Bernat Gel
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/regioneR |
| Branch: RELEASE_3_8 |
| Last Commit: 1b54982 |
| Last Changed Date: 2018-10-30 11:41:57 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:51:12 -0400 (Tue, 16 Apr 2019).
| Package 1286/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| regioneR 1.14.0 Bernat Gel
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: regioneR |
| Version: 1.14.0 |
| Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:regioneR.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings regioneR_1.14.0.tar.gz |
| StartedAt: 2019-04-16 02:31:12 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 02:37:43 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 390.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: regioneR.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:regioneR.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings regioneR_1.14.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/regioneR.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (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 ‘1.14.0’
* 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 ‘regioneR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
circularRandomizeRegions 28.896 3.528 39.015
maskFromBSGenome 25.168 3.708 27.052
filterChromosomes 24.100 3.068 27.317
getMask 21.300 3.320 24.676
* 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-3.8-bioc/meat/regioneR.Rcheck/00check.log’
for details.
regioneR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL regioneR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/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 3.5.3 (2019-03-11) -- "Great Truth"
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(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, 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
>
> test_check("regioneR")
══ testthat results ═══════════════════════════════════════════════════════════
OK: 24 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
38.068 3.360 41.731
regioneR.Rcheck/regioneR-Ex.timings
| name | user | system | elapsed | |
| characterToBSGenome | 1.412 | 0.100 | 1.566 | |
| circularRandomizeRegions | 28.896 | 3.528 | 39.015 | |
| commonRegions | 0.244 | 0.000 | 0.245 | |
| createFunctionsList | 1.008 | 0.048 | 1.061 | |
| createRandomRegions | 0.236 | 0.000 | 0.238 | |
| emptyCacheRegioneR | 0.000 | 0.000 | 0.001 | |
| extendRegions | 0.124 | 0.008 | 0.138 | |
| filterChromosomes | 24.100 | 3.068 | 27.317 | |
| getChromosomesByOrganism | 0 | 0 | 0 | |
| getGenome | 0.032 | 0.000 | 0.030 | |
| getGenomeAndMask | 1.264 | 0.152 | 1.418 | |
| getMask | 21.300 | 3.320 | 24.676 | |
| joinRegions | 0.124 | 0.000 | 0.122 | |
| listChrTypes | 0.004 | 0.000 | 0.006 | |
| localZScore | 2.780 | 0.360 | 4.122 | |
| maskFromBSGenome | 25.168 | 3.708 | 27.052 | |
| meanDistance | 0.084 | 0.000 | 0.083 | |
| meanInRegions | 0.152 | 0.000 | 0.148 | |
| mergeRegions | 0.088 | 0.000 | 0.091 | |
| numOverlaps | 0.132 | 0.000 | 0.132 | |
| overlapGraphicalSummary | 0.064 | 0.000 | 0.064 | |
| overlapPermTest | 0.644 | 0.000 | 0.643 | |
| overlapRegions | 0.036 | 0.000 | 0.035 | |
| permTest | 0.924 | 0.000 | 0.924 | |
| plot.localZScoreResults | 1.328 | 0.000 | 1.342 | |
| plot.localZScoreResultsList | 2.220 | 0.008 | 2.230 | |
| plot.permTestResults | 1.692 | 0.004 | 1.703 | |
| plot.permTestResultsList | 1.692 | 0.000 | 1.695 | |
| plotRegions | 0.024 | 0.000 | 0.024 | |
| print.permTestResults | 0.880 | 0.000 | 0.881 | |
| randomizeRegions | 0.192 | 0.000 | 0.191 | |
| recomputePermTest | 0.760 | 0.000 | 0.758 | |
| resampleRegions | 0.028 | 0.000 | 0.031 | |
| splitRegions | 0.088 | 0.000 | 0.091 | |
| subtractRegions | 0.208 | 0.000 | 0.204 | |
| toDataframe | 0.016 | 0.000 | 0.018 | |
| toGRanges | 0.456 | 0.008 | 0.659 | |
| uniqueRegions | 0.404 | 0.000 | 0.408 | |