Package: DiffLogo

Version: 2.2.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings DiffLogo_2.2.0.tar.gz

StartedAt: 2018-04-11 22:56:26 -0400 (Wed, 11 Apr 2018)

EndedAt: 2018-04-11 22:57:01 -0400 (Wed, 11 Apr 2018)

EllapsedTime: 35.0 seconds

RetCode: 0

Status:  OK

CheckDir: DiffLogo.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings DiffLogo_2.2.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/DiffLogo.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (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 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-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.

> 
> proc.time()
   user  system elapsed 
  0.192   0.012   0.201 

name	user	system	elapsed
ASN	0	0	0
Alphabet	0.004	0.000	0.000
DNA	0	0	0
FULL_ALPHABET	0.000	0.000	0.001
RNA	0	0	0
calculatePvalue	0.028	0.000	0.029
createDiffLogoObject	0.116	0.000	0.114
diffLogo	0.156	0.000	0.154
diffLogoFromPwm	0.056	0.000	0.058
diffLogoTable	1.920	0.024	1.945
diffLogoTableConfiguration	0.000	0.000	0.002
differenceOfICs	0.356	0.004	0.361
drawDiffLogoTable	1.584	0.000	1.585
enrichDiffLogoObjectWithPvalues	0.248	0.000	0.247
enrichDiffLogoTableWithPvalues	3.324	0.000	3.322
extendPwmsFromAlignmentVector	0.060	0.000	0.063
getAlphabetFromCharacters	0.000	0.000	0.001
getAlphabetFromSequences	0.012	0.000	0.012
getPwmFromAlignment	0.420	0.000	0.418
getPwmFromAlignmentFile	0.028	0.000	0.028
getPwmFromFastaFile	0.016	0.000	0.015
getPwmFromFile	0.004	0.000	0.002
getPwmFromHomerFile	0.004	0.000	0.002
getPwmFromPfmOrJasparFile	0.000	0.000	0.002
getPwmFromPwmFile	0.000	0.000	0.002
getSequencesFromAlignmentFile	0.004	0.000	0.002
getSequencesFromFastaFile	0.000	0.000	0.002
informationContent	0.116	0.000	0.115
lossOfAbsICDifferences	0.056	0.000	0.056
multipleLocalPwmsAlignment	0.036	0.000	0.036
normalizePWM	0	0	0
normalizedDifferenceOfProbabilities	0.060	0.004	0.064
prepareDiffLogoTable	1.408	0.000	1.410
probabilities	0.040	0.004	0.045
seqLogo	0.048	0.000	0.045
shannonDivergence	0.056	0.000	0.055
sumOfAbsICDifferences	0.048	0.004	0.054
sumOfAbsProbabilityDifferences	0.056	0.000	0.059
sumProbabilities	0.040	0.004	0.046