Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-08-12 13:23:26 -0400 (Fri, 12 Aug 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4364
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4117
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4182
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for periodicDNA on merida1


To the developers/maintainers of the periodicDNA package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/periodicDNA.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? 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 1437/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
periodicDNA 1.6.0  (landing page)
Jacques Serizay
Snapshot Date: 2022-08-11 13:55:06 -0400 (Thu, 11 Aug 2022)
git_url: https://git.bioconductor.org/packages/periodicDNA
git_branch: RELEASE_3_15
git_last_commit: dd2df94
git_last_commit_date: 2022-04-26 12:08:09 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: periodicDNA
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:periodicDNA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings periodicDNA_1.6.0.tar.gz
StartedAt: 2022-08-12 06:00:31 -0400 (Fri, 12 Aug 2022)
EndedAt: 2022-08-12 06:09:05 -0400 (Fri, 12 Aug 2022)
EllapsedTime: 513.9 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: periodicDNA.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:periodicDNA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings periodicDNA_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/periodicDNA.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘periodicDNA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘periodicDNA’ version ‘1.6.0’
* 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 ‘periodicDNA’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘GenomicRanges::subtract’ by ‘magrittr::subtract’ when loading ‘periodicDNA’
See ‘/Users/biocbuild/bbs-3.15-bioc/meat/periodicDNA.Rcheck/00install.out’ for details.
* 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
getPeriodicity         20.007  0.906  21.180
plotPeriodicityResults  8.323  0.406   8.745
getPeriodicityTrack     8.335  0.150   8.517
plotAggregateCoverage   6.253  2.023   6.380
* 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
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/periodicDNA.Rcheck/00check.log’
for details.



Installation output

periodicDNA.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL periodicDNA
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘periodicDNA’ ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘GenomicRanges::subtract’ by ‘magrittr::subtract’ when loading ‘periodicDNA’
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘GenomicRanges::subtract’ by ‘magrittr::subtract’ when loading ‘periodicDNA’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘GenomicRanges::subtract’ by ‘magrittr::subtract’ when loading ‘periodicDNA’
** testing if installed package keeps a record of temporary installation path
* DONE (periodicDNA)

Tests output

periodicDNA.Rcheck/tests/testthat.Rout


R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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(periodicDNA)
Loading required package: Biostrings
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

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
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: XVector
Loading required package: GenomeInfoDb

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Loading required package: GenomicRanges
Loading required package: BSgenome
Loading required package: rtracklayer
Loading required package: BiocParallel
Warning message:
replacing previous import 'GenomicRanges::subtract' by 'magrittr::subtract' when loading 'periodicDNA' 
> library(BiocParallel)
> register(setUpBPPARAM(1), default = TRUE)
> 
> test_check("periodicDNA")
[ FAIL 0 | WARN 7 | SKIP 0 | PASS 6 ]

[ FAIL 0 | WARN 7 | SKIP 0 | PASS 6 ]
> 
> proc.time()
   user  system elapsed 
 55.818   3.877  58.847 

Example timings

periodicDNA.Rcheck/periodicDNA-Ex.timings

nameusersystemelapsed
ce11_ATACseq0.1090.0140.123
ce11_TSSs0.1080.0130.121
ce11_WW_10bp0.0570.0070.066
ce11_all_REs0.2310.0120.244
ce11_proms0.0700.0040.075
ce11_proms_seqs0.0830.0040.086
getPeriodicity20.007 0.90621.180
getPeriodicityTrack8.3350.1508.517
getPeriodicityWithIterations4.3480.0224.387
plotAggregateCoverage6.2532.0236.380
plotPeriodicityResults8.3230.4068.745
setUpBPPARAM0.0070.0000.007
theme_ggplot20.2490.0030.252