Back to Multiple platform build/check report for BioC 3.16:   simplified   long
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This page was generated on 2023-04-12 11:06:31 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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 lconway


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 2151/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
VplotR 1.8.0  (landing page)
Jacques Serizay
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/VplotR
git_branch: RELEASE_3_16
git_last_commit: ec8d656
git_last_commit_date: 2022-11-01 11:22:38 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    ERROR  
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: VplotR
Version: 1.8.0
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_1.8.0.tar.gz
StartedAt: 2023-04-10 23:19:20 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 23:24:03 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 282.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: VplotR.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### 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_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/VplotR.Rcheck’
* using R version 4.2.3 (2023-03-15)
* 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 ‘1.8.0’
* 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-3.16-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 8.339  0.747   9.097
nucleosomeEnrichment.Vmat    6.094  0.701   6.807
nucleosomeEnrichment         5.376  1.133   6.520
* 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-3.16-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 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 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, aperm, 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 18 | SKIP 0 | PASS 4 ]

[ FAIL 0 | WARN 18 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
 58.101   6.286  64.588 

Example timings

VplotR.Rcheck/VplotR-Ex.timings

nameusersystemelapsed
ABF1_sacCer30.0450.0050.050
ATAC_ce11_Serizay20200.1980.0090.207
CTCF_hg380.0280.0040.032
MNase_sacCer3_Henikoff20110.6370.0050.646
MNase_sacCer3_Henikoff2011_subset0.0580.0030.061
REB1_sacCer30.0140.0020.015
alignToTSS0.0720.0040.076
bam_test0.0370.0030.040
ce11_all_REs0.0240.0020.026
ce11_proms0.0130.0020.015
computeVmat1.7760.0751.855
deconvolveBidirectionalPromoters0.1160.0050.122
getFragmentsDistribution0.1360.0090.147
importPEBamFiles0.2100.0070.216
normalizeVmat1.5200.0681.591
nucleosomeEnrichment.GRanges8.3390.7479.097
nucleosomeEnrichment5.3761.1336.520
nucleosomeEnrichment.Vmat6.0940.7016.807
plotFootprint0.4240.0220.448
plotProfile0.6510.1610.814
plotVmat.GRanges1.0550.0401.097
plotVmat1.1500.1061.259
plotVmat.Vmat1.5580.1261.691
plotVmat.VmatList1.9500.0492.004
plotVmat.default1.4180.0821.504
plotVmat.list1.9440.1712.119
sampleGRanges.GRanges1.6330.2261.860
sampleGRanges1.8470.4452.296
shiftATACGranges0.0830.0030.086
shuffleVmat0.9110.0160.929
theme_ggplot20.1240.0030.126