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This page was generated on 2021-09-22 15:04:47 -0400 (Wed, 22 Sep 2021).

CHECK results for BRGenomics on nebbiolo1

To the developers/maintainers of the BRGenomics package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BRGenomics.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 213/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BRGenomics 1.4.0  (landing page)
Mike DeBerardine
Snapshot Date: 2021-09-21 04:50:12 -0400 (Tue, 21 Sep 2021)
git_url: https://git.bioconductor.org/packages/BRGenomics
git_branch: RELEASE_3_13
git_last_commit: b006074
git_last_commit_date: 2021-05-19 12:50:47 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: BRGenomics
Version: 1.4.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:BRGenomics.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings BRGenomics_1.4.0.tar.gz
StartedAt: 2021-09-21 09:05:30 -0400 (Tue, 21 Sep 2021)
EndedAt: 2021-09-21 09:14:57 -0400 (Tue, 21 Sep 2021)
EllapsedTime: 567.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: BRGenomics.Rcheck
Warnings: 1

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:BRGenomics.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings BRGenomics_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/BRGenomics.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.4.0’
* 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 ... WARNING
Missing link or links in documentation object 'getCountsByRegions.Rd':
  ‘[rtracklayer:export]{rtracklayer::import.bw}’

Missing link or links in documentation object 'import-functions.Rd':
  ‘[rtracklayer:export]{rtracklayer::import}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 19.778  0.136   19.93
* 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 WARNING
See
  ‘/home/biocbuild/bbs-3.13-bioc/meat/BRGenomics.Rcheck/00check.log’
for details.



Installation output

BRGenomics.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL BRGenomics
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
> 
> test_check("BRGenomics")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 576 ]
> 
> proc.time()
   user  system elapsed 
189.255  11.390 197.041 

Example timings

BRGenomics.Rcheck/BRGenomics-Ex.timings

nameusersystemelapsed
applyNFsGRanges0.3000.0080.308
binNDimensions0.4230.0400.463
bootstrap-signal-by-position0.3450.0030.349
genebodies0.2190.0040.223
getCountsByPositions0.5070.0000.508
getCountsByRegions0.1760.0240.200
getDESeqDataSet1.3820.0081.390
getDESeqResults19.778 0.13619.930
getMaxPositionsBySignal0.3280.0120.339
getPausingIndices0.6290.0080.638
getSpikeInCounts0.4300.3490.550
getSpikeInNFs0.8380.2860.890
getStrandedCoverage1.9740.0602.036
import-functions1.1390.0361.177
import_bam0.8320.0240.856
intersectByGene1.1920.0161.208
makeGRangesBRG0.4530.0040.457
mergeGRangesData1.3790.0001.380
mergeReplicates0.8460.0000.846
subsampleBySpikeIn1.1510.4061.264
subsampleGRanges0.0850.0160.101
subsetRegionsBySignal1.6950.1961.891
tidyChromosomes0.6830.0200.703