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This page was generated on 2025-08-04 12:08 -0400 (Mon, 04 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4796
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4536
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4578
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4519
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4517
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 576/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DiffLogo 2.33.0  (landing page)
Hendrik Treutler
Snapshot Date: 2025-08-03 13:25 -0400 (Sun, 03 Aug 2025)
git_url: https://git.bioconductor.org/packages/DiffLogo
git_branch: devel
git_last_commit: 344faf6
git_last_commit_date: 2025-04-15 10:53:31 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
taishanLinux (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: 2.33.0
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_2.33.0.tar.gz
StartedAt: 2025-08-03 20:43:27 -0400 (Sun, 03 Aug 2025)
EndedAt: 2025-08-03 20:44:16 -0400 (Sun, 03 Aug 2025)
EllapsedTime: 49.2 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_2.33.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/DiffLogo.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 ‘2.33.0’
* 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-3.22-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 ‘2.33.0’
** 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 4.5.1 (2025-06-13) -- "Great Square Root"
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 
  0.204   0.075   0.278 

Example timings

DiffLogo.Rcheck/DiffLogo-Ex.timings

nameusersystemelapsed
ASN0.0000.0010.001
Alphabet0.0010.0000.000
DNA0.0000.0010.003
FULL_ALPHABET0.0000.0000.001
RNA0.0000.0010.000
calculatePvalue0.0290.0030.032
createDiffLogoObject0.0620.0090.072
diffLogo0.0540.0070.062
diffLogoFromPwm0.0560.0100.066
diffLogoTable1.1540.0891.258
diffLogoTableConfiguration0.0010.0000.001
differenceOfICs0.3460.0120.360
drawDiffLogoTable1.1090.0681.180
enrichDiffLogoObjectWithPvalues0.1920.0150.208
enrichDiffLogoTableWithPvalues3.1280.0983.237
extendPwmsFromAlignmentVector0.0430.0040.047
getAlphabetFromCharacters000
getAlphabetFromSequences000
getPwmFromAlignment0.4070.0550.464
getPwmFromAlignmentFile0.0040.0010.005
getPwmFromFastaFile0.0120.0010.014
getPwmFromFile0.0020.0010.003
getPwmFromHomerFile0.0020.0010.003
getPwmFromPfmOrJasparFile0.0030.0010.004
getPwmFromPwmFile0.0030.0010.003
getSequencesFromAlignmentFile0.0020.0010.003
getSequencesFromFastaFile0.0020.0000.003
informationContent0.0740.0050.080
lossOfAbsICDifferences0.0620.0110.074
multipleLocalPwmsAlignment0.0380.0020.041
normalizePWM000
normalizedDifferenceOfProbabilities0.0550.0050.061
prepareDiffLogoTable0.9270.0460.976
probabilities0.0430.0040.047
seqLogo0.0390.0050.043
shannonDivergence0.0520.0050.058
sumOfAbsICDifferences0.0550.0050.061
sumOfAbsProbabilityDifferences0.0640.0160.081
sumProbabilities0.0440.0040.048