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CHECK report for PWMEnrich on veracruz1

This page was generated on 2018-04-12 13:35:40 -0400 (Thu, 12 Apr 2018).

Package 1092/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PWMEnrich 4.14.0
Robert Stojnic
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/PWMEnrich
Branch: RELEASE_3_6
Last Commit: 8531fcc
Last Changed Date: 2017-10-30 12:39:43 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 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
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: PWMEnrich
Version: 4.14.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PWMEnrich_4.14.0.tar.gz
StartedAt: 2018-04-12 08:03:15 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 08:05:17 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 121.6 seconds
RetCode: 0
Status:  OK 
CheckDir: PWMEnrich.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings PWMEnrich_4.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/PWMEnrich.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘4.14.0’
* 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 ... NOTE
  installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc       1.4Mb
    extdata   3.4Mb
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/PWMEnrich.Rcheck/00check.log’
for details.



Installation output

PWMEnrich.Rcheck/00install.out

* installing *source* package ‘PWMEnrich’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (PWMEnrich)

Tests output

PWMEnrich.Rcheck/tests/test-all.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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: 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, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, 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 FAILED: 0
Warning message:
Placing tests in `inst/tests` is deprecated. Please use `tests/testthat` instead 
> 
> 
> proc.time()
   user  system elapsed 
  5.814   0.176   6.084 

Example timings

PWMEnrich.Rcheck/PWMEnrich-Ex.timings

nameusersystemelapsed
PFMtoPWM2.6170.3893.074
PWMUnscaled0.3300.0080.340
getBackgroundFrequencies000
groupReport-commaMotifEnrichmentResults-method2.8660.0422.956
makeBackground0.0050.0010.005
makePWMCutoffBackground0.0000.0000.001
makePWMEmpiricalBackground0.0010.0000.001
makePWMGEVBackground0.0000.0000.001
makePWMLognBackground0.0000.0000.001
makePWMPvalCutoffBackground0.0000.0000.001
makePWMPvalCutoffBackgroundFromSeq0.0010.0010.001
makePriors0.0020.0000.001
motifDiffEnrichment2.7330.0092.774
motifEnrichment4.0630.0254.148
motifIC0.0520.0030.056
motifRankingForGroup-commaMotifEnrichmentResults-method2.2810.0072.335
motifRankingForSequence-commaMotifEnrichmentResults-method2.2540.0092.302
motifScores4.7360.0384.865
motifSimilarity0.1190.0010.121
plot0.1810.0050.193
plotMotifScores0.0770.0030.081
plotTopMotifsGroup-commaMotifEnrichmentResults-method2.6390.0152.707
plotTopMotifsSequence-commaMotifEnrichmentResults-method2.3940.0202.467
readMotifs0.1610.0150.181
registerCoresPWMEnrich000
reverseComplement0.0210.0020.023
scanWithPWM0.0430.0010.045
sequenceReport-commaMotifEnrichmentResults-method3.1770.0643.299
toPWM2.4850.3912.936
useBigMemoryPWMEnrich000