Back to Multiple platform build/check report for BioC 3.15
ABCDEFGHIJKLMNOPQRSTU[V]WXYZ

This page was generated on 2022-06-24 12:06:59 -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 palomino3


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: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:VplotR.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings VplotR_1.6.0.tar.gz
StartedAt: 2022-06-24 05:52:49 -0400 (Fri, 24 Jun 2022)
EndedAt: 2022-06-24 05:58:51 -0400 (Fri, 24 Jun 2022)
EllapsedTime: 362.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: VplotR.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:VplotR.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings VplotR_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/VplotR.Rcheck'
* using R version 4.2.0 (2022-04-22 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 '1.6.0'
* 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 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-3.15-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 10.00   0.61   11.00
nucleosomeEnrichment.Vmat     7.90   0.66    8.57
nucleosomeEnrichment          5.77   0.65    6.45
* 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-3.15-bioc/meat/VplotR.Rcheck/00check.log'
for details.



Installation output

VplotR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL VplotR
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.15-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 4.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics"
Copyright (C) 2022 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, 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 15 | SKIP 0 | PASS 4 ]

[ FAIL 0 | WARN 15 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
  77.71    6.03   84.09 

Example timings

VplotR.Rcheck/VplotR-Ex.timings

nameusersystemelapsed
ABF1_sacCer30.080.020.10
ATAC_ce11_Serizay20200.230.000.23
CTCF_hg380.040.000.03
MNase_sacCer3_Henikoff20110.070.010.10
MNase_sacCer3_Henikoff2011_subset0.050.020.06
REB1_sacCer30.020.010.03
alignToTSS0.110.020.12
bam_test0.030.000.04
ce11_all_REs0.010.020.03
ce11_proms0.020.010.03
computeVmat2.010.022.03
deconvolveBidirectionalPromoters0.110.000.11
getFragmentsDistribution0.160.000.16
importPEBamFiles0.280.030.31
normalizeVmat2.030.032.06
nucleosomeEnrichment.GRanges10.00 0.6111.00
nucleosomeEnrichment5.770.656.45
nucleosomeEnrichment.Vmat7.900.668.57
plotFootprint0.550.030.57
plotProfile0.860.060.93
plotVmat.GRanges1.780.071.84
plotVmat1.690.061.75
plotVmat.Vmat2.390.302.69
plotVmat.VmatList3.270.093.36
plotVmat.default2.150.162.31
plotVmat.list3.240.173.41
sampleGRanges.GRanges3.200.153.35
sampleGRanges3.000.253.25
shiftATACGranges0.050.050.10
shuffleVmat1.390.151.57
theme_ggplot20.170.000.18