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CHECK report for DiffLogo on merida1

This page was generated on 2021-02-22 12:42:27 -0500 (Mon, 22 Feb 2021).

To the developers/maintainers of the DiffLogo package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 479/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DiffLogo 2.14.0
Hendrik Treutler
Snapshot Date: 2021-02-21 14:52:07 -0500 (Sun, 21 Feb 2021)
URL: https://git.bioconductor.org/packages/DiffLogo
Branch: RELEASE_3_12
Last Commit: 7edeada
Last Changed Date: 2020-10-27 11:08:01 -0500 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: DiffLogo
Version: 2.14.0
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_2.14.0.tar.gz
StartedAt: 2021-02-22 01:16:34 -0500 (Mon, 22 Feb 2021)
EndedAt: 2021-02-22 01:17:20 -0500 (Mon, 22 Feb 2021)
EllapsedTime: 46.4 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_2.14.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/DiffLogo.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (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 ‘2.14.0’
* 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 ... NOTE
diffLogo: no visible global function definition for ‘is’
preconditionTransformPWM: no visible global function definition for
  ‘is’
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/DiffLogo.Rcheck/00check.log’
for details.



Installation output

DiffLogo.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL DiffLogo
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/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 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 
  0.283   0.068   0.326 

Example timings

DiffLogo.Rcheck/DiffLogo-Ex.timings

nameusersystemelapsed
ASN0.0000.0010.001
Alphabet000
DNA0.0000.0010.001
FULL_ALPHABET0.0000.0010.001
RNA0.0010.0010.000
calculatePvalue0.0290.0030.032
createDiffLogoObject0.0750.0090.084
diffLogo0.0600.0070.068
diffLogoFromPwm0.0690.0070.076
diffLogoTable1.7880.0841.875
diffLogoTableConfiguration0.0010.0010.003
differenceOfICs0.3470.0090.359
drawDiffLogoTable1.6950.0721.769
enrichDiffLogoObjectWithPvalues0.2600.0150.275
enrichDiffLogoTableWithPvalues4.4080.1154.528
extendPwmsFromAlignmentVector0.0830.0030.087
getAlphabetFromCharacters0.0010.0010.001
getAlphabetFromSequences0.0010.0000.001
getPwmFromAlignment0.4840.0460.534
getPwmFromAlignmentFile0.010.000.01
getPwmFromFastaFile0.0230.0000.023
getPwmFromFile0.0030.0000.005
getPwmFromHomerFile0.0020.0000.003
getPwmFromPfmOrJasparFile0.0040.0010.004
getPwmFromPwmFile0.0030.0000.003
getSequencesFromAlignmentFile0.0020.0000.003
getSequencesFromFastaFile0.0030.0000.003
informationContent0.0850.0040.089
lossOfAbsICDifferences0.0720.0100.083
multipleLocalPwmsAlignment0.0500.0020.051
normalizePWM0.0010.0000.000
normalizedDifferenceOfProbabilities0.0740.0050.079
prepareDiffLogoTable1.4230.0241.449
probabilities0.0480.0030.051
seqLogo0.0460.0030.049
shannonDivergence0.0640.0040.067
sumOfAbsICDifferences0.0710.0040.076
sumOfAbsProbabilityDifferences0.0700.0110.081
sumProbabilities0.0510.0030.054