Back to Multiple platform build/check report for BioC 3.16:   simplified   long
ABCDEFGHIJKLMNOPQRSTU[V]WXYZ

This page was generated on 2023-04-12 11:05:57 -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 palomino4


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: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:VplotR.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings VplotR_1.8.0.tar.gz
StartedAt: 2023-04-11 07:09:53 -0400 (Tue, 11 Apr 2023)
EndedAt: 2023-04-11 07:15:17 -0400 (Tue, 11 Apr 2023)
EllapsedTime: 323.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: VplotR.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:VplotR.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings VplotR_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/VplotR.Rcheck'
* using R version 4.2.3 (2023-03-15 ucrt)
* using platform: x86_64-w64-mingw32 (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 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 'F:/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 9.36   0.54    9.97
nucleosomeEnrichment.Vmat    6.58   0.64    7.22
nucleosomeEnrichment         6.01   0.64    6.65
* 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
  'F:/biocbuild/bbs-3.16-bioc/meat/VplotR.Rcheck/00check.log'
for details.



Installation output

VplotR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL VplotR
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.16-bioc/R/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 ucrt) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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

Attaching package: 'IRanges'

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

    windows

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 
  69.00    5.92   75.54 

Example timings

VplotR.Rcheck/VplotR-Ex.timings

nameusersystemelapsed
ABF1_sacCer30.060.000.07
ATAC_ce11_Serizay20200.220.020.23
CTCF_hg380.020.030.04
MNase_sacCer3_Henikoff20110.080.000.08
MNase_sacCer3_Henikoff2011_subset0.050.000.04
REB1_sacCer30.010.000.02
alignToTSS0.100.010.11
bam_test0.030.000.03
ce11_all_REs0.010.020.03
ce11_proms0.020.000.02
computeVmat1.840.031.87
deconvolveBidirectionalPromoters0.100.010.11
getFragmentsDistribution0.120.000.13
importPEBamFiles0.280.000.29
normalizeVmat1.630.041.66
nucleosomeEnrichment.GRanges9.360.549.97
nucleosomeEnrichment6.010.646.65
nucleosomeEnrichment.Vmat6.580.647.22
plotFootprint0.440.110.55
plotProfile0.700.080.78
plotVmat.GRanges1.380.031.41
plotVmat1.290.081.37
plotVmat.Vmat1.690.271.95
plotVmat.VmatList2.550.202.75
plotVmat.default1.860.121.99
plotVmat.list2.400.082.48
sampleGRanges.GRanges1.880.111.99
sampleGRanges2.000.172.18
shiftATACGranges0.070.000.07
shuffleVmat0.970.161.13
theme_ggplot20.220.080.31