Package: DiffLogo

Version: 2.10.0

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:DiffLogo.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings DiffLogo_2.10.0.tar.gz

StartedAt: 2020-04-15 03:18:07 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 03:18:42 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 34.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: DiffLogo.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:DiffLogo.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings DiffLogo_2.10.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/DiffLogo.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘2.10.0’
* 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 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
  ‘/home/biocbuild/bbs-3.10-bioc/meat/DiffLogo.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL DiffLogo
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/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-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 
  0.240   0.024   0.261 

name	user	system	elapsed
ASN	0	0	0
Alphabet	0	0	0
DNA	0	0	0
FULL_ALPHABET	0.000	0.000	0.001
RNA	0.000	0.000	0.001
calculatePvalue	0.040	0.000	0.043
createDiffLogoObject	0.092	0.012	0.122
diffLogo	0.096	0.000	0.093
diffLogoFromPwm	0.076	0.008	0.085
diffLogoTable	1.656	0.024	1.679
diffLogoTableConfiguration	0.004	0.000	0.001
differenceOfICs	0.348	0.004	0.351
drawDiffLogoTable	1.628	0.008	1.639
enrichDiffLogoObjectWithPvalues	0.284	0.000	0.286
enrichDiffLogoTableWithPvalues	4.436	0.008	4.452
extendPwmsFromAlignmentVector	0.040	0.000	0.047
getAlphabetFromCharacters	0	0	0
getAlphabetFromSequences	0.000	0.000	0.001
getPwmFromAlignment	0.524	0.008	0.540
getPwmFromAlignmentFile	0.012	0.000	0.009
getPwmFromFastaFile	0.012	0.004	0.024
getPwmFromFile	0.004	0.000	0.004
getPwmFromHomerFile	0.004	0.000	0.002
getPwmFromPfmOrJasparFile	0.004	0.000	0.003
getPwmFromPwmFile	0.004	0.000	0.003
getSequencesFromAlignmentFile	0.004	0.000	0.002
getSequencesFromFastaFile	0.004	0.000	0.002
informationContent	0.100	0.004	0.104
lossOfAbsICDifferences	0.092	0.000	0.091
multipleLocalPwmsAlignment	0.100	0.000	0.102
normalizePWM	0	0	0
normalizedDifferenceOfProbabilities	0.084	0.000	0.083
prepareDiffLogoTable	1.428	0.004	1.432
probabilities	0.060	0.004	0.065
seqLogo	0.068	0.000	0.068
shannonDivergence	0.072	0.008	0.082
sumOfAbsICDifferences	0.080	0.004	0.084
sumOfAbsProbabilityDifferences	0.080	0.004	0.086
sumProbabilities	0.048	0.004	0.050