Back to Multiple platform build/check report for BioC 3.18:   simplified   long
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This page was generated on 2024-03-04 11:37:17 -0500 (Mon, 04 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4692
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4445
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 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 564/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DiffLogo 2.26.0  (landing page)
Hendrik Treutler
Snapshot Date: 2024-03-03 14:05:05 -0500 (Sun, 03 Mar 2024)
git_url: https://git.bioconductor.org/packages/DiffLogo
git_branch: RELEASE_3_18
git_last_commit: cf17c71
git_last_commit_date: 2023-10-24 10:45:18 -0500 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows 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
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

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: 2.26.0
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_2.26.0.tar.gz
StartedAt: 2024-03-03 20:12:47 -0500 (Sun, 03 Mar 2024)
EndedAt: 2024-03-03 20:13:29 -0500 (Sun, 03 Mar 2024)
EllapsedTime: 41.9 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_2.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/DiffLogo.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘DiffLogo/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DiffLogo’ version ‘2.26.0’
* 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 ... 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 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 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.18-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/4.3-x86_64/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 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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 
  0.212   0.082   0.282 

Example timings

DiffLogo.Rcheck/DiffLogo-Ex.timings

nameusersystemelapsed
ASN0.0000.0010.001
Alphabet0.0000.0000.001
DNA0.0010.0000.000
FULL_ALPHABET0.0010.0000.001
RNA0.0000.0000.001
calculatePvalue0.0290.0020.032
createDiffLogoObject0.0580.0090.068
diffLogo0.0590.0080.068
diffLogoFromPwm0.0550.0080.063
diffLogoTable1.1940.1011.309
diffLogoTableConfiguration0.0010.0010.002
differenceOfICs0.3410.0150.359
drawDiffLogoTable1.0980.0761.180
enrichDiffLogoObjectWithPvalues0.2060.0180.233
enrichDiffLogoTableWithPvalues3.2810.1233.434
extendPwmsFromAlignmentVector0.0520.0060.059
getAlphabetFromCharacters0.0010.0000.000
getAlphabetFromSequences000
getPwmFromAlignment0.4200.0620.487
getPwmFromAlignmentFile0.0050.0010.006
getPwmFromFastaFile0.0140.0010.015
getPwmFromFile0.0030.0010.004
getPwmFromHomerFile0.0020.0010.003
getPwmFromPfmOrJasparFile0.0030.0010.004
getPwmFromPwmFile0.0030.0000.003
getSequencesFromAlignmentFile0.0010.0000.002
getSequencesFromFastaFile0.0010.0010.002
informationContent0.0720.0040.076
lossOfAbsICDifferences0.0580.0090.066
multipleLocalPwmsAlignment0.0400.0030.043
normalizePWM0.0010.0000.001
normalizedDifferenceOfProbabilities0.0570.0050.065
prepareDiffLogoTable0.8800.0400.925
probabilities0.0450.0060.051
seqLogo0.0400.0040.044
shannonDivergence0.0550.0060.061
sumOfAbsICDifferences0.0590.0070.070
sumOfAbsProbabilityDifferences0.0610.0150.076
sumProbabilities0.0400.0040.045