Package: DiffLogo

Version: 2.10.0

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_2.10.0.tar.gz

StartedAt: 2020-04-15 01:50:57 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 01:51:44 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 47.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: DiffLogo.Rcheck

Warnings: 1

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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_2.10.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/DiffLogo.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘2.10.0’
* 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 ... WARNING
Documented arguments not in \usage in documentation object 'diffLogoTableConfiguration':
  ‘...’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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: 1 WARNING
See
  ‘/Users/biocbuild/bbs-3.10-bioc/meat/DiffLogo.Rcheck/00check.log’
for details.

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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 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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 
  0.307   0.084   0.361 

name	user	system	elapsed
ASN	0.000	0.000	0.001
Alphabet	0.000	0.001	0.000
DNA	0.000	0.000	0.001
FULL_ALPHABET	0.001	0.001	0.001
RNA	0.001	0.000	0.000
calculatePvalue	0.024	0.003	0.027
createDiffLogoObject	0.082	0.010	0.095
diffLogo	0.072	0.010	0.084
diffLogoFromPwm	0.077	0.007	0.087
diffLogoTable	1.894	0.091	2.004
diffLogoTableConfiguration	0.002	0.001	0.003
differenceOfICs	0.395	0.011	0.418
drawDiffLogoTable	1.845	0.071	1.930
enrichDiffLogoObjectWithPvalues	0.295	0.020	0.316
enrichDiffLogoTableWithPvalues	4.700	0.082	4.840
extendPwmsFromAlignmentVector	0.058	0.001	0.061
getAlphabetFromCharacters	0.001	0.000	0.001
getAlphabetFromSequences	0.001	0.001	0.001
getPwmFromAlignment	0.527	0.089	0.628
getPwmFromAlignmentFile	0.011	0.000	0.011
getPwmFromFastaFile	0.017	0.001	0.019
getPwmFromFile	0.004	0.000	0.003
getPwmFromHomerFile	0.002	0.000	0.002
getPwmFromPfmOrJasparFile	0.003	0.000	0.003
getPwmFromPwmFile	0.004	0.001	0.005
getSequencesFromAlignmentFile	0.001	0.000	0.001
getSequencesFromFastaFile	0.002	0.001	0.003
informationContent	0.096	0.003	0.100
lossOfAbsICDifferences	0.106	0.008	0.115
multipleLocalPwmsAlignment	0.059	0.001	0.061
normalizePWM	0.001	0.000	0.001
normalizedDifferenceOfProbabilities	0.070	0.003	0.073
prepareDiffLogoTable	1.689	0.027	1.736
probabilities	0.057	0.011	0.069
seqLogo	0.057	0.002	0.059
shannonDivergence	0.072	0.004	0.080
sumOfAbsICDifferences	0.079	0.003	0.083
sumOfAbsProbabilityDifferences	0.080	0.003	0.086
sumProbabilities	0.058	0.004	0.062