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CHECK report for PWMEnrich on malbec1

This page was generated on 2020-04-15 12:07:00 -0400 (Wed, 15 Apr 2020).

Package 1334/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PWMEnrich 4.22.0
Robert Stojnic
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/PWMEnrich
Branch: RELEASE_3_10
Last Commit: de4c88d
Last Changed Date: 2019-10-29 13:08:32 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: PWMEnrich
Version: 4.22.0
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:PWMEnrich.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings PWMEnrich_4.22.0.tar.gz
StartedAt: 2020-04-15 01:21:11 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 01:23:11 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 120.0 seconds
RetCode: 0
Status:  OK 
CheckDir: PWMEnrich.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:PWMEnrich.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings PWMEnrich_4.22.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/PWMEnrich.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (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 ‘4.22.0’
* 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 ... NOTE
'library' or 'require' calls in package code:
  ‘PWMEnrich.Dmelanogaster.background’ ‘PWMEnrich.Hsapiens.background’
  ‘PWMEnrich.Mmusculus.background’ ‘parallel’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
colMedians: no visible binding for global variable ‘median’
getPromoters: no visible global function definition for
  ‘providerVersion’
getPromoters: no visible global function definition for ‘data’
gevPerSequence: no visible global function definition for ‘predict.lm’
logNormPval: no visible global function definition for ‘plnorm’
makePWMGEVBackground : <anonymous>: no visible global function
  definition for ‘lm’
makePWMLognBackground : dlnorm.lcen: no visible global function
  definition for ‘dlnorm’
makePWMLognBackground : dlnorm.lcen: no visible global function
  definition for ‘plnorm’
makePWMLognBackground: no visible global function definition for
  ‘quantile’
makePWMLognBackground: no visible global function definition for
  ‘median’
makePWMLognBackground: no visible global function definition for
  ‘optimize’
makePWMPvalCutoffBackground: no visible global function definition for
  ‘quantile’
makePWMPvalCutoffBackground: no visible global function definition for
  ‘ecdf’
makePWMPvalCutoffBackgroundFromSeq: no visible global function
  definition for ‘na.omit’
makePWMPvalCutoffBackgroundFromSeq: no visible global function
  definition for ‘quantile’
makePWMPvalCutoffBackgroundFromSeq: no visible global function
  definition for ‘ecdf’
motifEcdf : <anonymous>: no visible global function definition for
  ‘na.omit’
motifEcdf: no visible binding for global variable ‘ecdf’
motifEnrichment: no visible binding for global variable ‘qlnorm’
motifEnrichment : <anonymous>: no visible global function definition
  for ‘pchisq’
motifScores: no visible global function definition for ‘mclapply’
motifScoresBigMemory: no visible global function definition for
  ‘mclapply’
plotMotifScores: no visible global function definition for ‘palette’
plotMotifScores: no visible global function definition for ‘col2rgb’
plotMotifScores: no visible global function definition for ‘rgb’
plotMotifScores: no visible global function definition for ‘par’
plotMotifScores: no visible global function definition for ‘lines’
plotMotifScores: no visible global function definition for ‘polygon’
plotMotifScores: no visible global function definition for ‘rect’
plotMotifScores: no visible global function definition for ‘text’
registerCoresPWMEnrich: no visible global function definition for
  ‘detectCores’
tryAllMotifAlignments : <anonymous>: no visible global function
  definition for ‘cor’
Undefined global functions or variables:
  col2rgb cor data detectCores dlnorm ecdf lines lm mclapply median
  na.omit optimize palette par pchisq plnorm polygon predict.lm
  providerVersion qlnorm quantile rect rgb text
Consider adding
  importFrom("grDevices", "col2rgb", "palette", "rgb")
  importFrom("graphics", "lines", "par", "polygon", "rect", "text")
  importFrom("stats", "cor", "dlnorm", "ecdf", "lm", "median", "na.omit",
             "optimize", "pchisq", "plnorm", "predict.lm", "qlnorm",
             "quantile")
  importFrom("utils", "data")
to your NAMESPACE file.
* 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 ... OK
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.10-bioc/meat/PWMEnrich.Rcheck/00check.log’
for details.



Installation output

PWMEnrich.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL PWMEnrich
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/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 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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, 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
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

> 
> test_package("PWMEnrich")
Calculating motif enrichment scores ...
Calculating motif enrichment scores ...
NOTE: Using the 'default' algorithm to infer background parameters,
      appropriate for all organisms except human.
Calculating motif enrichment scores ...
Calculating motif enrichment scores ...
Calculating motif enrichment scores ...
Calculating motif enrichment scores ...
Calculating motif enrichment scores ...
Calculating motif enrichment scores ...
Calculating motif enrichment scores ...
Calculating motif enrichment scores ...
NOTE: Using the 'default' algorithm to infer background parameters,
      appropriate for all organisms except human.
Calculating motif enrichment scores ...
Calculating motif enrichment scores ...
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 48 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
Warning message:
Placing tests in `inst/tests` is deprecated. Please use `tests/testthat` instead 
> 
> 
> proc.time()
   user  system elapsed 
  6.524   0.180   6.841 

Example timings

PWMEnrich.Rcheck/PWMEnrich-Ex.timings

nameusersystemelapsed
PFMtoPWM2.2000.3322.656
PWMUnscaled0.3320.0320.365
getBackgroundFrequencies000
groupReport-commaMotifEnrichmentResults-method2.5720.0002.601
makeBackground0.0040.0000.009
makePWMCutoffBackground0.0000.0000.001
makePWMEmpiricalBackground0.0000.0000.001
makePWMGEVBackground000
makePWMLognBackground000
makePWMPvalCutoffBackground0.0000.0000.001
makePWMPvalCutoffBackgroundFromSeq0.0000.0000.001
makePriors0.0000.0000.002
motifDiffEnrichment3.4960.0003.502
motifEnrichment4.0840.0044.481
motifIC0.0720.0000.250
motifRankingForGroup-commaMotifEnrichmentResults-method2.2400.0002.245
motifRankingForSequence-commaMotifEnrichmentResults-method2.3600.0002.363
motifScores4.7280.0124.755
motifSimilarity0.0400.0040.046
plot0.1640.0000.167
plotMotifScores0.0520.0040.058
plotTopMotifsGroup-commaMotifEnrichmentResults-method2.4960.0002.499
plotTopMotifsSequence-commaMotifEnrichmentResults-method2.2000.0082.211
readMotifs0.0760.0120.099
registerCoresPWMEnrich000
reverseComplement0.0160.0000.019
scanWithPWM0.0320.0040.037
sequenceReport-commaMotifEnrichmentResults-method3.5000.0483.554
toPWM2.6120.2482.866
useBigMemoryPWMEnrich000