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CHECK report for PWMEnrich on tokay1

This page was generated on 2021-05-06 12:32:55 -0400 (Thu, 06 May 2021).

To the developers/maintainers of the PWMEnrich package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1418/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PWMEnrich 4.26.0  (landing page)
Diego Diez
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/PWMEnrich
Branch: RELEASE_3_12
Last Commit: 5544f38
Last Changed Date: 2020-10-27 10:46:10 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: PWMEnrich
Version: 4.26.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PWMEnrich.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings PWMEnrich_4.26.0.tar.gz
StartedAt: 2021-05-06 05:51:03 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 05:53:52 -0400 (Thu, 06 May 2021)
EllapsedTime: 168.5 seconds
RetCode: 0
Status:   OK   
CheckDir: PWMEnrich.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PWMEnrich.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings PWMEnrich_4.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/PWMEnrich.Rcheck'
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'PWMEnrich/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PWMEnrich' version '4.26.0'
* 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 '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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test-all.R'
 OK
** running tests for arch 'x64' ...
  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:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/PWMEnrich_4.26.0.tar.gz && rm -rf PWMEnrich.buildbin-libdir && mkdir PWMEnrich.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=PWMEnrich.buildbin-libdir PWMEnrich_4.26.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL PWMEnrich_4.26.0.zip && rm PWMEnrich_4.26.0.tar.gz PWMEnrich_4.26.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  204k  100  204k    0     0  7263k      0 --:--:-- --:--:-- --:--:-- 7577k

install for i386

* installing *source* package 'PWMEnrich' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'PWMEnrich'
    finding HTML links ... done
    DNAStringSetToList                      html  
    MotifEnrichmentReport-class             html  
    MotifEnrichmentResults-class            html  
    PFMtoPWM                                html  
    PWM-class                               html  
    PWMCutoffBackground-class               html  
    PWMEmpiricalBackground-class            html  
    PWMEnrich-package                       html  
    PWMGEVBackground-class                  html  
    PWMLognBackground-class                 html  
    PWMUnscaled                             html  
    affinitySequenceSet                     html  
    as.data.frame-MotifEnrichmentReport-method
                                            html  
    cloverPvalue1seq                        html  
    cloverScore                             html  
    colMedians                              html  
    colSds                                  html  
    concatenateSequences                    html  
    cutoffZscore                            html  
    cutoffZscoreSequenceSet                 html  
    divideRows                              html  
    dot-inputPFMfromMatrixOrPWM             html  
    dot-inputParamMotifs                    html  
    dot-inputParamSequences                 html  
    dot-normalize.bg.seq                    html  
    dot-normargPfm                          html  
    dot-normargPriorParams                  html  
    empiricalPvalue                         html  
    empiricalPvalueSequenceSet              html  
    getBackgroundFrequencies                html  
    getPromoters                            html  
    gevPerSequence                          html  
    groupReport-MotifEnrichmentResults-method
                                            html  
    keepFinite                              html  
    logNormPval                             html  
    logNormPvalSequenceSet                  html  
    makeBackground                          html  
    makePWMCutoffBackground                 html  
    makePWMEmpiricalBackground              html  
    makePWMGEVBackground                    html  
    makePWMLognBackground                   html  
    makePWMPvalCutoffBackground             html  
    makePWMPvalCutoffBackgroundFromSeq      html  
    makePriors                              html  
    makeStartEndPos                         html  
    matrixShuffleZscorePerSequence          html  
    maxAligned                              html  
    motifDiffEnrichment                     html  
    motifEcdf                               html  
    motifEnrichment                         html  
    motifIC                                 html  
    motifPrAUC                              html  
    motifRankingForGroup-MotifEnrichmentResults-method
                                            html  
    motifRankingForSequence-MotifEnrichmentResults-method
                                            html  
    motifRecoveryAUC                        html  
    motifScores                             html  
    motifScoresBigMemory                    html  
    motifSimilarity                         html  
    operators-MotifEnrichmentReport         html  
    operators-MotifEnrichmentResults        html  
    operators-PWM                           html  
    operators-PWMCutoffBackground           html  
    operators-PWMEmpiricalBackground        html  
    operators-PWMGEVBackground              html  
    operators-PWMLognBackground             html  
    plot-MotifEnrichmentReport-missing-method
                                            html  
    plot-PWM-missing-method                 html  
    plotMotifScores                         html  
    plotMultipleMotifs                      html  
    plotPFM                                 html  
    plotTopMotifsGroup-MotifEnrichmentResults-method
                                            html  
    plotTopMotifsSequence-MotifEnrichmentResults-method
                                            html  
    rankingProcessAndReturn                 html  
    readJASPAR                              html  
    readMotifs                              html  
    readTRANSFAC                            html  
    registerCoresPWMEnrich                  html  
    reverseComplement-PWM-method            html  
    scanWithPWM                             html  
    seqLogoGrid                             html  
    sequenceReport-MotifEnrichmentResults-method
                                            html  
    show-MotifEnrichmentReport-method       html  
    show-MotifEnrichmentResults-method      html  
    show-PWM-method                         html  
    show-PWMCutoffBackground-method         html  
    show-PWMEmpiricalBackground-method      html  
    show-PWMGEVBackground-method            html  
    show-PWMLognBackground-method           html  
    subsetting-PWMCutoffBackground          html  
    subsetting-PWMEmpiricalBackground       html  
    subsetting-PWMGEVBackground             html  
    subsetting-PWMLognBackground            html  
    toPWM                                   html  
    tryAllMotifAlignments                   html  
    useBigMemoryPWMEnrich                   html  
** 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

