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CHECK report for DiffLogo on merida1

This page was generated on 2019-04-16 11:58:58 -0400 (Tue, 16 Apr 2019).

Package 411/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DiffLogo 2.6.0
Hendrik Treutler
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/DiffLogo
Branch: RELEASE_3_8
Last Commit: b40ac15
Last Changed Date: 2018-10-30 11:41:59 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: DiffLogo
Version: 2.6.0
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_2.6.0.tar.gz
StartedAt: 2019-04-15 23:31:15 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 23:32:02 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 47.2 seconds
RetCode: 0
Status:  OK 
CheckDir: DiffLogo.Rcheck
Warnings: 0

Command output

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### Running 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_2.6.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/DiffLogo.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘2.6.0’
* 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
* 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


Installation output

DiffLogo.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL DiffLogo
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘DiffLogo’ ...
** 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
* DONE (DiffLogo)

Tests output

DiffLogo.Rcheck/tests/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
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 
  0.237   0.060   0.269 

Example timings

DiffLogo.Rcheck/DiffLogo-Ex.timings

nameusersystemelapsed
ASN0.0010.0000.002
Alphabet0.0000.0000.001
DNA000
FULL_ALPHABET0.0000.0010.001
RNA0.0000.0000.001
calculatePvalue0.0270.0020.028
createDiffLogoObject0.0870.0100.100
diffLogo0.0810.0100.093
diffLogoFromPwm0.0770.0080.086
diffLogoTable2.0830.0902.194
diffLogoTableConfiguration0.0020.0010.003
differenceOfICs0.4030.0120.418
drawDiffLogoTable2.2130.0562.286
enrichDiffLogoObjectWithPvalues0.2350.0170.254
enrichDiffLogoTableWithPvalues4.3250.1304.497
extendPwmsFromAlignmentVector0.0790.0010.081
getAlphabetFromCharacters0.0010.0000.001
getAlphabetFromSequences0.0010.0010.001
getPwmFromAlignment0.5150.0870.609
getPwmFromAlignmentFile0.0090.0010.009
getPwmFromFastaFile0.0240.0000.026
getPwmFromFile0.0030.0000.004
getPwmFromHomerFile0.0020.0000.002
getPwmFromPfmOrJasparFile0.0030.0000.003
getPwmFromPwmFile0.0050.0010.005
getSequencesFromAlignmentFile0.0020.0000.003
getSequencesFromFastaFile0.0020.0000.003
informationContent0.0810.0050.087
lossOfAbsICDifferences0.0770.0040.082
multipleLocalPwmsAlignment0.0590.0030.062
normalizePWM0.0010.0000.001
normalizedDifferenceOfProbabilities0.0650.0020.068
prepareDiffLogoTable1.7540.0231.797
probabilities0.0510.0070.059
seqLogo0.0540.0020.057
shannonDivergence0.0690.0040.073
sumOfAbsICDifferences0.0700.0040.075
sumOfAbsProbabilityDifferences0.0740.0040.079
sumProbabilities0.0580.0020.061