Bernat Gel
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/regioneR |
| Branch: RELEASE_3_10 |
| Last Commit: 6c60b03 |
| Last Changed Date: 2020-01-14 08:07:30 -0400 (Tue, 14 Jan 2020) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:09:56 -0400 (Wed, 15 Apr 2020).
| Package 1408/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| regioneR 1.18.1 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: regioneR |
| Version: 1.18.1 |
| Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:regioneR.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings regioneR_1.18.1.tar.gz |
| StartedAt: 2020-04-15 02:55:57 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 03:02:41 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 404.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: regioneR.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:regioneR.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings regioneR_1.18.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/regioneR.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.18.1’
* 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 ... NOTE
Found the following apparent S3 methods exported but not registered:
print.permTestResults
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getChromosomesByOrganism: no visible global function definition for
‘as.roman’
Undefined global functions or variables:
as.roman
Consider adding
importFrom("utils", "as.roman")
to your NAMESPACE file.
* 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 28.172 3.600 41.372
filterChromosomes 27.336 3.384 30.848
getMask 26.692 3.380 30.177
maskFromBSGenome 24.924 3.300 25.804
localZScore 4.660 0.220 6.498
* 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: 3 NOTEs
See
‘/home/biocbuild/bbs-3.10-bioc/meat/regioneR.Rcheck/00check.log’
for details.
regioneR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL regioneR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’ * installing *source* package ‘regioneR’ ... ** 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 (regioneR)
regioneR.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-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, 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("regioneR")
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 89 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
42.948 3.892 47.186
regioneR.Rcheck/regioneR-Ex.timings
| name | user | system | elapsed | |
| characterToBSGenome | 1.396 | 0.120 | 1.846 | |
| circularRandomizeRegions | 28.172 | 3.600 | 41.372 | |
| commonRegions | 0.232 | 0.000 | 0.230 | |
| createFunctionsList | 1.252 | 0.088 | 1.341 | |
| createRandomRegions | 0.316 | 0.000 | 0.318 | |
| emptyCacheRegioneR | 0.004 | 0.000 | 0.001 | |
| extendRegions | 0.200 | 0.008 | 0.211 | |
| filterChromosomes | 27.336 | 3.384 | 30.848 | |
| getChromosomesByOrganism | 0.000 | 0.000 | 0.001 | |
| getGenome | 0.112 | 0.000 | 0.112 | |
| getGenomeAndMask | 0.856 | 0.064 | 0.921 | |
| getMask | 26.692 | 3.380 | 30.177 | |
| joinRegions | 0.164 | 0.004 | 0.169 | |
| listChrTypes | 0.012 | 0.000 | 0.011 | |
| localZScore | 4.660 | 0.220 | 6.498 | |
| maskFromBSGenome | 24.924 | 3.300 | 25.804 | |
| meanDistance | 0.120 | 0.004 | 0.123 | |
| meanInRegions | 0.176 | 0.000 | 0.174 | |
| mergeRegions | 0.136 | 0.000 | 0.136 | |
| numOverlaps | 0.216 | 0.000 | 0.216 | |
| overlapGraphicalSummary | 0.084 | 0.000 | 0.084 | |
| overlapPermTest | 2.2 | 0.0 | 2.2 | |
| overlapRegions | 0.08 | 0.00 | 0.08 | |
| permTest | 1.848 | 0.000 | 1.848 | |
| plot.localZScoreResults | 1.892 | 0.000 | 1.905 | |
| plot.localZScoreResultsList | 3.240 | 0.000 | 3.251 | |
| plot.permTestResults | 2.788 | 0.000 | 2.788 | |
| plot.permTestResultsList | 2.460 | 0.000 | 2.461 | |
| plotRegions | 0.056 | 0.000 | 0.054 | |
| print.permTestResults | 1.888 | 0.000 | 1.892 | |
| randomizeRegions | 0.344 | 0.004 | 0.345 | |
| recomputePermTest | 0.944 | 0.000 | 0.952 | |
| resampleRegions | 0.032 | 0.000 | 0.036 | |
| splitRegions | 0.064 | 0.000 | 0.064 | |
| subtractRegions | 0.164 | 0.000 | 0.164 | |
| toDataframe | 0.016 | 0.000 | 0.015 | |
| toGRanges | 0.496 | 0.032 | 0.681 | |
| uniqueRegions | 0.344 | 0.000 | 0.344 | |