Bernat Gel
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/regioneR |
| Branch: RELEASE_3_9 |
| Last Commit: f141ad6 |
| Last Changed Date: 2019-09-26 08:38:35 -0400 (Thu, 26 Sep 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:55:24 -0400 (Wed, 16 Oct 2019).
| Package 1351/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| regioneR 1.16.5 Bernat Gel
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: regioneR |
| Version: 1.16.5 |
| 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_1.16.5.tar.gz |
| StartedAt: 2019-10-16 06:08:36 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 06:20:32 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 716.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: regioneR.Rcheck |
| Warnings: 0 |
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### 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_1.16.5.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/regioneR.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.16.5’
* 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 ... 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
maskFromBSGenome 61.801 12.316 70.506
circularRandomizeRegions 63.207 10.257 77.389
filterChromosomes 61.534 10.409 73.967
getMask 59.734 9.720 73.118
localZScore 4.490 0.694 7.558
* 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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.9-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/3.6/Resources/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 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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: 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: 24 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
83.963 12.222 96.985
regioneR.Rcheck/regioneR-Ex.timings
| name | user | system | elapsed | |
| characterToBSGenome | 2.102 | 0.540 | 2.648 | |
| circularRandomizeRegions | 63.207 | 10.257 | 77.389 | |
| commonRegions | 0.389 | 0.005 | 0.421 | |
| createFunctionsList | 0.973 | 0.279 | 1.252 | |
| createRandomRegions | 0.228 | 0.002 | 0.231 | |
| emptyCacheRegioneR | 0.001 | 0.001 | 0.002 | |
| extendRegions | 0.146 | 0.002 | 0.152 | |
| filterChromosomes | 61.534 | 10.409 | 73.967 | |
| getChromosomesByOrganism | 0.001 | 0.001 | 0.003 | |
| getGenome | 0.109 | 0.007 | 0.117 | |
| getGenomeAndMask | 0.755 | 0.229 | 1.278 | |
| getMask | 59.734 | 9.720 | 73.118 | |
| joinRegions | 0.155 | 0.002 | 0.157 | |
| listChrTypes | 0.006 | 0.000 | 0.006 | |
| localZScore | 4.490 | 0.694 | 7.558 | |
| maskFromBSGenome | 61.801 | 12.316 | 70.506 | |
| meanDistance | 0.099 | 0.000 | 0.100 | |
| meanInRegions | 0.138 | 0.000 | 0.139 | |
| mergeRegions | 0.108 | 0.001 | 0.110 | |
| numOverlaps | 0.233 | 0.000 | 0.234 | |
| overlapGraphicalSummary | 0.073 | 0.001 | 0.075 | |
| overlapPermTest | 0.899 | 0.004 | 0.904 | |
| overlapRegions | 0.063 | 0.001 | 0.064 | |
| permTest | 2.208 | 0.222 | 2.431 | |
| plot.localZScoreResults | 1.634 | 0.042 | 1.677 | |
| plot.localZScoreResultsList | 3.320 | 0.009 | 3.330 | |
| plot.permTestResults | 2.275 | 0.008 | 2.286 | |
| plot.permTestResultsList | 2.285 | 0.010 | 2.310 | |
| plotRegions | 0.034 | 0.001 | 0.036 | |
| print.permTestResults | 1.352 | 0.003 | 1.355 | |
| randomizeRegions | 0.226 | 0.001 | 0.228 | |
| recomputePermTest | 0.970 | 0.005 | 0.976 | |
| resampleRegions | 0.044 | 0.000 | 0.045 | |
| splitRegions | 0.089 | 0.001 | 0.091 | |
| subtractRegions | 0.218 | 0.002 | 0.220 | |
| toDataframe | 0.019 | 0.001 | 0.019 | |
| toGRanges | 0.634 | 0.020 | 0.805 | |
| uniqueRegions | 0.492 | 0.002 | 0.494 | |