Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-07-16 11:41 -0400 (Tue, 16 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4677 |
palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4416 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4444 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4393 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 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 1591/2243 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
PWMEnrich 4.41.0 (landing page) Diego Diez
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino6 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the PWMEnrich package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PWMEnrich.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. |
Package: PWMEnrich |
Version: 4.41.0 |
Command: C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:PWMEnrich.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings PWMEnrich_4.41.0.tar.gz |
StartedAt: 2024-07-16 02:58:38 -0400 (Tue, 16 Jul 2024) |
EndedAt: 2024-07-16 03:00:14 -0400 (Tue, 16 Jul 2024) |
EllapsedTime: 96.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: PWMEnrich.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:PWMEnrich.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings PWMEnrich_4.41.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/PWMEnrich.Rcheck' * using R version 4.4.1 (2024-06-14 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'PWMEnrich/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'PWMEnrich' version '4.41.0' * package encoding: UTF-8 * 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 whether package 'PWMEnrich' 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 ... OK * 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 ... OK * checking Rd files ... NOTE checkRd: (-1) plot-MotifEnrichmentReport-missing-method.Rd:31-47: Lost braces 31 | if(requireNamespace("PWMEnrich.Dmelanogaster.background")){ | ^ * 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 'test-all.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 NOTE See 'C:/Users/biocbuild/bbs-3.20-bioc/meat/PWMEnrich.Rcheck/00check.log' for details.
PWMEnrich.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL PWMEnrich ### ############################################################################## ############################################################################## * installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'PWMEnrich' ... ** 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 (PWMEnrich)
PWMEnrich.Rcheck/tests/test-all.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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. > library(testthat) > library(PWMEnrich) Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: Biostrings Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Loading required package: XVector Loading required package: GenomeInfoDb Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit > > test_package("PWMEnrich") No installed testthat tests found for PWMEnrich > > > proc.time() user system elapsed 2.60 0.26 2.85
PWMEnrich.Rcheck/PWMEnrich-Ex.timings
name | user | system | elapsed | |
PFMtoPWM | 0 | 0 | 0 | |
PWMUnscaled | 0.75 | 0.01 | 0.78 | |
getBackgroundFrequencies | 0 | 0 | 0 | |
groupReport-MotifEnrichmentResults-method | 1.55 | 0.10 | 1.64 | |
makeBackground | 0 | 0 | 0 | |
makePWMCutoffBackground | 0 | 0 | 0 | |
makePWMEmpiricalBackground | 0 | 0 | 0 | |
makePWMGEVBackground | 0 | 0 | 0 | |
makePWMLognBackground | 0 | 0 | 0 | |
makePWMPvalCutoffBackground | 0 | 0 | 0 | |
makePWMPvalCutoffBackgroundFromSeq | 0 | 0 | 0 | |
makePriors | 0 | 0 | 0 | |
motifDiffEnrichment | 1.67 | 0.00 | 1.67 | |
motifEnrichment | 2.39 | 0.03 | 2.44 | |
motifIC | 0.05 | 0.00 | 0.06 | |
motifRankingForGroup-MotifEnrichmentResults-method | 1.21 | 0.04 | 1.30 | |
motifRankingForSequence-MotifEnrichmentResults-method | 1.60 | 0.02 | 1.61 | |
motifScores | 2.67 | 0.04 | 2.75 | |
motifSimilarity | 0.03 | 0.00 | 0.03 | |
plot-PWM-missing-method | 0.14 | 0.02 | 0.15 | |
plotMotifScores | 0.06 | 0.00 | 0.07 | |
plotTopMotifsGroup-MotifEnrichmentResults-method | 1.40 | 0.03 | 1.43 | |
plotTopMotifsSequence-MotifEnrichmentResults-method | 1.53 | 0.00 | 1.55 | |
readMotifs | 0.04 | 0.03 | 0.08 | |
registerCoresPWMEnrich | 0 | 0 | 0 | |
reverseComplement-PWM-method | 0 | 0 | 0 | |
scanWithPWM | 0.02 | 0.00 | 0.04 | |
sequenceReport-MotifEnrichmentResults-method | 1.97 | 0.09 | 2.06 | |
toPWM | 0 | 0 | 0 | |
useBigMemoryPWMEnrich | 0 | 0 | 0 | |