Back to Multiple platform build/check report for BioC 3.16: simplified long |
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This page was generated on 2023-04-12 11:06:05 -0400 (Wed, 12 Apr 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
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 |
To the developers/maintainers of the DiffLogo package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 537/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
DiffLogo 2.22.0 (landing page) Hendrik Treutler
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
Package: DiffLogo |
Version: 2.22.0 |
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_2.22.0.tar.gz |
StartedAt: 2023-04-10 19:53:34 -0400 (Mon, 10 Apr 2023) |
EndedAt: 2023-04-10 19:54:12 -0400 (Mon, 10 Apr 2023) |
EllapsedTime: 38.4 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: DiffLogo.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### 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_2.22.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/DiffLogo.Rcheck’ * using R version 4.2.3 (2023-03-15) * 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 ‘2.22.0’ * 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-3.16-bioc/meat/DiffLogo.Rcheck/00check.log’ for details.
DiffLogo.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL DiffLogo ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/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)
DiffLogo.Rcheck/tests/testthat.Rout
R version 4.2.3 (2023-03-15) -- "Shortstop Beagle" Copyright (C) 2023 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 0.161 0.057 0.211
DiffLogo.Rcheck/DiffLogo-Ex.timings
name | user | system | elapsed | |
ASN | 0.000 | 0.001 | 0.001 | |
Alphabet | 0.001 | 0.000 | 0.000 | |
DNA | 0.001 | 0.001 | 0.001 | |
FULL_ALPHABET | 0.000 | 0.001 | 0.001 | |
RNA | 0 | 0 | 0 | |
calculatePvalue | 0.025 | 0.002 | 0.028 | |
createDiffLogoObject | 0.056 | 0.008 | 0.066 | |
diffLogo | 0.049 | 0.006 | 0.057 | |
diffLogoFromPwm | 0.047 | 0.005 | 0.052 | |
diffLogoTable | 0.879 | 0.061 | 0.941 | |
diffLogoTableConfiguration | 0.000 | 0.001 | 0.001 | |
differenceOfICs | 0.321 | 0.013 | 0.335 | |
drawDiffLogoTable | 0.911 | 0.063 | 0.977 | |
enrichDiffLogoObjectWithPvalues | 0.164 | 0.015 | 0.179 | |
enrichDiffLogoTableWithPvalues | 2.686 | 0.140 | 2.834 | |
extendPwmsFromAlignmentVector | 0.041 | 0.003 | 0.045 | |
getAlphabetFromCharacters | 0.001 | 0.000 | 0.000 | |
getAlphabetFromSequences | 0.000 | 0.000 | 0.001 | |
getPwmFromAlignment | 0.394 | 0.051 | 0.447 | |
getPwmFromAlignmentFile | 0.006 | 0.001 | 0.007 | |
getPwmFromFastaFile | 0.014 | 0.001 | 0.016 | |
getPwmFromFile | 0.003 | 0.000 | 0.003 | |
getPwmFromHomerFile | 0.002 | 0.000 | 0.005 | |
getPwmFromPfmOrJasparFile | 0.002 | 0.001 | 0.003 | |
getPwmFromPwmFile | 0.003 | 0.000 | 0.004 | |
getSequencesFromAlignmentFile | 0.001 | 0.000 | 0.001 | |
getSequencesFromFastaFile | 0.002 | 0.001 | 0.002 | |
informationContent | 0.074 | 0.003 | 0.078 | |
lossOfAbsICDifferences | 0.060 | 0.014 | 0.075 | |
multipleLocalPwmsAlignment | 0.028 | 0.002 | 0.030 | |
normalizePWM | 0.000 | 0.000 | 0.001 | |
normalizedDifferenceOfProbabilities | 0.052 | 0.003 | 0.055 | |
prepareDiffLogoTable | 0.600 | 0.033 | 0.633 | |
probabilities | 0.033 | 0.003 | 0.036 | |
seqLogo | 0.037 | 0.010 | 0.047 | |
shannonDivergence | 0.042 | 0.002 | 0.046 | |
sumOfAbsICDifferences | 0.052 | 0.006 | 0.058 | |
sumOfAbsProbabilityDifferences | 0.048 | 0.004 | 0.053 | |
sumProbabilities | 0.040 | 0.004 | 0.043 | |