Bernat Gel
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/karyoploteR |
| Branch: RELEASE_3_6 |
| Last Commit: 3473db9 |
| Last Changed Date: 2018-02-22 02:40:26 -0400 (Thu, 22 Feb 2018) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:15:51 -0400 (Thu, 12 Apr 2018).
| Package 729/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| karyoploteR 1.4.2 Bernat Gel
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
| Package: karyoploteR |
| Version: 1.4.2 |
| Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings karyoploteR_1.4.2.tar.gz |
| StartedAt: 2018-04-12 00:33:51 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 00:39:50 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 358.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: karyoploteR.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings karyoploteR_1.4.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/karyoploteR.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.4.2’
* 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 loading without being on the library search path ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
kpPlotDensity 24.260 2.772 32.549
getCytobands 5.908 0.072 50.741
* 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-3.6-bioc/meat/karyoploteR.Rcheck/00check.log’
for details.
karyoploteR.Rcheck/00install.out
* installing *source* package ‘karyoploteR’ ... ** R ** inst ** preparing 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 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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: 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, cbind, colMeans, colSums, colnames, 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
12.564 0.224 13.187
karyoploteR.Rcheck/karyoploteR-Ex.timings
| name | user | system | elapsed | |
| darker | 0.004 | 0.000 | 0.002 | |
| filterParams | 0.012 | 0.000 | 0.010 | |
| getChromosomeNamesBoundingBox | 0.872 | 0.004 | 0.878 | |
| getCytobandColors | 0.004 | 0.000 | 0.001 | |
| getCytobands | 5.908 | 0.072 | 50.741 | |
| getDefaultPlotParams | 0.896 | 0.000 | 0.898 | |
| getMainTitleBoundingBox | 0.028 | 0.004 | 0.031 | |
| getVariantsColors | 0.016 | 0.000 | 0.018 | |
| kpAbline | 1.004 | 0.048 | 1.083 | |
| kpAddBaseNumbers | 0.388 | 0.000 | 0.386 | |
| kpAddChromosomeNames | 0.032 | 0.000 | 0.032 | |
| kpAddCytobandLabels | 0.436 | 0.004 | 0.441 | |
| kpAddCytobands | 0.032 | 0.000 | 0.030 | |
| kpAddCytobandsAsLine | 0.028 | 0.004 | 0.032 | |
| kpAddLabels | 0.176 | 0.000 | 0.173 | |
| kpAddMainTitle | 0.028 | 0.000 | 0.031 | |
| kpArrows | 0.368 | 0.000 | 0.372 | |
| kpAxis | 0.296 | 0.000 | 0.297 | |
| kpBars | 0.196 | 0.000 | 0.195 | |
| kpDataBackground | 0.216 | 0.000 | 0.215 | |
| kpHeatmap | 0.148 | 0.000 | 0.146 | |
| kpLines | 0.204 | 0.000 | 0.204 | |
| kpPlotBAMDensity | 1.756 | 0.016 | 1.772 | |
| kpPlotCoverage | 3.648 | 0.004 | 3.655 | |
| kpPlotDensity | 24.260 | 2.772 | 32.549 | |
| kpPlotLinks | 0.812 | 0.004 | 0.818 | |
| kpPlotLoess | 0.056 | 0.000 | 0.057 | |
| kpPlotMarkers | 1.880 | 0.004 | 1.886 | |
| kpPlotRainfall | 0.504 | 0.000 | 0.506 | |
| kpPlotRegions | 3.428 | 0.000 | 3.432 | |
| kpPlotRibbon | 0.072 | 0.000 | 0.070 | |
| kpPoints | 0.188 | 0.000 | 0.189 | |
| kpPolygon | 0.196 | 0.004 | 0.197 | |
| kpRect | 0.352 | 0.000 | 0.351 | |
| kpSegments | 0.176 | 0.000 | 0.174 | |
| kpText | 0.180 | 0.000 | 0.179 | |
| lighter | 0.000 | 0.000 | 0.001 | |
| plotDefaultPlotParams | 0.168 | 0.000 | 0.170 | |
| plotKaryotype | 1.236 | 0.008 | 1.261 | |
| prepareParameters2 | 0.052 | 0.000 | 0.050 | |
| prepareParameters4 | 0.036 | 0.000 | 0.035 | |