Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:46 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 564/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
DiffLogo 2.31.0 (landing page) Hendrik Treutler
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: DiffLogo |
Version: 2.31.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:DiffLogo.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings DiffLogo_2.31.0.tar.gz |
StartedAt: 2024-12-24 06:09:52 -0000 (Tue, 24 Dec 2024) |
EndedAt: 2024-12-24 06:10:26 -0000 (Tue, 24 Dec 2024) |
EllapsedTime: 34.0 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: DiffLogo.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:DiffLogo.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings DiffLogo_2.31.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/DiffLogo.Rcheck’ * using R Under development (unstable) (2024-11-24 r87369) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘DiffLogo/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘DiffLogo’ version ‘2.31.0’ * 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 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 ‘/home/biocbuild/bbs-3.21-bioc/meat/DiffLogo.Rcheck/00check.log’ for details.
DiffLogo.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL DiffLogo ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/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)
DiffLogo.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-unknown-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 0.205 0.027 0.215
DiffLogo.Rcheck/DiffLogo-Ex.timings
name | user | system | elapsed | |
ASN | 0.000 | 0.000 | 0.001 | |
Alphabet | 0 | 0 | 0 | |
DNA | 0 | 0 | 0 | |
FULL_ALPHABET | 0 | 0 | 0 | |
RNA | 0.001 | 0.000 | 0.000 | |
calculatePvalue | 0.037 | 0.000 | 0.037 | |
createDiffLogoObject | 0.082 | 0.000 | 0.085 | |
diffLogo | 0.063 | 0.012 | 0.075 | |
diffLogoFromPwm | 0.068 | 0.000 | 0.069 | |
diffLogoTable | 1.750 | 0.044 | 1.798 | |
diffLogoTableConfiguration | 0.001 | 0.000 | 0.000 | |
differenceOfICs | 0.350 | 0.008 | 0.359 | |
drawDiffLogoTable | 1.710 | 0.008 | 1.722 | |
enrichDiffLogoObjectWithPvalues | 0.259 | 0.004 | 0.263 | |
enrichDiffLogoTableWithPvalues | 4.387 | 0.000 | 4.397 | |
extendPwmsFromAlignmentVector | 0.072 | 0.004 | 0.076 | |
getAlphabetFromCharacters | 0.000 | 0.000 | 0.001 | |
getAlphabetFromSequences | 0.001 | 0.000 | 0.000 | |
getPwmFromAlignment | 0.459 | 0.024 | 0.484 | |
getPwmFromAlignmentFile | 0.008 | 0.000 | 0.009 | |
getPwmFromFastaFile | 0.018 | 0.000 | 0.020 | |
getPwmFromFile | 0.004 | 0.000 | 0.005 | |
getPwmFromHomerFile | 0.002 | 0.000 | 0.003 | |
getPwmFromPfmOrJasparFile | 0.003 | 0.000 | 0.004 | |
getPwmFromPwmFile | 0.003 | 0.000 | 0.004 | |
getSequencesFromAlignmentFile | 0.001 | 0.000 | 0.001 | |
getSequencesFromFastaFile | 0.002 | 0.000 | 0.002 | |
informationContent | 0.082 | 0.000 | 0.083 | |
lossOfAbsICDifferences | 0.073 | 0.000 | 0.073 | |
multipleLocalPwmsAlignment | 0.049 | 0.004 | 0.053 | |
normalizePWM | 0 | 0 | 0 | |
normalizedDifferenceOfProbabilities | 0.069 | 0.000 | 0.069 | |
prepareDiffLogoTable | 1.407 | 0.028 | 1.438 | |
probabilities | 0.050 | 0.000 | 0.049 | |
seqLogo | 0.049 | 0.000 | 0.049 | |
shannonDivergence | 0.073 | 0.000 | 0.074 | |
sumOfAbsICDifferences | 0.065 | 0.004 | 0.069 | |
sumOfAbsProbabilityDifferences | 0.07 | 0.00 | 0.07 | |
sumProbabilities | 0.046 | 0.004 | 0.049 | |