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CHECK report for PWMEnrich on malbec2

This page was generated on 2019-10-16 12:01:16 -0400 (Wed, 16 Oct 2019).

Package 1280/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PWMEnrich 4.20.0
Robert Stojnic
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/PWMEnrich
Branch: RELEASE_3_9
Last Commit: ab13907
Last Changed Date: 2019-05-02 11:53:36 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: PWMEnrich
Version: 4.20.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:PWMEnrich.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings PWMEnrich_4.20.0.tar.gz
StartedAt: 2019-10-16 04:10:50 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 04:12:47 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 116.5 seconds
RetCode: 0
Status:  OK 
CheckDir: PWMEnrich.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:PWMEnrich.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings PWMEnrich_4.20.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/PWMEnrich.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘4.20.0’
* 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 : : 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 : : 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 : : 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 : : 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-3.9-bioc/meat/PWMEnrich.Rcheck/00check.log’
for details.



Installation output

PWMEnrich.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL PWMEnrich
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-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 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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 
  5.396   0.158   6.031 

Example timings

PWMEnrich.Rcheck/PWMEnrich-Ex.timings

nameusersystemelapsed
PFMtoPWM2.3200.2802.934
PWMUnscaled0.3300.0200.351
getBackgroundFrequencies000
groupReport-commaMotifEnrichmentResults-method3.0420.0163.073
makeBackground0.0020.0000.017
makePWMCutoffBackground000
makePWMEmpiricalBackground0.0000.0000.001
makePWMGEVBackground000
makePWMLognBackground000
makePWMPvalCutoffBackground0.0010.0000.000
makePWMPvalCutoffBackgroundFromSeq000
makePriors0.0010.0000.001
motifDiffEnrichment2.1450.0002.145
motifEnrichment2.8350.0002.845
motifIC0.0390.0000.055
motifRankingForGroup-commaMotifEnrichmentResults-method1.9920.0122.004
motifRankingForSequence-commaMotifEnrichmentResults-method2.0420.0082.063
motifScores4.8190.0164.889
motifSimilarity0.0750.0000.075
plot0.2390.0070.246
plotMotifScores0.0880.0000.088
plotTopMotifsGroup-commaMotifEnrichmentResults-method2.7300.0042.735
plotTopMotifsSequence-commaMotifEnrichmentResults-method1.9160.0001.916
readMotifs0.0820.0070.102
registerCoresPWMEnrich000
reverseComplement0.0240.0000.024
scanWithPWM0.0560.0000.056
sequenceReport-commaMotifEnrichmentResults-method2.4800.0162.496
toPWM2.1970.1882.385
useBigMemoryPWMEnrich000