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CHECK report for DiffLogo on celaya2

This page was generated on 2019-10-16 12:56:20 -0400 (Wed, 16 Oct 2019).

Package 436/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DiffLogo 2.8.0
Hendrik Treutler
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/DiffLogo
Branch: RELEASE_3_9
Last Commit: b31a93c
Last Changed Date: 2019-05-02 11:53:57 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: DiffLogo
Version: 2.8.0
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_2.8.0.tar.gz
StartedAt: 2019-10-16 02:14:26 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 02:15:24 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 57.3 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_2.8.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/DiffLogo.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘2.8.0’
* 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
Examples with CPU or elapsed time > 5s
                                user system elapsed
enrichDiffLogoTableWithPvalues 4.879  0.334   5.214
* 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/3.6/Resources/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)

Tests output

DiffLogo.Rcheck/tests/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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 
  0.376   0.141   0.467 

Example timings

DiffLogo.Rcheck/DiffLogo-Ex.timings

nameusersystemelapsed
ASN0.0020.0010.002
Alphabet0.0010.0000.001
DNA0.0000.0010.001
FULL_ALPHABET0.0010.0010.001
RNA0.0010.0010.001
calculatePvalue0.0380.0060.044
createDiffLogoObject0.1030.0170.124
diffLogo0.0910.0160.108
diffLogoFromPwm0.0830.0090.094
diffLogoTable2.0230.1592.184
diffLogoTableConfiguration0.0020.0010.003
differenceOfICs0.4210.0200.447
drawDiffLogoTable1.9400.1412.084
enrichDiffLogoObjectWithPvalues0.2660.0280.294
enrichDiffLogoTableWithPvalues4.8790.3345.214
extendPwmsFromAlignmentVector0.0420.0020.046
getAlphabetFromCharacters0.0010.0000.001
getAlphabetFromSequences000
getPwmFromAlignment0.5320.1720.706
getPwmFromAlignmentFile0.0120.0010.012
getPwmFromFastaFile0.0230.0010.025
getPwmFromFile0.0050.0020.008
getPwmFromHomerFile0.0040.0010.005
getPwmFromPfmOrJasparFile0.0050.0000.006
getPwmFromPwmFile0.0050.0010.006
getSequencesFromAlignmentFile0.0020.0010.003
getSequencesFromFastaFile0.0030.0010.003
informationContent0.0950.0060.105
lossOfAbsICDifferences0.1360.0260.164
multipleLocalPwmsAlignment0.0690.0010.071
normalizePWM0.0000.0010.001
normalizedDifferenceOfProbabilities0.0820.0090.092
prepareDiffLogoTable1.4740.0941.568
probabilities0.0640.0220.093
seqLogo0.0540.0110.068
shannonDivergence0.0710.0090.082
sumOfAbsICDifferences0.0790.0050.086
sumOfAbsProbabilityDifferences0.0850.0110.097
sumProbabilities0.0610.0060.067