Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-08-04 12:12 -0400 (Mon, 04 Aug 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4796 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4536 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4578 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4519 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4517 |
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 1328/2313 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MOSClip 1.3.2 (landing page) Paolo Martini
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | 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 | ![]() | ||||||||
taishan | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: MOSClip |
Version: 1.3.2 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:MOSClip.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings MOSClip_1.3.2.tar.gz |
StartedAt: 2025-08-01 08:36:31 -0000 (Fri, 01 Aug 2025) |
EndedAt: 2025-08-01 08:46:10 -0000 (Fri, 01 Aug 2025) |
EllapsedTime: 578.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MOSClip.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:MOSClip.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings MOSClip_1.3.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/MOSClip.Rcheck’ * using R version 4.5.0 (2025-04-11) * 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 ‘MOSClip/DESCRIPTION’ ... OK * this is package ‘MOSClip’ version ‘1.3.2’ * 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 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: 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 7.897 0.075 7.988 annotePathwayToFather 7.393 0.148 7.562 plotModuleReport 7.205 0.020 7.243 resampling-Survival 6.673 0.020 6.711 resampling-TwoClass 6.541 0.004 6.564 plotModuleHeat 5.656 0.088 5.770 multiPathwayModuleReport 5.182 0.080 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 ‘/home/biocbuild/bbs-3.22-bioc/meat/MOSClip.Rcheck/00check.log’ for details.
MOSClip.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL MOSClip ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘MOSClip’ ... ** this is package ‘MOSClip’ version ‘1.3.2’ ** 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 4.5.0 (2025-04-11) -- "How About a Twenty-Six" Copyright (C) 2025 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(MOSClip) > > test_check("MOSClip") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 198 ] > > proc.time() user system elapsed 99.347 1.866 106.271
MOSClip.Rcheck/MOSClip-Ex.timings
name | user | system | elapsed | |
annotePathwayToFather | 7.393 | 0.148 | 7.562 | |
availableOmicMethods | 0.001 | 0.000 | 0.000 | |
computeFreqs | 0.003 | 0.000 | 0.003 | |
computeOmicsIntersections | 0.004 | 0.000 | 0.004 | |
downloadPathwayRelationFromReactome | 0.055 | 0.008 | 0.062 | |
evaluateResampling | 7.897 | 0.075 | 7.988 | |
makeOmics | 0.263 | 0.001 | 0.263 | |
minOrNA | 0 | 0 | 0 | |
multiOmicsSurvivalModuleTest | 2.105 | 0.004 | 2.112 | |
multiOmicsSurvivalPathwayTest | 0.355 | 0.007 | 0.363 | |
multiOmicsTwoClassModuleTest | 2.038 | 0.019 | 2.061 | |
multiOmicsTwoClassPathwayTest | 0.399 | 0.000 | 0.400 | |
multiPathwayModuleReport | 5.182 | 0.080 | 5.271 | |
multiPathwayReport | 0.756 | 0.012 | 0.769 | |
plotFrequencies | 0.355 | 0.000 | 0.356 | |
plotModuleHeat | 5.656 | 0.088 | 5.770 | |
plotModuleInGraph | 2.582 | 0.020 | 2.607 | |
plotModuleKM | 3.916 | 0.020 | 3.946 | |
plotModuleReport | 7.205 | 0.020 | 7.243 | |
plotMultiPathwayReport | 1.939 | 0.000 | 1.944 | |
plotPathwayHeat | 2.671 | 0.024 | 2.701 | |
plotPathwayKM | 1.890 | 0.000 | 1.894 | |
resampling-Survival | 6.673 | 0.020 | 6.711 | |
resampling-TwoClass | 6.541 | 0.004 | 6.564 | |
runSupertest | 0.164 | 0.000 | 0.165 | |
showMOSpalette | 0.072 | 0.004 | 0.076 | |
showModule | 2.146 | 0.000 | 2.152 | |
showOmics | 0.046 | 0.000 | 0.046 | |
showPathway | 0.436 | 0.000 | 0.438 | |
stripModulesFromPathways | 0 | 0 | 0 | |
summarizeOmicsResByMinPvalue | 0 | 0 | 0 | |