Package: DiffLogo

Version: 2.8.0

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_2.8.0.tar.gz

StartedAt: 2019-10-16 02:14:26 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 02:15:24 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 57.3 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_2.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/DiffLogo.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘2.8.0’
* 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
Examples with CPU or elapsed time > 5s
                                user system elapsed
enrichDiffLogoTableWithPvalues 4.879  0.334   5.214
* 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’ ...
** 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 (DiffLogo)

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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 
  0.376   0.141   0.467 

name	user	system	elapsed
ASN	0.002	0.001	0.002
Alphabet	0.001	0.000	0.001
DNA	0.000	0.001	0.001
FULL_ALPHABET	0.001	0.001	0.001
RNA	0.001	0.001	0.001
calculatePvalue	0.038	0.006	0.044
createDiffLogoObject	0.103	0.017	0.124
diffLogo	0.091	0.016	0.108
diffLogoFromPwm	0.083	0.009	0.094
diffLogoTable	2.023	0.159	2.184
diffLogoTableConfiguration	0.002	0.001	0.003
differenceOfICs	0.421	0.020	0.447
drawDiffLogoTable	1.940	0.141	2.084
enrichDiffLogoObjectWithPvalues	0.266	0.028	0.294
enrichDiffLogoTableWithPvalues	4.879	0.334	5.214
extendPwmsFromAlignmentVector	0.042	0.002	0.046
getAlphabetFromCharacters	0.001	0.000	0.001
getAlphabetFromSequences	0	0	0
getPwmFromAlignment	0.532	0.172	0.706
getPwmFromAlignmentFile	0.012	0.001	0.012
getPwmFromFastaFile	0.023	0.001	0.025
getPwmFromFile	0.005	0.002	0.008
getPwmFromHomerFile	0.004	0.001	0.005
getPwmFromPfmOrJasparFile	0.005	0.000	0.006
getPwmFromPwmFile	0.005	0.001	0.006
getSequencesFromAlignmentFile	0.002	0.001	0.003
getSequencesFromFastaFile	0.003	0.001	0.003
informationContent	0.095	0.006	0.105
lossOfAbsICDifferences	0.136	0.026	0.164
multipleLocalPwmsAlignment	0.069	0.001	0.071
normalizePWM	0.000	0.001	0.001
normalizedDifferenceOfProbabilities	0.082	0.009	0.092
prepareDiffLogoTable	1.474	0.094	1.568
probabilities	0.064	0.022	0.093
seqLogo	0.054	0.011	0.068
shannonDivergence	0.071	0.009	0.082
sumOfAbsICDifferences	0.079	0.005	0.086
sumOfAbsProbabilityDifferences	0.085	0.011	0.097
sumProbabilities	0.061	0.006	0.067