Bernat Gel
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/CopyNumberPlots |
| Branch: RELEASE_3_10 |
| Last Commit: f27c5fc |
| Last Changed Date: 2019-12-23 10:11:11 -0400 (Mon, 23 Dec 2019) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:49:15 -0400 (Wed, 15 Apr 2020).
| Package 361/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| CopyNumberPlots 1.2.3 Bernat Gel
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: CopyNumberPlots |
| Version: 1.2.3 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CopyNumberPlots.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CopyNumberPlots_1.2.3.tar.gz |
| StartedAt: 2020-04-15 01:26:59 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 01:32:44 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 345.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CopyNumberPlots.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CopyNumberPlots.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CopyNumberPlots_1.2.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/CopyNumberPlots.Rcheck’ * using R version 3.6.3 (2020-02-29) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘CopyNumberPlots/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘CopyNumberPlots’ version ‘1.2.3’ * 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 ‘CopyNumberPlots’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * 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 files in ‘vignettes’ ... OK * checking examples ... OK * 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: OK
CopyNumberPlots.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CopyNumberPlots ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘CopyNumberPlots’ ... ** 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 (CopyNumberPlots)
CopyNumberPlots.Rcheck/tests/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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(CopyNumberPlots)
Loading required package: 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("CopyNumberPlots")
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 26 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
17.563 0.820 18.527
CopyNumberPlots.Rcheck/CopyNumberPlots-Ex.timings
| name | user | system | elapsed | |
| EnsemblStyle | 0.400 | 0.010 | 0.415 | |
| UCSCStyle | 0.266 | 0.010 | 0.278 | |
| Ztree2Hclust | 0.008 | 0.001 | 0.010 | |
| colByCopyNumber | 0.554 | 0.016 | 0.573 | |
| computeHclustPlotOrder | 0.005 | 0.001 | 0.007 | |
| getBAFColumn | 0.004 | 0.000 | 0.004 | |
| getChrColumn | 0.002 | 0.000 | 0.003 | |
| getColumn | 0.003 | 0.001 | 0.004 | |
| getCopyNumberColors | 0.000 | 0.000 | 0.001 | |
| getCopyNumberColumn | 0.002 | 0.000 | 0.002 | |
| getEndColumn | 0.002 | 0.000 | 0.003 | |
| getIDColumn | 0.002 | 0.000 | 0.002 | |
| getLOHColumn | 0.003 | 0.000 | 0.002 | |
| getLRRColumn | 0.003 | 0.000 | 0.003 | |
| getPosColumn | 0.003 | 0.000 | 0.002 | |
| getSegmentValueColumn | 0.003 | 0.000 | 0.002 | |
| getStartColumn | 0.003 | 0.000 | 0.003 | |
| loadCopyNumberCalls | 0.029 | 0.000 | 0.029 | |
| loadCopyNumberCallsCNVkit | 0.021 | 0.001 | 0.022 | |
| loadCopyNumberCallsCnmops | 0.260 | 0.005 | 0.267 | |
| loadCopyNumberCallsDECoN | 0.091 | 0.014 | 0.107 | |
| loadCopyNumberCallsDNAcopy | 1.168 | 0.011 | 1.189 | |
| loadCopyNumberCallsPanelcnmops | 0.457 | 0.007 | 0.474 | |
| loadCopyNumberCallsSeg | 0.024 | 0.001 | 0.025 | |
| loadCopyNumberCallspennCNV | 0.058 | 0.001 | 0.059 | |
| loadSNPData | 0.075 | 0.001 | 0.078 | |
| loadSNPDataDNAcopy | 1.742 | 0.009 | 1.772 | |
| loadSNPDataFromVCF | 0.000 | 0.000 | 0.001 | |
| plotBAF | 1.350 | 0.091 | 1.470 | |
| plotCopyNumberCalls | 0.743 | 0.080 | 0.828 | |
| plotCopyNumberCallsAsLines | 1.042 | 0.004 | 1.059 | |
| plotCopyNumberSummary | 2.340 | 0.006 | 2.364 | |
| plotLRR | 0.536 | 0.003 | 0.545 | |
| plotSingleCellCopyNumberCalls | 0.055 | 0.001 | 0.057 | |
| plotSingleCellCopyNumberSummary | 0.038 | 0.000 | 0.039 | |
| prepareLabels | 0.086 | 0.000 | 0.086 | |
| readHDF5Ztree | 0.000 | 0.000 | 0.001 | |
| removeNAs | 0.242 | 0.001 | 0.245 | |
| transformChr | 0.005 | 0.000 | 0.005 | |