Bernat Gel
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/regioneR |
| Branch: master |
| Last Commit: debe68a |
| Last Changed Date: 2019-02-12 11:30:59 -0400 (Tue, 12 Feb 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 11:42:02 -0400 (Tue, 09 Apr 2019).
| Package 1325/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| regioneR 1.15.2 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 | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
| Package: regioneR |
| Version: 1.15.2 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:regioneR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings regioneR_1.15.2.tar.gz |
| StartedAt: 2019-04-09 03:08:01 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 03:14:44 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 402.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: regioneR.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:regioneR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings regioneR_1.15.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/regioneR.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.15.2’
* 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
circularRandomizeRegions 26.442 3.511 33.737
maskFromBSGenome 23.631 3.771 31.711
filterChromosomes 23.179 3.185 26.551
getMask 22.799 3.248 26.048
* 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
‘/home/biocbuild/bbs-3.9-bioc/meat/regioneR.Rcheck/00check.log’
for details.
regioneR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL regioneR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-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 Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
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, 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
32.926 3.245 41.617
regioneR.Rcheck/regioneR-Ex.timings
| name | user | system | elapsed | |
| characterToBSGenome | 1.044 | 0.056 | 1.102 | |
| circularRandomizeRegions | 26.442 | 3.511 | 33.737 | |
| commonRegions | 0.169 | 0.000 | 0.169 | |
| createFunctionsList | 0.518 | 0.048 | 0.566 | |
| createRandomRegions | 0.109 | 0.000 | 0.109 | |
| emptyCacheRegioneR | 0.001 | 0.000 | 0.000 | |
| extendRegions | 0.073 | 0.000 | 0.099 | |
| filterChromosomes | 23.179 | 3.185 | 26.551 | |
| getChromosomesByOrganism | 0.001 | 0.000 | 0.001 | |
| getGenome | 0.078 | 0.004 | 0.082 | |
| getGenomeAndMask | 0.787 | 0.068 | 0.859 | |
| getMask | 22.799 | 3.248 | 26.048 | |
| joinRegions | 0.114 | 0.000 | 0.114 | |
| listChrTypes | 0.007 | 0.000 | 0.007 | |
| localZScore | 3.001 | 0.271 | 4.359 | |
| maskFromBSGenome | 23.631 | 3.771 | 31.711 | |
| meanDistance | 0.057 | 0.000 | 0.057 | |
| meanInRegions | 0.086 | 0.003 | 0.089 | |
| mergeRegions | 0.054 | 0.000 | 0.245 | |
| numOverlaps | 0.182 | 0.000 | 0.183 | |
| overlapGraphicalSummary | 0.092 | 0.000 | 0.124 | |
| overlapPermTest | 0.729 | 0.001 | 1.243 | |
| overlapRegions | 0.045 | 0.000 | 0.045 | |
| permTest | 1.017 | 0.000 | 1.018 | |
| plot.localZScoreResults | 0.818 | 0.000 | 0.818 | |
| plot.localZScoreResultsList | 1.948 | 0.000 | 1.949 | |
| plot.permTestResults | 1.199 | 0.000 | 1.342 | |
| plot.permTestResultsList | 1.141 | 0.000 | 1.141 | |
| plotRegions | 0.021 | 0.000 | 0.020 | |
| print.permTestResults | 0.724 | 0.000 | 0.723 | |
| randomizeRegions | 0.122 | 0.000 | 0.122 | |
| recomputePermTest | 0.592 | 0.000 | 0.591 | |
| resampleRegions | 0.022 | 0.000 | 0.022 | |
| splitRegions | 0.041 | 0.004 | 0.044 | |
| subtractRegions | 0.102 | 0.000 | 0.102 | |
| toDataframe | 0.008 | 0.000 | 0.008 | |
| toGRanges | 0.395 | 0.000 | 1.099 | |
| uniqueRegions | 0.284 | 0.000 | 0.284 | |