Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-12-23 11:47 -0500 (Mon, 23 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" | 4372 |
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 1298/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
monaLisa 1.13.0 (landing page) Michael Stadler
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: monaLisa |
Version: 1.13.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:monaLisa.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings monaLisa_1.13.0.tar.gz |
StartedAt: 2024-12-23 09:46:51 -0000 (Mon, 23 Dec 2024) |
EndedAt: 2024-12-23 09:54:32 -0000 (Mon, 23 Dec 2024) |
EllapsedTime: 461.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: monaLisa.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:monaLisa.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings monaLisa_1.13.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/monaLisa.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 ‘monaLisa/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘monaLisa’ version ‘1.13.0’ * 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 ...Warning: program compiled against libxml 212 using older 211 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 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 ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: getKmerFreq.Rd: DNAStringSet Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * 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 5.974 0.08 6.067 * 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 NOTE See ‘/home/biocbuild/bbs-3.21-bioc/meat/monaLisa.Rcheck/00check.log’ for details.
monaLisa.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL monaLisa ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’ * installing *source* package ‘monaLisa’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading No methods found in package ‘Biostrings’ for request: ‘pattern’ when loading ‘TFBSTools’ ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location No methods found in package ‘Biostrings’ for request: ‘pattern’ when loading ‘TFBSTools’ ** testing if installed package can be loaded from final location No methods found in package ‘Biostrings’ for request: ‘pattern’ when loading ‘TFBSTools’ ** testing if installed package keeps a record of temporary installation path * DONE (monaLisa)
monaLisa.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. > library(testthat) > library(monaLisa) No methods found in package 'Biostrings' for request: 'pattern' when loading 'TFBSTools' > > 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 66.118 5.364 69.490
monaLisa.Rcheck/monaLisa-Ex.timings
name | user | system | elapsed | |
annoSeqlogo | 0.324 | 0.017 | 0.366 | |
bin | 0.009 | 0.000 | 0.009 | |
calcBinnedKmerEnr | 2.062 | 0.079 | 2.145 | |
calcBinnedMotifEnrHomer | 0.006 | 0.001 | 0.005 | |
calcBinnedMotifEnrR | 0.831 | 0.079 | 0.913 | |
dumpJaspar | 0.031 | 0.004 | 0.042 | |
findHomer | 0.000 | 0.005 | 0.005 | |
findMotifHits-methods | 0.360 | 0.019 | 0.381 | |
getColsByBin | 0.004 | 0.000 | 0.004 | |
getKmerFreq | 0.039 | 0.000 | 0.040 | |
getSetZeroBin | 0.002 | 0.000 | 0.002 | |
homerToPFMatrixList | 0.063 | 0.000 | 0.063 | |
motifKmerSimilarity | 0.025 | 0.000 | 0.025 | |
motifSimilarity | 0.008 | 0.003 | 0.011 | |
parseHomerOutput | 0.011 | 0.000 | 0.013 | |
plotBinDensity | 0.014 | 0.000 | 0.014 | |
plotBinDiagnostics | 0.772 | 0.008 | 0.781 | |
plotBinHist | 0.005 | 0.004 | 0.009 | |
plotBinScatter | 0.007 | 0.000 | 0.007 | |
plotMotifHeatmaps | 5.974 | 0.080 | 6.067 | |
plotSelectionProb | 1.202 | 0.020 | 1.225 | |
plotStabilityPaths | 0.910 | 0.052 | 0.964 | |
prepareHomer | 0.070 | 0.004 | 0.073 | |
randLassoStabSel | 1.52 | 0.44 | 1.90 | |
sampleRandomRegions | 0.588 | 0.395 | 0.075 | |
seqLogoGrob | 0.296 | 0.115 | 0.417 | |