Bernat Gel
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/regioneR |
| Branch: master |
| Last Commit: d69c54a |
| Last Changed Date: 2020-01-14 08:02:03 -0500 (Tue, 14 Jan 2020) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-16 13:41:55 -0500 (Thu, 16 Jan 2020).
| Package 1405/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| regioneR 1.19.1 Bernat Gel
| malbec2 | Linux (Ubuntu 18.04.3 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: 1.19.1 |
| 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_1.19.1.tar.gz |
| StartedAt: 2020-01-16 08:05:17 -0500 (Thu, 16 Jan 2020) |
| EndedAt: 2020-01-16 08:17:07 -0500 (Thu, 16 Jan 2020) |
| EllapsedTime: 710.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: regioneR.Rcheck |
| Warnings: 0 |
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### Running command:
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### /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_1.19.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/regioneR.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.19.1’
* 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 (user + system) or elapsed time > 5s
user system elapsed
maskFromBSGenome 54.360 12.153 63.903
circularRandomizeRegions 54.242 10.070 66.267
filterChromosomes 52.121 10.590 63.841
getMask 48.732 9.590 59.100
localZScore 7.201 0.985 11.282
plot.localZScoreResultsList 5.111 0.013 5.125
* 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
‘/Users/biocbuild/bbs-3.11-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/4.0/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 Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
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: 89 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
80.488 12.084 93.409
regioneR.Rcheck/regioneR-Ex.timings
| name | user | system | elapsed | |
| characterToBSGenome | 2.101 | 0.534 | 2.641 | |
| circularRandomizeRegions | 54.242 | 10.070 | 66.267 | |
| commonRegions | 0.538 | 0.031 | 0.568 | |
| createFunctionsList | 1.497 | 0.308 | 1.805 | |
| createRandomRegions | 0.426 | 0.005 | 0.465 | |
| emptyCacheRegioneR | 0.000 | 0.000 | 0.001 | |
| extendRegions | 0.282 | 0.002 | 0.285 | |
| filterChromosomes | 52.121 | 10.590 | 63.841 | |
| getChromosomesByOrganism | 0.003 | 0.001 | 0.004 | |
| getGenome | 0.170 | 0.006 | 0.177 | |
| getGenomeAndMask | 0.923 | 0.320 | 1.374 | |
| getMask | 48.732 | 9.590 | 59.100 | |
| joinRegions | 0.243 | 0.002 | 0.244 | |
| listChrTypes | 0.017 | 0.001 | 0.018 | |
| localZScore | 7.201 | 0.985 | 11.282 | |
| maskFromBSGenome | 54.360 | 12.153 | 63.903 | |
| meanDistance | 0.197 | 0.001 | 0.198 | |
| meanInRegions | 0.278 | 0.003 | 0.283 | |
| mergeRegions | 0.159 | 0.001 | 0.161 | |
| numOverlaps | 0.416 | 0.001 | 0.418 | |
| overlapGraphicalSummary | 0.138 | 0.002 | 0.140 | |
| overlapPermTest | 3.647 | 0.044 | 3.733 | |
| overlapRegions | 0.099 | 0.001 | 0.100 | |
| permTest | 2.656 | 0.048 | 2.729 | |
| plot.localZScoreResults | 2.804 | 0.006 | 2.815 | |
| plot.localZScoreResultsList | 5.111 | 0.013 | 5.125 | |
| plot.permTestResults | 3.892 | 0.012 | 3.910 | |
| plot.permTestResultsList | 4.357 | 0.012 | 4.371 | |
| plotRegions | 0.091 | 0.001 | 0.093 | |
| print.permTestResults | 2.551 | 0.007 | 2.557 | |
| randomizeRegions | 0.441 | 0.002 | 0.443 | |
| recomputePermTest | 1.493 | 0.008 | 1.501 | |
| resampleRegions | 0.092 | 0.001 | 0.092 | |
| splitRegions | 0.143 | 0.001 | 0.145 | |
| subtractRegions | 0.396 | 0.002 | 0.398 | |
| toDataframe | 0.032 | 0.001 | 0.032 | |
| toGRanges | 0.781 | 0.046 | 0.961 | |
| uniqueRegions | 0.813 | 0.004 | 0.816 | |