BioC 3.6: CHECK report for DiffLogo on malbec1

Package: DiffLogo

Version: 2.00.1

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings DiffLogo_2.00.1.tar.gz

StartedAt: 2017-08-15 22:38:17 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 22:38:49 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 32.0 seconds

RetCode: 0

Status:  OK

CheckDir: DiffLogo.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings DiffLogo_2.00.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/DiffLogo.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘2.00.1’
* 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 loading without being on the library search path ... 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 installed files from ‘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

* installing *source* package ‘DiffLogo’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DiffLogo)

name	user	system	elapsed
ASN	0.000	0.004	0.001
Alphabet	0	0	0
DNA	0	0	0
FULL_ALPHABET	0.000	0.004	0.000
RNA	0	0	0
calculatePvalue	0.028	0.000	0.029
createDiffLogoObject	0.112	0.000	0.113
diffLogo	0.152	0.000	0.151
diffLogoFromPwm	0.056	0.000	0.057
diffLogoTable	1.776	0.004	1.782
diffLogoTableConfiguration	0.000	0.000	0.001
differenceOfICs	0.336	0.004	0.337
drawDiffLogoTable	1.880	0.000	1.885
enrichDiffLogoObjectWithPvalues	0.216	0.000	0.216
enrichDiffLogoTableWithPvalues	2.952	0.000	2.953
extendPwmsFromAlignmentVector	0.052	0.000	0.051
getAlphabetFromCharacters	0.000	0.000	0.001
getAlphabetFromSequences	0.012	0.000	0.011
getPwmFromAlignment	0.392	0.000	0.391
getPwmFromAlignmentFile	0.04	0.00	0.04
getPwmFromFastaFile	0.020	0.000	0.022
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	0.004
getSequencesFromAlignmentFile	0.048	0.000	0.047
getSequencesFromFastaFile	0.000	0.000	0.002
informationContent	0.100	0.000	0.097
lossOfAbsICDifferences	0.080	0.000	0.081
multipleLocalPwmsAlignment	0.056	0.000	0.057
normalizePWM	0.000	0.000	0.001
normalizedDifferenceOfProbabilities	0.076	0.004	0.081
prepareDiffLogoTable	1.56	0.00	1.56
probabilities	0.048	0.000	0.046
seqLogo	0.044	0.000	0.045
shannonDivergence	0.056	0.000	0.057
sumOfAbsICDifferences	0.056	0.000	0.054
sumOfAbsProbabilityDifferences	0.060	0.000	0.058
sumProbabilities	0.044	0.000	0.047