Bernat Gel
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/regioneR |
| Branch: RELEASE_3_6 |
| Last Commit: 8fe51e6 |
| Last Changed Date: 2017-10-30 12:40:50 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:13:28 -0400 (Thu, 12 Apr 2018).
| Package 1155/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| regioneR 1.10.0 Bernat Gel
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: regioneR |
| Version: 1.10.0 |
| Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings regioneR_1.10.0.tar.gz |
| StartedAt: 2018-04-12 02:17:23 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 02:22:14 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 290.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: regioneR.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings regioneR_1.10.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/regioneR.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.10.0’
* 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
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
‘memoise’ ‘GenomicRanges’ ‘BSgenome’ ‘rtracklayer’ ‘parallel’
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
filterChromosomes 21.216 3.240 24.519
circularRandomizeRegions 20.884 3.012 28.659
getMask 16.468 2.804 19.328
maskFromBSGenome 16.204 2.836 19.083
* 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-3.6-bioc/meat/regioneR.Rcheck/00check.log’
for details.
regioneR.Rcheck/00install.out
* installing *source* package ‘regioneR’ ... ** R ** inst ** preparing 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 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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: memoise
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, cbind, colMeans, colSums, colnames, 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
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: rtracklayer
>
> test_check("regioneR")
══ testthat results ═══════════════════════════════════════════════════════════
OK: 24 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
29.472 2.912 32.418
regioneR.Rcheck/regioneR-Ex.timings
| name | user | system | elapsed | |
| characterToBSGenome | 0.536 | 0.052 | 0.614 | |
| circularRandomizeRegions | 20.884 | 3.012 | 28.659 | |
| commonRegions | 0.272 | 0.000 | 0.273 | |
| createFunctionsList | 1.720 | 0.128 | 1.852 | |
| createRandomRegions | 0.080 | 0.000 | 0.081 | |
| emptyCacheRegioneR | 0.000 | 0.000 | 0.001 | |
| extendRegions | 0.152 | 0.000 | 0.152 | |
| filterChromosomes | 21.216 | 3.240 | 24.519 | |
| getChromosomesByOrganism | 0.000 | 0.000 | 0.001 | |
| getGenome | 0.028 | 0.000 | 0.029 | |
| getGenomeAndMask | 0.908 | 0.124 | 1.038 | |
| getMask | 16.468 | 2.804 | 19.328 | |
| joinRegions | 0.088 | 0.000 | 0.091 | |
| listChrTypes | 0.008 | 0.004 | 0.015 | |
| localZScore | 2.908 | 0.216 | 3.859 | |
| maskFromBSGenome | 16.204 | 2.836 | 19.083 | |
| meanDistance | 0.060 | 0.000 | 0.059 | |
| meanInRegions | 0.148 | 0.000 | 0.147 | |
| mergeRegions | 0.076 | 0.000 | 0.073 | |
| numOverlaps | 0.128 | 0.000 | 0.127 | |
| overlapGraphicalSummary | 0.112 | 0.000 | 0.111 | |
| overlapPermTest | 0.580 | 0.000 | 0.581 | |
| overlapRegions | 0.040 | 0.000 | 0.037 | |
| permTest | 1.096 | 0.004 | 1.103 | |
| plot.localZScoreResults | 0.968 | 0.000 | 0.972 | |
| plot.localZScoreResultsList | 2.220 | 0.004 | 2.230 | |
| plot.permTestResults | 1.540 | 0.004 | 1.542 | |
| plot.permTestResultsList | 1.620 | 0.000 | 1.622 | |
| plotRegions | 0.028 | 0.000 | 0.029 | |
| print.permTestResults | 0.876 | 0.000 | 0.880 | |
| randomizeRegions | 0.140 | 0.000 | 0.141 | |
| recomputePermTest | 0.552 | 0.000 | 0.551 | |
| resampleRegions | 0.028 | 0.000 | 0.028 | |
| splitRegions | 0.056 | 0.000 | 0.056 | |
| subtractRegions | 0.108 | 0.000 | 0.108 | |
| toDataframe | 0.008 | 0.000 | 0.010 | |
| toGRanges | 0.012 | 0.000 | 0.012 | |
| uniqueRegions | 0.588 | 0.048 | 0.641 | |