Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-10-16 11:39 -0400 (Thu, 16 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4833 |
merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4586 |
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 1339/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MOSClip 1.2.3 (landing page) Paolo Martini
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the MOSClip package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MOSClip.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: MOSClip |
Version: 1.2.3 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MOSClip.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MOSClip_1.2.3.tar.gz |
StartedAt: 2025-10-14 06:51:21 -0400 (Tue, 14 Oct 2025) |
EndedAt: 2025-10-14 07:07:44 -0400 (Tue, 14 Oct 2025) |
EllapsedTime: 983.8 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MOSClip.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MOSClip.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MOSClip_1.2.3.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/MOSClip.Rcheck’ * using R version 4.5.1 RC (2025-06-05 r88288) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘MOSClip/DESCRIPTION’ ... OK * this is package ‘MOSClip’ version ‘1.2.3’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 27 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * 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 ‘MOSClip’ 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 ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: makeOmics.Rd: ExperimentList, DataFrame-class 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed evaluateResampling 13.241 0.314 13.609 annotePathwayToFather 12.512 0.485 13.118 plotModuleReport 12.119 0.082 12.286 resampling-TwoClass 10.976 0.081 11.777 resampling-Survival 10.984 0.071 11.162 plotModuleHeat 10.450 0.163 11.000 multiPathwayModuleReport 9.700 0.106 9.933 plotModuleKM 7.885 0.103 8.196 plotModuleInGraph 4.967 0.062 5.271 * 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 ‘/Users/biocbuild/bbs-3.21-bioc/meat/MOSClip.Rcheck/00check.log’ for details.
MOSClip.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MOSClip ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’ * installing *source* package ‘MOSClip’ ... ** this is package ‘MOSClip’ version ‘1.2.3’ ** using staged installation ** R ** data ** 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 (MOSClip)
MOSClip.Rcheck/tests/testthat.Rout
R version 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" Copyright (C) 2025 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(MOSClip) > > test_check("MOSClip") [ FAIL 0 | WARN 1 | SKIP 0 | PASS 198 ] [ FAIL 0 | WARN 1 | SKIP 0 | PASS 198 ] > > proc.time() user system elapsed 172.797 4.681 189.007
MOSClip.Rcheck/MOSClip-Ex.timings
name | user | system | elapsed | |
annotePathwayToFather | 12.512 | 0.485 | 13.118 | |
availableOmicMethods | 0.001 | 0.001 | 0.002 | |
computeFreqs | 0.004 | 0.001 | 0.005 | |
computeOmicsIntersections | 0.007 | 0.001 | 0.008 | |
downloadPathwayRelationFromReactome | 0.151 | 0.112 | 0.264 | |
evaluateResampling | 13.241 | 0.314 | 13.609 | |
makeOmics | 0.466 | 0.006 | 0.474 | |
minOrNA | 0 | 0 | 0 | |
multiOmicsSurvivalModuleTest | 3.787 | 0.087 | 3.922 | |
multiOmicsSurvivalPathwayTest | 0.593 | 0.016 | 0.613 | |
multiOmicsTwoClassModuleTest | 3.775 | 0.084 | 3.890 | |
multiOmicsTwoClassPathwayTest | 0.595 | 0.020 | 0.619 | |
multiPathwayModuleReport | 9.700 | 0.106 | 9.933 | |
multiPathwayReport | 1.319 | 0.031 | 1.374 | |
plotFrequencies | 0.997 | 0.010 | 1.021 | |
plotModuleHeat | 10.450 | 0.163 | 11.000 | |
plotModuleInGraph | 4.967 | 0.062 | 5.271 | |
plotModuleKM | 7.885 | 0.103 | 8.196 | |
plotModuleReport | 12.119 | 0.082 | 12.286 | |
plotMultiPathwayReport | 3.204 | 0.042 | 3.272 | |
plotPathwayHeat | 4.303 | 0.062 | 4.400 | |
plotPathwayKM | 3.924 | 0.035 | 3.982 | |
resampling-Survival | 10.984 | 0.071 | 11.162 | |
resampling-TwoClass | 10.976 | 0.081 | 11.777 | |
runSupertest | 0.264 | 0.004 | 0.281 | |
showMOSpalette | 0.032 | 0.001 | 0.035 | |
showModule | 3.854 | 0.064 | 4.131 | |
showOmics | 0.077 | 0.008 | 0.087 | |
showPathway | 0.601 | 0.012 | 0.640 | |
stripModulesFromPathways | 0.001 | 0.001 | 0.002 | |
summarizeOmicsResByMinPvalue | 0.000 | 0.000 | 0.001 | |