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 01:24:41 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 01:25:37 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 56.3 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_2.7.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/DiffLogo.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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
Examples with CPU or elapsed time > 5s
                                user system elapsed
enrichDiffLogoTableWithPvalues 5.122   0.34   5.461
* 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 Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
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 
  0.381   0.149   0.474 

name	user	system	elapsed
ASN	0.001	0.002	0.002
Alphabet	0.001	0.000	0.000
DNA	0.001	0.000	0.001
FULL_ALPHABET	0.001	0.001	0.001
RNA	0.000	0.000	0.001
calculatePvalue	0.022	0.002	0.025
createDiffLogoObject	0.105	0.021	0.128
diffLogo	0.080	0.014	0.094
diffLogoFromPwm	0.071	0.015	0.086
diffLogoTable	2.328	0.179	2.508
diffLogoTableConfiguration	0.002	0.002	0.004
differenceOfICs	0.420	0.032	0.454
drawDiffLogoTable	2.060	0.141	2.203
enrichDiffLogoObjectWithPvalues	0.347	0.059	0.405
enrichDiffLogoTableWithPvalues	5.122	0.340	5.461
extendPwmsFromAlignmentVector	0.067	0.003	0.072
getAlphabetFromCharacters	0.001	0.000	0.001
getAlphabetFromSequences	0.000	0.000	0.001
getPwmFromAlignment	0.597	0.151	0.750
getPwmFromAlignmentFile	0.006	0.000	0.007
getPwmFromFastaFile	0.025	0.001	0.027
getPwmFromFile	0.003	0.001	0.004
getPwmFromHomerFile	0.003	0.001	0.004
getPwmFromPfmOrJasparFile	0.004	0.000	0.005
getPwmFromPwmFile	0.003	0.000	0.004
getSequencesFromAlignmentFile	0.002	0.000	0.002
getSequencesFromFastaFile	0.002	0.000	0.002
informationContent	0.069	0.006	0.075
lossOfAbsICDifferences	0.063	0.004	0.068
multipleLocalPwmsAlignment	0.083	0.025	0.109
normalizePWM	0.000	0.000	0.001
normalizedDifferenceOfProbabilities	0.065	0.006	0.071
prepareDiffLogoTable	1.432	0.053	1.484
probabilities	0.050	0.005	0.055
seqLogo	0.062	0.028	0.091
shannonDivergence	0.075	0.008	0.083
sumOfAbsICDifferences	0.085	0.006	0.091
sumOfAbsProbabilityDifferences	0.092	0.006	0.099
sumProbabilities	0.060	0.005	0.064