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This page was generated on 2022-03-14 11:08:22 -0400 (Mon, 14 Mar 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" 4335
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4061
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" 4073
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" 4134
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 riesling1


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? here 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 2061/2090HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
VplotR 1.5.1  (landing page)
Jacques Serizay
Snapshot Date: 2022-03-13 13:55:13 -0400 (Sun, 13 Mar 2022)
git_url: https://git.bioconductor.org/packages/VplotR
git_branch: master
git_last_commit: b1f537c
git_last_commit_date: 2021-11-21 01:03:46 -0400 (Sun, 21 Nov 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  
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: VplotR
Version: 1.5.1
Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:VplotR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings VplotR_1.5.1.tar.gz
StartedAt: 2022-03-13 20:23:06 -0400 (Sun, 13 Mar 2022)
EndedAt: 2022-03-13 20:27:23 -0400 (Sun, 13 Mar 2022)
EllapsedTime: 257.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: VplotR.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:VplotR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings VplotR_1.5.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/VplotR.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'VplotR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'VplotR' version '1.5.1'
* 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 'D:/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 7.53   1.56    9.09
nucleosomeEnrichment.Vmat    4.98   1.50    6.49
nucleosomeEnrichment         4.57   1.73    6.30
* 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
  'D:/biocbuild/bbs-3.15-bioc/meat/VplotR.Rcheck/00check.log'
for details.



Installation output

VplotR.Rcheck/00install.out

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


* installing to library 'D:/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
  converting help for package 'VplotR'
    finding HTML links ... done
    ABF1_sacCer3                            html  
    ATAC_ce11_Serizay2020                   html  
    CTCF_hg38                               html  
    MNase_sacCer3_Henikoff2011              html  
    MNase_sacCer3_Henikoff2011_subset       html  
    REB1_sacCer3                            html  
    alignToTSS                              html  
    bam_test                                html  
    ce11_all_REs                            html  
    ce11_proms                              html  
    computeNucleosomeEnrichmentOverBackground
                                            html  
    computeVmat                             html  
    deconvolveBidirectionalPromoters        html  
    getCuts                                 html  
    getFragmentsDistribution                html  
    importPEBamFiles                        html  
    normalizeVmat                           html  
    nucleosomeEnrichment.GRanges            html  
    nucleosomeEnrichment                    html  
    nucleosomeEnrichment.Vmat               html  
    plotFootprint                           html  
    plotProfile                             html  
    plotVmat.GRanges                        html  
    plotVmat                                html  
    plotVmat.Vmat                           html  
    plotVmat.VmatList                       html  
    plotVmat.default                        html  
    plotVmat.list                           html  
    sampleGRanges.GRanges                   html  
    sampleGRanges                           html  
    shiftATACGranges                        html  
    shuffleVmat                             html  
    theme_ggplot2                           html  
** 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)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'netresponse' is missing or broken
 done

Tests output

VplotR.Rcheck/tests/testthat.Rout


R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 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 
  46.93    7.18   54.06 

Example timings

VplotR.Rcheck/VplotR-Ex.timings

nameusersystemelapsed
ABF1_sacCer30.050.020.06
ATAC_ce11_Serizay20200.690.020.71
CTCF_hg380.030.000.03
MNase_sacCer3_Henikoff20110.070.000.07
MNase_sacCer3_Henikoff2011_subset0.040.010.06
REB1_sacCer30.000.020.02
alignToTSS0.070.010.07
bam_test0.030.020.05
ce11_all_REs0.000.030.03
ce11_proms0.010.000.01
computeVmat1.910.182.10
deconvolveBidirectionalPromoters0.120.000.12
getFragmentsDistribution0.160.020.17
importPEBamFiles0.250.000.25
normalizeVmat0.890.040.92
nucleosomeEnrichment.GRanges7.531.569.09
nucleosomeEnrichment4.571.736.30
nucleosomeEnrichment.Vmat4.981.506.49
plotFootprint0.310.030.34
plotProfile0.490.070.55
plotVmat.GRanges1.010.061.07
plotVmat1.080.111.19
plotVmat.Vmat1.500.151.66
plotVmat.VmatList1.890.182.06
plotVmat.default1.310.071.39
plotVmat.list1.850.141.99
sampleGRanges.GRanges2.080.662.73
sampleGRanges2.040.722.77
shiftATACGranges0.050.020.06
shuffleVmat0.750.060.81
theme_ggplot20.080.000.08