Package: DiffLogo

Version: 2.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DiffLogo_2.2.0.tar.gz

StartedAt: 2018-04-12 02:52:24 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 02:53:05 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 40.9 seconds

RetCode: 0

Status:  OK

CheckDir: DiffLogo.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DiffLogo_2.2.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/DiffLogo.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 ‘DiffLogo/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DiffLogo’ version ‘2.2.0’
* 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 ‘DiffLogo’ 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 loading without being on the library search path ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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

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

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.

> 
> proc.time()
   user  system elapsed 
  0.230   0.042   0.264 

name	user	system	elapsed
ASN	0.001	0.000	0.001
Alphabet	0.000	0.000	0.001
DNA	0.001	0.000	0.001
FULL_ALPHABET	0.001	0.001	0.001
RNA	0	0	0
calculatePvalue	0.029	0.003	0.032
createDiffLogoObject	0.125	0.006	0.132
diffLogo	0.204	0.009	0.215
diffLogoFromPwm	0.060	0.004	0.067
diffLogoTable	2.212	0.029	2.273
diffLogoTableConfiguration	0.003	0.001	0.002
differenceOfICs	0.322	0.009	0.339
drawDiffLogoTable	2.072	0.021	2.119
enrichDiffLogoObjectWithPvalues	0.326	0.008	0.341
enrichDiffLogoTableWithPvalues	3.899	0.019	3.987
extendPwmsFromAlignmentVector	0.072	0.000	0.073
getAlphabetFromCharacters	0.001	0.000	0.000
getAlphabetFromSequences	0.009	0.000	0.010
getPwmFromAlignment	0.422	0.059	0.503
getPwmFromAlignmentFile	0.036	0.000	0.038
getPwmFromFastaFile	0.019	0.000	0.019
getPwmFromFile	0.004	0.001	0.004
getPwmFromHomerFile	0.002	0.000	0.003
getPwmFromPfmOrJasparFile	0.002	0.000	0.002
getPwmFromPwmFile	0.004	0.000	0.004
getSequencesFromAlignmentFile	0.002	0.000	0.003
getSequencesFromFastaFile	0.002	0.000	0.003
informationContent	0.076	0.004	0.084
lossOfAbsICDifferences	0.049	0.002	0.054
multipleLocalPwmsAlignment	0.055	0.001	0.056
normalizePWM	0.001	0.000	0.000
normalizedDifferenceOfProbabilities	0.061	0.002	0.067
prepareDiffLogoTable	1.541	0.013	1.578
probabilities	0.045	0.001	0.047
seqLogo	0.045	0.002	0.047
shannonDivergence	0.056	0.002	0.059
sumOfAbsICDifferences	0.057	0.002	0.067
sumOfAbsProbabilityDifferences	0.063	0.005	0.073
sumProbabilities	0.040	0.002	0.043