Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-06-07 20:24 -0400 (Fri, 07 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4755
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4489
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4520
kjohnson3macOS 13.6.5 Venturaarm644.4.0 (2024-04-24) -- "Puppy Cup" 4466
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 574/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DiffLogo 2.28.0  (landing page)
Hendrik Treutler
Snapshot Date: 2024-06-05 14:00:26 -0400 (Wed, 05 Jun 2024)
git_url: https://git.bioconductor.org/packages/DiffLogo
git_branch: RELEASE_3_19
git_last_commit: 7ff879d
git_last_commit_date: 2024-04-30 10:45:43 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows 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 13.6.5 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published


CHECK results for DiffLogo on nebbiolo1

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: 2.28.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:DiffLogo.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings DiffLogo_2.28.0.tar.gz
StartedAt: 2024-06-05 22:31:11 -0400 (Wed, 05 Jun 2024)
EndedAt: 2024-06-05 22:32:19 -0400 (Wed, 05 Jun 2024)
EllapsedTime: 68.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: DiffLogo.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:DiffLogo.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings DiffLogo_2.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/DiffLogo.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘DiffLogo/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DiffLogo’ version ‘2.28.0’
* 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 loading without being on the library search path ... 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 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/DiffLogo.Rcheck/00check.log’
for details.


Installation output

DiffLogo.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL DiffLogo
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-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 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 
  0.186   0.012   0.188 

Example timings

DiffLogo.Rcheck/DiffLogo-Ex.timings

nameusersystemelapsed
ASN0.0000.0010.001
Alphabet000
DNA000
FULL_ALPHABET0.0000.0010.000
RNA0.0000.0010.000
calculatePvalue0.0340.0010.034
createDiffLogoObject0.0630.0000.063
diffLogo0.0550.0040.059
diffLogoFromPwm0.0550.0030.058
diffLogoTable1.0780.0131.090
diffLogoTableConfiguration0.0000.0010.001
differenceOfICs0.3030.0030.306
drawDiffLogoTable1.0470.0041.050
enrichDiffLogoObjectWithPvalues0.1870.0040.191
enrichDiffLogoTableWithPvalues3.0190.0003.020
extendPwmsFromAlignmentVector0.0600.0040.065
getAlphabetFromCharacters0.0010.0000.001
getAlphabetFromSequences0.0000.0000.001
getPwmFromAlignment0.3940.0110.406
getPwmFromAlignmentFile0.0040.0000.005
getPwmFromFastaFile0.0110.0000.011
getPwmFromFile0.0020.0000.003
getPwmFromHomerFile0.0010.0000.002
getPwmFromPfmOrJasparFile0.0020.0000.002
getPwmFromPwmFile0.0020.0000.002
getSequencesFromAlignmentFile0.0010.0000.001
getSequencesFromFastaFile0.0010.0000.001
informationContent0.0730.0000.073
lossOfAbsICDifferences0.0570.0040.061
multipleLocalPwmsAlignment0.030.000.03
normalizePWM000
normalizedDifferenceOfProbabilities0.0590.0000.058
prepareDiffLogoTable0.7240.0030.728
probabilities0.0430.0010.044
seqLogo0.0440.0030.048
shannonDivergence0.0540.0000.054
sumOfAbsICDifferences0.0580.0010.058
sumOfAbsProbabilityDifferences0.0530.0030.057
sumProbabilities0.0460.0010.046