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This page was generated on 2021-10-22 12:05:07 -0400 (Fri, 22 Oct 2021).

CHECK results for PWMEnrich on merida1

To the developers/maintainers of the PWMEnrich package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PWMEnrich.git to
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raw results

Package 1486/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PWMEnrich 4.29.1  (landing page)
Diego Diez
Snapshot Date: 2021-10-21 14:50:08 -0400 (Thu, 21 Oct 2021)
git_url: https://git.bioconductor.org/packages/PWMEnrich
git_branch: master
git_last_commit: 96da45d
git_last_commit_date: 2021-06-19 02:32:14 -0400 (Sat, 19 Jun 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    NA  

Summary

Package: PWMEnrich
Version: 4.29.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PWMEnrich.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PWMEnrich_4.29.1.tar.gz
StartedAt: 2021-10-22 07:53:25 -0400 (Fri, 22 Oct 2021)
EndedAt: 2021-10-22 07:56:13 -0400 (Fri, 22 Oct 2021)
EllapsedTime: 167.6 seconds
RetCode: 0
Status:   OK  
CheckDir: PWMEnrich.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:PWMEnrich.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings PWMEnrich_4.29.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/PWMEnrich.Rcheck’
* using R version 4.1.1 Patched (2021-08-22 r80813)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PWMEnrich/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PWMEnrich’ version ‘4.29.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘PWMEnrich’ can be installed ... OK
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
motifScores     5.653  0.040   5.700
motifEnrichment 5.145  0.018   5.169
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.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: OK


Installation output

PWMEnrich.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL PWMEnrich
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘PWMEnrich’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (PWMEnrich)

Tests output

PWMEnrich.Rcheck/tests/test-all.Rout


R version 4.1.1 Patched (2021-08-22 r80813) -- "Kick Things"
Copyright (C) 2021 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(PWMEnrich)
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: Biostrings
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: XVector
Loading required package: GenomeInfoDb

Attaching package: 'Biostrings'

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

    strsplit

> 
> test_package("PWMEnrich")
No installed testthat tests found for PWMEnrich
> 
> 
> proc.time()
   user  system elapsed 
  4.681   0.354   4.972 

Example timings

PWMEnrich.Rcheck/PWMEnrich-Ex.timings

nameusersystemelapsed
PFMtoPWM000
PWMUnscaled1.0760.0541.133
getBackgroundFrequencies000
groupReport-MotifEnrichmentResults-method3.2520.0973.355
makeBackground0.0040.0000.005
makePWMCutoffBackground0.0000.0010.000
makePWMEmpiricalBackground0.0010.0000.001
makePWMGEVBackground0.0000.0000.001
makePWMLognBackground000
makePWMPvalCutoffBackground000
makePWMPvalCutoffBackgroundFromSeq000
makePriors0.0010.0000.002
motifDiffEnrichment3.8240.0333.861
motifEnrichment5.1450.0185.169
motifIC0.0660.0020.069
motifRankingForGroup-MotifEnrichmentResults-method2.8030.0082.815
motifRankingForSequence-MotifEnrichmentResults-method2.5470.0082.558
motifScores5.6530.0405.700
motifSimilarity0.0730.0010.073
plot-PWM-missing-method0.2080.0210.230
plotMotifScores0.0930.0020.096
plotTopMotifsGroup-MotifEnrichmentResults-method2.8100.0172.832
plotTopMotifsSequence-MotifEnrichmentResults-method3.0550.0303.091
readMotifs0.1030.0190.122
registerCoresPWMEnrich000
reverseComplement-PWM-method0.0220.0010.023
scanWithPWM0.0590.0010.060
sequenceReport-MotifEnrichmentResults-method4.0440.0714.121
toPWM0.0010.0000.000
useBigMemoryPWMEnrich0.0010.0010.001