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CHECK report for DiffLogo on machv2

This page was generated on 2020-10-17 11:58:23 -0400 (Sat, 17 Oct 2020).

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 474/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DiffLogo 2.12.2
Hendrik Treutler
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/DiffLogo
Branch: RELEASE_3_11
Last Commit: df91b9a
Last Changed Date: 2020-06-03 04:25:02 -0400 (Wed, 03 Jun 2020)
malbec2 Linux (Ubuntu 18.04.4 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
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: DiffLogo
Version: 2.12.2
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_2.12.2.tar.gz
StartedAt: 2020-10-17 00:31:44 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 00:32:37 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 53.1 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_2.12.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-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 ‘2.12.2’
* 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
Examples with CPU (user + system) or elapsed time > 5s
                                user system elapsed
enrichDiffLogoTableWithPvalues 5.328   0.15   5.482
* 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-3.11-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 
  0.302   0.071   0.350 

Example timings

DiffLogo.Rcheck/DiffLogo-Ex.timings

nameusersystemelapsed
ASN0.0010.0010.002
Alphabet0.0000.0010.001
DNA0.0000.0010.001
FULL_ALPHABET0.0010.0010.002
RNA0.0010.0010.001
calculatePvalue0.0280.0030.031
createDiffLogoObject0.0970.0120.109
diffLogo0.0850.0100.095
diffLogoFromPwm0.0790.0100.091
diffLogoTable2.1560.1192.277
diffLogoTableConfiguration0.0020.0020.003
differenceOfICs0.4040.0120.421
drawDiffLogoTable2.1160.0972.215
enrichDiffLogoObjectWithPvalues0.3260.0240.351
enrichDiffLogoTableWithPvalues5.3280.1505.482
extendPwmsFromAlignmentVector0.0770.0040.081
getAlphabetFromCharacters0.0000.0000.001
getAlphabetFromSequences0.0010.0000.001
getPwmFromAlignment0.4810.0740.556
getPwmFromAlignmentFile0.0060.0010.006
getPwmFromFastaFile0.0220.0000.023
getPwmFromFile0.0030.0000.003
getPwmFromHomerFile0.0020.0000.003
getPwmFromPfmOrJasparFile0.0040.0010.004
getPwmFromPwmFile0.0040.0010.005
getSequencesFromAlignmentFile0.0010.0000.002
getSequencesFromFastaFile0.0020.0000.003
informationContent0.0960.0050.101
lossOfAbsICDifferences0.0740.0100.085
multipleLocalPwmsAlignment0.0630.0030.066
normalizePWM0.0010.0010.001
normalizedDifferenceOfProbabilities0.0710.0060.076
prepareDiffLogoTable1.7760.0441.820
probabilities0.0610.0040.064
seqLogo0.0540.0060.060
shannonDivergence0.0730.0060.079
sumOfAbsICDifferences0.0760.0040.081
sumOfAbsProbabilityDifferences0.0790.0100.089
sumProbabilities0.0570.0040.102