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This page was generated on 2023-10-20 09:38:14 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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

Package 2198/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
VplotR 1.10.0  (landing page)
Jacques Serizay
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/VplotR
git_branch: RELEASE_3_17
git_last_commit: 6b367d8
git_last_commit_date: 2023-04-25 11:21:54 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

CHECK results for VplotR on kjohnson2


To the developers/maintainers of the VplotR package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: VplotR
Version: 1.10.0
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_1.10.0.tar.gz
StartedAt: 2023-10-19 09:48:54 -0400 (Thu, 19 Oct 2023)
EndedAt: 2023-10-19 09:58:55 -0400 (Thu, 19 Oct 2023)
EllapsedTime: 600.6 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_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/VplotR.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘VplotR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘VplotR’ version ‘1.10.0’
* 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-3.17-bioc-mac-arm64/meat/VplotR.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data      2.8Mb
    figures   2.1Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 9.115  0.684  17.443
nucleosomeEnrichment.Vmat    7.267  0.700  14.159
nucleosomeEnrichment         6.074  1.001  12.813
plotVmat.list                2.816  0.071   5.211
plotVmat.VmatList            2.734  0.116   5.196
* 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, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/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/4.3-arm64/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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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 object is masked from 'package:utils':

    findMatches

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 
 74.460   4.507 139.801 

Example timings

VplotR.Rcheck/VplotR-Ex.timings

nameusersystemelapsed
ABF1_sacCer30.0830.0100.166
ATAC_ce11_Serizay20200.2610.0130.492
CTCF_hg380.0290.0040.061
MNase_sacCer3_Henikoff20110.0920.0060.175
MNase_sacCer3_Henikoff2011_subset0.0620.0030.116
REB1_sacCer30.0160.0030.032
alignToTSS0.0950.0050.180
bam_test0.0410.0050.078
ce11_all_REs0.1080.0060.203
ce11_proms0.0180.0040.038
computeVmat1.9780.0463.587
deconvolveBidirectionalPromoters0.1360.0060.250
getFragmentsDistribution0.1600.0110.309
importPEBamFiles0.2630.0100.482
normalizeVmat1.7400.0393.117
nucleosomeEnrichment.GRanges 9.115 0.68417.443
nucleosomeEnrichment 6.074 1.00112.813
nucleosomeEnrichment.Vmat 7.267 0.70014.159
plotFootprint0.5520.0301.026
plotProfile0.8740.0841.695
plotVmat.GRanges1.5370.0352.846
plotVmat1.5450.0612.886
plotVmat.Vmat1.8770.1163.634
plotVmat.VmatList2.7340.1165.196
plotVmat.default1.9720.0963.823
plotVmat.list2.8160.0715.211
sampleGRanges.GRanges2.1490.3704.574
sampleGRanges2.1720.3934.500
shiftATACGranges0.0900.0050.165
shuffleVmat1.1490.0532.094
theme_ggplot20.1640.0070.302