| Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-22 12:06 -0400 (Wed, 22 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4890 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4680 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4625 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4642 |
| 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 1346/2355 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| monaLisa 1.15.3 (landing page) Michael Stadler
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
|
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: 1.15.3 |
| 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_1.15.3.tar.gz |
| StartedAt: 2025-10-21 20:49:08 -0400 (Tue, 21 Oct 2025) |
| EndedAt: 2025-10-21 20:51:21 -0400 (Tue, 21 Oct 2025) |
| EllapsedTime: 133.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: monaLisa.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### 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_1.15.3.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/monaLisa.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘monaLisa/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘monaLisa’ version ‘1.15.3’
* 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
* 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/4.5-arm64/Resources/library’ * installing *source* package ‘monaLisa’ ... ** this is package ‘monaLisa’ version ‘1.15.3’ ** 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 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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 1 | SKIP 1 | PASS 646 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test_Homer.R:150:1'
[ FAIL 0 | WARN 1 | SKIP 1 | PASS 646 ]
>
> proc.time()
user system elapsed
21.088 2.049 22.617
monaLisa.Rcheck/monaLisa-Ex.timings
| name | user | system | elapsed | |
| annoSeqlogo | 0.046 | 0.005 | 0.057 | |
| bin | 0.003 | 0.000 | 0.003 | |
| calcBinnedKmerEnr | 0.194 | 0.011 | 0.203 | |
| calcBinnedMotifEnrHomer | 0.001 | 0.003 | 0.014 | |
| calcBinnedMotifEnrR | 0.209 | 0.006 | 0.214 | |
| dumpJaspar | 0.017 | 0.001 | 0.019 | |
| findHomer | 0.001 | 0.001 | 0.001 | |
| findMotifHits-methods | 0.076 | 0.003 | 0.078 | |
| getColsByBin | 0.001 | 0.000 | 0.001 | |
| getKmerFreq | 0.010 | 0.001 | 0.011 | |
| getSetZeroBin | 0.000 | 0.000 | 0.001 | |
| homerToPFMatrixList | 0.018 | 0.002 | 0.021 | |
| motifKmerSimilarity | 0.006 | 0.001 | 0.008 | |
| motifSimilarity | 0.003 | 0.001 | 0.003 | |
| parseHomerOutput | 0.005 | 0.000 | 0.006 | |
| plotBinDensity | 0.200 | 0.019 | 0.219 | |
| plotBinDiagnostics | 0.456 | 0.010 | 0.466 | |
| plotBinHist | 0.165 | 0.001 | 0.166 | |
| plotBinScatter | 0.102 | 0.001 | 0.102 | |
| plotMotifHeatmaps | 1.372 | 0.021 | 1.394 | |
| plotSelectionProb | 0.454 | 0.006 | 0.460 | |
| plotStabilityPaths | 0.368 | 0.019 | 0.389 | |
| prepareHomer | 0.045 | 0.003 | 0.047 | |
| randLassoStabSel | 0.897 | 0.131 | 0.890 | |
| sampleRandomRegions | 0.015 | 0.009 | 0.025 | |
| seqLogoGrob | 0.055 | 0.017 | 0.074 | |