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CHECK report for BRGenomics on malbec2

This page was generated on 2020-10-17 11:54:29 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE BRGenomics PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 203/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BRGenomics 1.0.3
Mike DeBerardine
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/BRGenomics
Branch: RELEASE_3_11
Last Commit: 50f2560
Last Changed Date: 2020-08-28 13:05:31 -0400 (Fri, 28 Aug 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BRGenomics
Version: 1.0.3
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:BRGenomics.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings BRGenomics_1.0.3.tar.gz
StartedAt: 2020-10-16 23:25:18 -0400 (Fri, 16 Oct 2020)
EndedAt: 2020-10-16 23:32:01 -0400 (Fri, 16 Oct 2020)
EllapsedTime: 403.0 seconds
RetCode: 0
Status:  OK 
CheckDir: BRGenomics.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:BRGenomics.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings BRGenomics_1.0.3.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/BRGenomics.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BRGenomics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BRGenomics’ version ‘1.0.3’
* 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 ‘BRGenomics’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                  user system elapsed
getDESeqResults 15.125  0.024  15.161
* 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: OK


Installation output

BRGenomics.Rcheck/00install.out

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### Running command:
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###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL BRGenomics
###
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘BRGenomics’ ...
** using staged installation
** R
** data
** 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 (BRGenomics)

Tests output

BRGenomics.Rcheck/tests/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
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.

> Sys.setenv("R_TESTS" = "")
> library(testthat)
> library(BRGenomics)
Loading required package: rtracklayer
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("BRGenomics")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 576 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
147.963   5.720 151.585 

Example timings

BRGenomics.Rcheck/BRGenomics-Ex.timings

nameusersystemelapsed
applyNFsGRanges0.4140.0000.415
binNDimensions0.4990.0320.531
bootstrap-signal-by-position0.5070.0160.522
genebodies0.1720.0000.172
getCountsByPositions0.4590.0040.463
getCountsByRegions0.1670.0240.192
getDESeqDataSet0.6350.0080.643
getDESeqResults15.125 0.02415.161
getMaxPositionsBySignal0.3130.0000.313
getPausingIndices0.6120.0040.616
getSpikeInCounts0.3740.2700.472
getSpikeInNFs0.8000.1840.894
getStrandedCoverage1.8200.0641.884
import-functions1.6570.0361.867
import_bam0.8070.0361.003
intersectByGene1.3910.0081.399
makeGRangesBRG0.5680.0040.572
mergeGRangesData1.5990.0121.612
mergeReplicates0.7390.0000.739
subsampleBySpikeIn0.8300.2730.936
subsampleGRanges0.0730.0040.076
subsetRegionsBySignal0.6830.0240.707
tidyChromosomes0.8010.0240.825