Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-06-24 12:08:19 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4156
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4221
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 VplotR on merida1


To the developers/maintainers of the VplotR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/VplotR.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 2110/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
VplotR 1.6.0  (landing page)
Jacques Serizay
Snapshot Date: 2022-06-23 13:55:15 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/VplotR
git_branch: RELEASE_3_15
git_last_commit: e48df2f
git_last_commit_date: 2022-04-26 12:07:30 -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    NA  

Summary

Package: VplotR
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:VplotR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings VplotR_1.6.0.tar.gz
StartedAt: 2022-06-24 10:29:14 -0400 (Fri, 24 Jun 2022)
EndedAt: 2022-06-24 10:39:23 -0400 (Fri, 24 Jun 2022)
EllapsedTime: 608.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: VplotR.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:VplotR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings VplotR_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/VplotR.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘VplotR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘VplotR’ 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 ‘VplotR’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘GenomicRanges::subtract’ by ‘magrittr::subtract’ when loading ‘VplotR’
See ‘/Users/biocbuild/bbs-3.15-bioc/meat/VplotR.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
nucleosomeEnrichment.GRanges 14.993  1.282  16.411
nucleosomeEnrichment.Vmat    12.808  0.889  15.625
nucleosomeEnrichment         10.511  1.578  13.710
sampleGRanges.GRanges         5.523  0.560   6.864
sampleGRanges                 5.412  0.599   6.797
plotVmat.VmatList             5.034  0.125   5.856
plotVmat.list                 5.016  0.115   5.807
* 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/VplotR.Rcheck/00check.log’
for details.



Installation output

VplotR.Rcheck/00install.out

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


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

Tests output

VplotR.Rcheck/tests/testthat.Rout


R version 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"
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(VplotR)
Loading required package: GenomicRanges
Loading required package: stats4
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

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: ggplot2
Warning message:
replacing previous import 'GenomicRanges::subtract' by 'magrittr::subtract' when loading 'VplotR' 
> 
> test_check("VplotR")
[ FAIL 0 | WARN 15 | SKIP 0 | PASS 4 ]

[ FAIL 0 | WARN 15 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
130.211   7.397 158.770 

Example timings

VplotR.Rcheck/VplotR-Ex.timings

nameusersystemelapsed
ABF1_sacCer30.1050.0030.109
ATAC_ce11_Serizay20200.3730.0140.389
CTCF_hg380.0470.0030.050
MNase_sacCer3_Henikoff20110.1460.0050.151
MNase_sacCer3_Henikoff2011_subset0.1070.0030.111
REB1_sacCer30.0290.0030.031
alignToTSS0.8000.0060.814
bam_test0.0640.0030.073
ce11_all_REs0.0410.0040.047
ce11_proms0.0290.0030.031
computeVmat3.0350.0613.135
deconvolveBidirectionalPromoters0.2080.0060.216
getFragmentsDistribution0.2290.0120.242
importPEBamFiles0.4340.0100.445
normalizeVmat2.0660.0742.236
nucleosomeEnrichment.GRanges14.993 1.28216.411
nucleosomeEnrichment10.511 1.57813.710
nucleosomeEnrichment.Vmat12.808 0.88915.625
plotFootprint0.8870.0181.024
plotProfile1.2450.1781.643
plotVmat.GRanges2.7160.0323.040
plotVmat2.7070.0343.257
plotVmat.Vmat3.4330.0793.891
plotVmat.VmatList5.0340.1255.856
plotVmat.default3.4300.0563.970
plotVmat.list5.0160.1155.807
sampleGRanges.GRanges5.5230.5606.864
sampleGRanges5.4120.5996.797
shiftATACGranges0.1460.0030.182
shuffleVmat1.9120.0112.230
theme_ggplot20.2270.0030.263