Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-09-20 12:04 -0400 (Sat, 20 Sep 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4814 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4603 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4547 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4553 |
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 1341/2333 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MOSClip 1.3.2 (landing page) Paolo Martini
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
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: 1.3.2 |
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_1.3.2.tar.gz |
StartedAt: 2025-09-19 22:23:29 -0400 (Fri, 19 Sep 2025) |
EndedAt: 2025-09-19 22:32:26 -0400 (Fri, 19 Sep 2025) |
EllapsedTime: 537.0 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: MOSClip.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### 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_1.3.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/MOSClip.Rcheck’ * using R version 4.5.1 Patched (2025-09-10 r88807) * 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 ‘1.3.2’ * 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 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 6.370 0.209 6.597 annotePathwayToFather 6.290 0.242 6.571 plotModuleReport 5.327 0.053 5.402 resampling-Survival 5.103 0.042 5.175 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-PlottingMO.R:36:9'): Plots with two class object work ──────── class(res.pathwayHeat) not identical to c("gg", "ggplot"). Lengths differ: 5 is not 2 ── Failure ('test-PlottingMO.R:50:9'): Plots with two class object work ──────── class(res.pathwayHeat_nopalette) not identical to c("gg", "ggplot"). Lengths differ: 5 is not 2 ── Failure ('test-PlottingMO.R:107:9'): Plots with two class object work ─────── class(res.moduleHeat) not identical to c("gg", "ggplot"). Lengths differ: 5 is not 2 [ FAIL 3 | WARN 2 | SKIP 0 | PASS 195 ] Error: Test failures Execution halted * 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 ERROR, 1 NOTE See ‘/Users/biocbuild/bbs-3.22-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 ‘1.3.2’ ** 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.fail
R version 4.5.1 Patched (2025-09-10 r88807) -- "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 3 | WARN 2 | SKIP 0 | PASS 195 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-PlottingMO.R:36:9'): Plots with two class object work ──────── class(res.pathwayHeat) not identical to c("gg", "ggplot"). Lengths differ: 5 is not 2 ── Failure ('test-PlottingMO.R:50:9'): Plots with two class object work ──────── class(res.pathwayHeat_nopalette) not identical to c("gg", "ggplot"). Lengths differ: 5 is not 2 ── Failure ('test-PlottingMO.R:107:9'): Plots with two class object work ─────── class(res.moduleHeat) not identical to c("gg", "ggplot"). Lengths differ: 5 is not 2 [ FAIL 3 | WARN 2 | SKIP 0 | PASS 195 ] Error: Test failures Execution halted
MOSClip.Rcheck/MOSClip-Ex.timings
name | user | system | elapsed | |
annotePathwayToFather | 6.290 | 0.242 | 6.571 | |
availableOmicMethods | 0.001 | 0.001 | 0.001 | |
computeFreqs | 0.002 | 0.001 | 0.002 | |
computeOmicsIntersections | 0.002 | 0.000 | 0.003 | |
downloadPathwayRelationFromReactome | 0.074 | 0.033 | 0.108 | |
evaluateResampling | 6.370 | 0.209 | 6.597 | |
makeOmics | 0.226 | 0.003 | 0.230 | |
minOrNA | 0.001 | 0.000 | 0.000 | |
multiOmicsSurvivalModuleTest | 1.556 | 0.033 | 1.595 | |
multiOmicsSurvivalPathwayTest | 0.353 | 0.018 | 0.373 | |
multiOmicsTwoClassModuleTest | 1.557 | 0.046 | 1.608 | |
multiOmicsTwoClassPathwayTest | 0.283 | 0.010 | 0.293 | |
multiPathwayModuleReport | 3.825 | 0.059 | 3.897 | |
multiPathwayReport | 0.558 | 0.018 | 0.577 | |
plotFrequencies | 0.433 | 0.006 | 0.440 | |
plotModuleHeat | 4.822 | 0.108 | 4.956 | |
plotModuleInGraph | 2.113 | 0.042 | 2.168 | |
plotModuleKM | 3.604 | 0.085 | 3.714 | |
plotModuleReport | 5.327 | 0.053 | 5.402 | |
plotMultiPathwayReport | 1.533 | 0.025 | 1.570 | |
plotPathwayHeat | 2.367 | 0.055 | 2.444 | |
plotPathwayKM | 1.991 | 0.030 | 2.035 | |
resampling-Survival | 5.103 | 0.042 | 5.175 | |
resampling-TwoClass | 4.914 | 0.044 | 4.983 | |
runSupertest | 0.124 | 0.002 | 0.129 | |
showMOSpalette | 0.012 | 0.001 | 0.014 | |
showModule | 1.663 | 0.027 | 1.701 | |
showOmics | 0.048 | 0.002 | 0.050 | |
showPathway | 0.353 | 0.011 | 0.365 | |
stripModulesFromPathways | 0.000 | 0.000 | 0.001 | |
summarizeOmicsResByMinPvalue | 0 | 0 | 0 | |