.024 | 0.000 | 0.025 | |
| getVariantsColors | 0.002 | 0.000 | 0.002 | |
| kpAbline | 1.163 | 0.138 | 1.303 | |
| kpAddBaseNumbers | 0.244 | 0.028 | 0.274 | |
| kpAddChromosomeNames | 0.027 | 0.004 | 0.031 | |
| kpAddCytobandLabels | 0.265 | 0.013 | 0.279 | |
| kpAddCytobands | 0.024 | 0.001 | 0.024 | |
| kpAddCytobandsAsLine | 0.024 | 0.001 | 0.025 | |
| kpAddLabels | 0.059 | 0.001 | 0.060 | |
| kpAddMainTitle | 0.023 | 0.001 | 0.024 | |
| kpArea | 0.204 | 0.004 | 0.209 | |
| kpArrows | 0.125 | 0.004 | 0.129 | |
| kpAxis | 0.764 | 0.015 | 0.782 | |
| kpBars | 0.123 | 0.001 | 0.125 | |
| kpDataBackground | 0.130 | 0.001 | 0.131 | |
| kpHeatmap | 0.085 | 0.001 | 0.086 | |
| kpLines | 0.164 | 0.008 | 0.171 | |
| kpPlotBAMDensity | 1.285 | 0.034 | 1.322 | |
| kpPlotCoverage | 3.489 | 0.014 | 3.532 | |
| kpPlotDensity | 58.701 | 4.660 | 63.787 | |
| kpPlotGenes | 18.110 | 0.306 | 18.504 | |
| kpPlotLinks | 0.659 | 0.004 | 0.663 | |
| kpPlotLoess | 0.068 | 0.001 | 0.069 | |
| kpPlotMarkers | 1.405 | 0.005 | 1.428 | |
| kpPlotNames | 0.096 | 0.001 | 0.097 | |
| kpPlotRainfall | 0.791 | 0.012 | 0.808 | |
| kpPlotRegions | 4.373 | 0.010 | 4.412 | |
| kpPlotRibbon | 0.081 | 0.002 | 0.082 | |
| kpPlotTranscripts | 6.862 | 0.031 | 6.936 | |
| kpPoints | 0.236 | 0.001 | 0.241 | |
| kpPolygon | 0.201 | 0.003 | 0.213 | |
| kpRect | 0.489 | 0.002 | 0.495 | |
| kpSegments | 0.191 | 0.001 | 0.195 | |
| kpText | 0.202 | 0.001 | 0.204 | |
| lighter | 0.001 | 0.000 | 0.001 | |
| makeGenesDataFromTxDb | 5.320 | 0.096 | 5.453 | |
| plotDefaultPlotParams | 0.127 | 0.001 | 0.128 | |
| plotKaryotype | 1.666 | 0.023 | 1.715 | |
| prepareParameters2 | 0.045 | 0.001 | 0.047 | |
| prepareParameters4 | 0.034 | 0.001 | 0.035 | |