install for x64

* installing *source* package 'PWMEnrich' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'PWMEnrich' as PWMEnrich_4.26.0.zip
* DONE (PWMEnrich)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'PWMEnrich' successfully unpacked and MD5 sums checked

Tests output

PWMEnrich.Rcheck/tests_i386/test-all.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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: grid
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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 object is masked from 'package:base':

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

Loading required package: XVector

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 
   2.93    0.17    3.09 

PWMEnrich.Rcheck/tests_x64/test-all.Rout


R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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(PWMEnrich)
Loading required package: grid
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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 object is masked from 'package:base':

    expand.grid

Loading required package: IRanges

Attaching package: 'IRanges'

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

    windows

Loading required package: XVector

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 
   2.89    0.17    3.04 

Example timings

PWMEnrich.Rcheck/examples_i386/PWMEnrich-Ex.timings

nameusersystemelapsed
PFMtoPWM000
PWMUnscaled0.340.060.64
getBackgroundFrequencies000
groupReport-MotifEnrichmentResults-method2.120.112.50
makeBackground0.020.000.02
makePWMCutoffBackground000
makePWMEmpiricalBackground000
makePWMGEVBackground000
makePWMLognBackground000
makePWMPvalCutoffBackground000
makePWMPvalCutoffBackgroundFromSeq000
makePriors000
motifDiffEnrichment2.390.002.39
motifEnrichment3.360.003.41
motifIC0.040.020.11
motifRankingForGroup-MotifEnrichmentResults-method1.750.001.75
motifRankingForSequence-MotifEnrichmentResults-method1.830.001.83
motifScores4.070.034.11
motifSimilarity0.050.000.05
plot-PWM-missing-method0.190.000.18
plotMotifScores0.060.000.07
plotTopMotifsGroup-MotifEnrichmentResults-method1.970.021.98
plotTopMotifsSequence-MotifEnrichmentResults-method2.920.032.95
readMotifs0.100.010.11
registerCoresPWMEnrich000
reverseComplement-PWM-method000
scanWithPWM0.030.000.03
sequenceReport-MotifEnrichmentResults-method2.760.022.78
toPWM000
useBigMemoryPWMEnrich000

PWMEnrich.Rcheck/examples_x64/PWMEnrich-Ex.timings

nameusersystemelapsed
PFMtoPWM000
PWMUnscaled0.330.010.34
getBackgroundFrequencies000
groupReport-MotifEnrichmentResults-method2.470.032.50
makeBackground000
makePWMCutoffBackground000
makePWMEmpiricalBackground000
makePWMGEVBackground000
makePWMLognBackground000
makePWMPvalCutoffBackground000
makePWMPvalCutoffBackgroundFromSeq000
makePriors000
motifDiffEnrichment2.470.002.46
motifEnrichment3.610.023.64
motifIC0.030.000.04
motifRankingForGroup-MotifEnrichmentResults-method1.910.001.90
motifRankingForSequence-MotifEnrichmentResults-method1.980.001.99
motifScores3.830.003.82
motifSimilarity0.030.000.04
plot-PWM-missing-method0.20.00.2
plotMotifScores0.050.000.05
plotTopMotifsGroup-MotifEnrichmentResults-method2.030.002.03
plotTopMotifsSequence-MotifEnrichmentResults-method2.080.002.08
readMotifs0.070.020.09
registerCoresPWMEnrich000
reverseComplement-PWM-method0.020.000.02
scanWithPWM0.020.000.02
sequenceReport-MotifEnrichmentResults-method2.730.002.73
toPWM000
useBigMemoryPWMEnrich000