Package: DiffLogo

Version: 2.7.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:DiffLogo.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DiffLogo_2.7.0.tar.gz

StartedAt: 2019-04-09 00:29:39 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 00:30:23 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 43.8 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 --install=check:DiffLogo.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DiffLogo_2.7.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/DiffLogo.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘2.7.0’
* 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 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 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

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL DiffLogo
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘DiffLogo’ ...
** 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
* DONE (DiffLogo)

R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
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 
  0.260   0.074   0.299 

name	user	system	elapsed
ASN	0.001	0.000	0.002
Alphabet	0.001	0.000	0.001
DNA	0.000	0.001	0.000
FULL_ALPHABET	0.001	0.000	0.002
RNA	0	0	0
calculatePvalue	0.025	0.002	0.027
createDiffLogoObject	0.085	0.010	0.096
diffLogo	0.066	0.007	0.072
diffLogoFromPwm	0.074	0.009	0.086
diffLogoTable	1.922	0.083	2.025
diffLogoTableConfiguration	0.001	0.000	0.002
differenceOfICs	0.384	0.010	0.400
drawDiffLogoTable	1.982	0.060	2.068
enrichDiffLogoObjectWithPvalues	0.264	0.021	0.286
enrichDiffLogoTableWithPvalues	4.201	0.128	4.376
extendPwmsFromAlignmentVector	0.068	0.004	0.074
getAlphabetFromCharacters	0.001	0.001	0.001
getAlphabetFromSequences	0.001	0.000	0.000
getPwmFromAlignment	0.492	0.083	0.580
getPwmFromAlignmentFile	0.009	0.001	0.009
getPwmFromFastaFile	0.02	0.00	0.02
getPwmFromFile	0.003	0.001	0.003
getPwmFromHomerFile	0.002	0.000	0.002
getPwmFromPfmOrJasparFile	0.004	0.000	0.005
getPwmFromPwmFile	0.004	0.001	0.004
getSequencesFromAlignmentFile	0.002	0.000	0.002
getSequencesFromFastaFile	0.002	0.001	0.003
informationContent	0.080	0.004	0.086
lossOfAbsICDifferences	0.061	0.005	0.065
multipleLocalPwmsAlignment	0.056	0.006	0.062
normalizePWM	0	0	0
normalizedDifferenceOfProbabilities	0.072	0.003	0.074
prepareDiffLogoTable	1.537	0.035	1.582
probabilities	0.048	0.003	0.052
seqLogo	0.045	0.003	0.047
shannonDivergence	0.060	0.003	0.064
sumOfAbsICDifferences	0.060	0.004	0.068
sumOfAbsProbabilityDifferences	0.069	0.006	0.077
sumProbabilities	0.050	0.003	0.053