Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 1305/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
monaLisa 1.12.0 (landing page) Michael Stadler
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the monaLisa package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/monaLisa.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: monaLisa |
Version: 1.12.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:monaLisa.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings monaLisa_1.12.0.tar.gz |
StartedAt: 2024-12-20 06:17:56 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 06:29:54 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 718.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: monaLisa.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:monaLisa.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings monaLisa_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/monaLisa.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘monaLisa/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘monaLisa’ version ‘1.12.0’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘monaLisa’ 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 ... 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed plotMotifHeatmaps 10.695 0.148 11.201 * 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: OK
monaLisa.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL monaLisa ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘monaLisa’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (monaLisa)
monaLisa.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 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(monaLisa) > > test_check("monaLisa") [ FAIL 0 | WARN 0 | SKIP 1 | PASS 541 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • empty test (1): 'test_Homer.R:136:1' [ FAIL 0 | WARN 0 | SKIP 1 | PASS 541 ] > > proc.time() user system elapsed 103.816 6.940 110.625
monaLisa.Rcheck/monaLisa-Ex.timings
name | user | system | elapsed | |
annoSeqlogo | 1.242 | 0.027 | 1.279 | |
bin | 0.012 | 0.003 | 0.016 | |
calcBinnedKmerEnr | 1.416 | 0.040 | 1.460 | |
calcBinnedMotifEnrHomer | 0.006 | 0.013 | 0.028 | |
calcBinnedMotifEnrR | 1.572 | 0.117 | 1.693 | |
dumpJaspar | 0.056 | 0.003 | 0.061 | |
findHomer | 0.002 | 0.008 | 0.011 | |
findMotifHits-methods | 0.611 | 0.004 | 0.617 | |
getColsByBin | 0.006 | 0.001 | 0.007 | |
getKmerFreq | 0.062 | 0.001 | 0.063 | |
getSetZeroBin | 0.004 | 0.000 | 0.004 | |
homerToPFMatrixList | 0.104 | 0.008 | 0.112 | |
motifKmerSimilarity | 0.046 | 0.001 | 0.048 | |
motifSimilarity | 0.019 | 0.001 | 0.021 | |
parseHomerOutput | 0.017 | 0.002 | 0.019 | |
plotBinDensity | 0.022 | 0.002 | 0.025 | |
plotBinDiagnostics | 1.467 | 0.031 | 1.504 | |
plotBinHist | 0.014 | 0.002 | 0.016 | |
plotBinScatter | 0.011 | 0.002 | 0.013 | |
plotMotifHeatmaps | 10.695 | 0.148 | 11.201 | |
plotSelectionProb | 1.897 | 0.020 | 2.139 | |
plotStabilityPaths | 1.505 | 0.015 | 1.590 | |
prepareHomer | 0.111 | 0.009 | 0.120 | |
randLassoStabSel | 3.181 | 0.876 | 2.898 | |
sampleRandomRegions | 0.126 | 0.031 | 0.159 | |
seqLogoGrob | 0.328 | 0.089 | 0.425 | |