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CHECK report for DiffLogo on malbec1

This page was generated on 2019-04-16 11:51:34 -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: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:DiffLogo.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings DiffLogo_2.6.0.tar.gz
StartedAt: 2019-04-15 23:30:58 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 23:31:32 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 34.2 seconds
RetCode: 0
Status:  OK 
CheckDir: DiffLogo.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:DiffLogo.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings DiffLogo_2.6.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/DiffLogo.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘2.6.0’
* 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 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:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL DiffLogo
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/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-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 
  0.156   0.008   0.161 

Example timings

DiffLogo.Rcheck/DiffLogo-Ex.timings

nameusersystemelapsed
ASN000
Alphabet000
DNA000
FULL_ALPHABET0.0000.0040.000
RNA000
calculatePvalue0.0480.0000.048
createDiffLogoObject0.0960.0000.116
diffLogo0.0840.0040.089
diffLogoFromPwm0.0880.0000.088
diffLogoTable2.100.022.12
diffLogoTableConfiguration0.0000.0000.001
differenceOfICs0.4000.0040.406
drawDiffLogoTable2.1560.0042.161
enrichDiffLogoObjectWithPvalues0.2560.0000.257
enrichDiffLogoTableWithPvalues3.5040.0003.506
extendPwmsFromAlignmentVector0.0360.0000.051
getAlphabetFromCharacters0.0040.0000.000
getAlphabetFromSequences000
getPwmFromAlignment0.3600.0200.386
getPwmFromAlignmentFile0.0040.0000.005
getPwmFromFastaFile0.0120.0000.012
getPwmFromFile0.0040.0000.003
getPwmFromHomerFile0.0000.0000.002
getPwmFromPfmOrJasparFile0.0040.0000.002
getPwmFromPwmFile0.0040.0000.002
getSequencesFromAlignmentFile0.0000.0000.001
getSequencesFromFastaFile0.0000.0000.001
informationContent0.0680.0000.071
lossOfAbsICDifferences0.0560.0000.053
multipleLocalPwmsAlignment0.0360.0040.042
normalizePWM000
normalizedDifferenceOfProbabilities0.0560.0040.057
prepareDiffLogoTable0.8800.0080.889
probabilities0.0440.0040.047
seqLogo0.0400.0000.042
shannonDivergence0.0560.0000.053
sumOfAbsICDifferences0.0520.0000.054
sumOfAbsProbabilityDifferences0.0520.0040.055
sumProbabilities0.0440.0000.043