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This page was generated on 2025-04-22 13:16 -0400 (Tue, 22 Apr 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4831
palomino7Windows Server 2022 Datacenterx644.5.0 RC (2025-04-04 r88126 ucrt) -- "How About a Twenty-Six" 4573
lconwaymacOS 12.7.1 Montereyx86_644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4599
kjohnson3macOS 13.7.1 Venturaarm644.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six" 4553
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4570
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 583/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DiffLogo 2.32.0  (landing page)
Hendrik Treutler
Snapshot Date: 2025-04-21 13:40 -0400 (Mon, 21 Apr 2025)
git_url: https://git.bioconductor.org/packages/DiffLogo
git_branch: RELEASE_3_21
git_last_commit: e640352
git_last_commit_date: 2025-04-15 10:53:31 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  YES
palomino7Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  YES
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  YES
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    WARNINGS    OK  YES
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    WARNINGS  


CHECK results for DiffLogo on lconway

To the developers/maintainers of the DiffLogo package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/DiffLogo.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: DiffLogo
Version: 2.32.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DiffLogo.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DiffLogo_2.32.0.tar.gz
StartedAt: 2025-04-21 20:20:10 -0400 (Mon, 21 Apr 2025)
EndedAt: 2025-04-21 20:20:50 -0400 (Mon, 21 Apr 2025)
EllapsedTime: 39.8 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: DiffLogo.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:DiffLogo.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings DiffLogo_2.32.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/DiffLogo.Rcheck’
* using R version 4.5.0 RC (2025-04-04 r88126)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DiffLogo/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DiffLogo’ version ‘2.32.0’
* checking package namespace information ... NOTE
Found export directive that requires package ‘methods’:
  ‘exportClasses’
Remove all such namespace directives (if obsolete) or ensure that the
DESCRIPTION Depends or Imports field contains ‘methods’.
* 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 code 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 ... WARNING
Warning: S4 exports specified in 'NAMESPACE' but not defined in package ‘DiffLogo’
* 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 ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/DiffLogo.Rcheck/00check.log’
for details.


Installation output

DiffLogo.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘DiffLogo’ ...
** this is package ‘DiffLogo’ version ‘2.32.0’
** 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 4.5.0 RC (2025-04-04 r88126) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 
  0.171   0.068   0.230 

Example timings

DiffLogo.Rcheck/DiffLogo-Ex.timings

nameusersystemelapsed
ASN0.0000.0010.001
Alphabet0.0000.0010.002
DNA000
FULL_ALPHABET000
RNA0.0000.0000.001
calculatePvalue0.0270.0030.029
createDiffLogoObject0.0490.0070.057
diffLogo0.0510.0080.060
diffLogoFromPwm0.0530.0090.062
diffLogoTable1.0620.0791.145
diffLogoTableConfiguration0.0000.0000.001
differenceOfICs0.3250.0140.340
drawDiffLogoTable1.0630.0681.140
enrichDiffLogoObjectWithPvalues0.1960.0170.215
enrichDiffLogoTableWithPvalues2.9550.0893.058
extendPwmsFromAlignmentVector0.0410.0050.048
getAlphabetFromCharacters0.0000.0000.001
getAlphabetFromSequences0.0010.0000.000
getPwmFromAlignment0.3980.0340.436
getPwmFromAlignmentFile0.0040.0010.005
getPwmFromFastaFile0.0090.0010.010
getPwmFromFile0.0020.0000.003
getPwmFromHomerFile0.0010.0000.002
getPwmFromPfmOrJasparFile0.0020.0000.003
getPwmFromPwmFile0.0020.0010.003
getSequencesFromAlignmentFile0.0010.0010.002
getSequencesFromFastaFile0.0010.0000.002
informationContent0.0790.0040.083
lossOfAbsICDifferences0.0610.0110.073
multipleLocalPwmsAlignment0.0320.0030.035
normalizePWM000
normalizedDifferenceOfProbabilities0.0520.0040.057
prepareDiffLogoTable0.8600.0370.902
probabilities0.0390.0040.042
seqLogo0.0410.0040.046
shannonDivergence0.0510.0050.056
sumOfAbsICDifferences0.0550.0040.060
sumOfAbsProbabilityDifferences0.0540.0120.066
sumProbabilities0.0380.0030.042