Bernat Gel
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/regioneR |
| Branch: RELEASE_3_7 |
| Last Commit: f7a3067 |
| Last Changed Date: 2018-06-06 03:21:30 -0400 (Wed, 06 Jun 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:54:33 -0400 (Wed, 17 Oct 2018).
| Package 1217/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| regioneR 1.12.0 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: regioneR |
| Version: 1.12.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:regioneR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings regioneR_1.12.0.tar.gz |
| StartedAt: 2018-10-16 23:36:44 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 23:46:27 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 583.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: regioneR.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:regioneR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings regioneR_1.12.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/regioneR.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 ‘regioneR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘regioneR’ version ‘1.12.0’
* 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 ‘regioneR’ 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:
‘memoise’ ‘GenomicRanges’ ‘BSgenome’ ‘rtracklayer’ ‘parallel’
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
maskFromBSGenome 59.811 6.972 64.836
circularRandomizeRegions 59.229 5.450 66.031
filterChromosomes 58.861 5.678 65.519
getMask 56.829 5.136 65.548
localZScore 3.713 0.369 5.649
* 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/regioneR.Rcheck/00check.log’
for details.
regioneR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL regioneR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘regioneR’ ... ** 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 (regioneR)
regioneR.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(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("regioneR")
══ testthat results ═══════════════════════════════════════════════════════════
OK: 24 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
75.542 6.127 82.448
regioneR.Rcheck/regioneR-Ex.timings
| name | user | system | elapsed | |
| characterToBSGenome | 1.912 | 0.216 | 2.267 | |
| circularRandomizeRegions | 59.229 | 5.450 | 66.031 | |
| commonRegions | 0.271 | 0.002 | 0.273 | |
| createFunctionsList | 0.685 | 0.080 | 0.768 | |
| createRandomRegions | 0.144 | 0.031 | 0.174 | |
| emptyCacheRegioneR | 0.002 | 0.000 | 0.002 | |
| extendRegions | 0.144 | 0.002 | 0.173 | |
| filterChromosomes | 58.861 | 5.678 | 65.519 | |
| getChromosomesByOrganism | 0.002 | 0.001 | 0.002 | |
| getGenome | 0.037 | 0.001 | 0.038 | |
| getGenomeAndMask | 1.250 | 0.234 | 1.494 | |
| getMask | 56.829 | 5.136 | 65.548 | |
| joinRegions | 0.123 | 0.001 | 0.126 | |
| listChrTypes | 0.011 | 0.000 | 0.012 | |
| localZScore | 3.713 | 0.369 | 5.649 | |
| maskFromBSGenome | 59.811 | 6.972 | 64.836 | |
| meanDistance | 0.102 | 0.001 | 0.121 | |
| meanInRegions | 0.195 | 0.004 | 0.214 | |
| mergeRegions | 0.110 | 0.001 | 0.120 | |
| numOverlaps | 0.221 | 0.002 | 0.233 | |
| overlapGraphicalSummary | 0.146 | 0.002 | 0.153 | |
| overlapPermTest | 0.976 | 0.006 | 0.996 | |
| overlapRegions | 0.063 | 0.000 | 0.063 | |
| permTest | 1.349 | 0.038 | 1.404 | |
| plot.localZScoreResults | 1.322 | 0.016 | 1.349 | |
| plot.localZScoreResultsList | 2.771 | 0.012 | 2.816 | |
| plot.permTestResults | 2.091 | 0.007 | 2.127 | |
| plot.permTestResultsList | 2.245 | 0.006 | 2.274 | |
| plotRegions | 0.039 | 0.001 | 0.040 | |
| print.permTestResults | 1.165 | 0.003 | 1.173 | |
| randomizeRegions | 0.202 | 0.001 | 0.205 | |
| recomputePermTest | 0.841 | 0.009 | 0.856 | |
| resampleRegions | 0.041 | 0.001 | 0.042 | |
| splitRegions | 0.081 | 0.001 | 0.083 | |
| subtractRegions | 0.211 | 0.003 | 0.215 | |
| toDataframe | 0.019 | 0.001 | 0.019 | |
| toGRanges | 0.021 | 0.001 | 0.022 | |
| uniqueRegions | 0.370 | 0.001 | 0.379 | |