BioC 3.6: CHECK report for DiffLogo on veracruz1

Package: DiffLogo

Version: 2.00.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DiffLogo_2.00.1.tar.gz

StartedAt: 2017-08-16 02:16:44 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 02:17:25 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 40.7 seconds

RetCode: 0

Status:  OK

CheckDir: DiffLogo.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings DiffLogo_2.00.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/DiffLogo.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘2.00.1’
* 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 sizes of PDF files under ‘inst/doc’ ... 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	0.001	0.000
Alphabet	0	0	0
DNA	0.001	0.000	0.001
FULL_ALPHABET	0.001	0.000	0.002
RNA	0	0	0
calculatePvalue	0.025	0.002	0.027
createDiffLogoObject	0.094	0.004	0.100
diffLogo	0.170	0.007	0.182
diffLogoFromPwm	0.056	0.003	0.060
diffLogoTable	1.716	0.022	1.788
diffLogoTableConfiguration	0.002	0.000	0.003
differenceOfICs	0.282	0.007	0.296
drawDiffLogoTable	1.730	0.021	1.802
enrichDiffLogoObjectWithPvalues	0.296	0.008	0.305
enrichDiffLogoTableWithPvalues	3.475	0.020	3.604
extendPwmsFromAlignmentVector	0.084	0.002	0.086
getAlphabetFromCharacters	0.001	0.000	0.001
getAlphabetFromSequences	0.015	0.000	0.016
getPwmFromAlignment	0.401	0.055	0.470
getPwmFromAlignmentFile	0.031	0.000	0.031
getPwmFromFastaFile	0.020	0.001	0.023
getPwmFromFile	0.002	0.000	0.002
getPwmFromHomerFile	0.003	0.000	0.003
getPwmFromPfmOrJasparFile	0.003	0.001	0.003
getPwmFromPwmFile	0.003	0.000	0.003
getSequencesFromAlignmentFile	0.002	0.000	0.002
getSequencesFromFastaFile	0.002	0.001	0.003
informationContent	0.071	0.002	0.075
lossOfAbsICDifferences	0.048	0.003	0.051
multipleLocalPwmsAlignment	0.047	0.001	0.047
normalizePWM	0.003	0.000	0.002
normalizedDifferenceOfProbabilities	0.055	0.002	0.056
prepareDiffLogoTable	1.448	0.014	1.493
probabilities	0.039	0.002	0.041
seqLogo	0.039	0.001	0.040
shannonDivergence	0.053	0.002	0.056
sumOfAbsICDifferences	0.050	0.002	0.051
sumOfAbsProbabilityDifferences	0.051	0.002	0.057
sumProbabilities	0.041	0.002	0.045