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This page was generated on 2025-10-16 11:39 -0400 (Thu, 16 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4833
merida1macOS 12.7.6 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4614
kjohnson1macOS 13.7.5 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4555
kunpeng2Linux (openEuler 24.03 LTS)aarch64R 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 1339/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MOSClip 1.2.3  (landing page)
Paolo Martini
Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025)
git_url: https://git.bioconductor.org/packages/MOSClip
git_branch: RELEASE_3_21
git_last_commit: 0b0ae8c
git_last_commit_date: 2025-09-22 10:37:16 -0400 (Mon, 22 Sep 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.7.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for MOSClip on merida1

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.

raw results


Summary

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

Command output

##############################################################################
##############################################################################
###
### 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.


Installation output

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)

Tests output

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 

Example timings

MOSClip.Rcheck/MOSClip-Ex.timings

nameusersystemelapsed
annotePathwayToFather12.512 0.48513.118
availableOmicMethods0.0010.0010.002
computeFreqs0.0040.0010.005
computeOmicsIntersections0.0070.0010.008
downloadPathwayRelationFromReactome0.1510.1120.264
evaluateResampling13.241 0.31413.609
makeOmics0.4660.0060.474
minOrNA000
multiOmicsSurvivalModuleTest3.7870.0873.922
multiOmicsSurvivalPathwayTest0.5930.0160.613
multiOmicsTwoClassModuleTest3.7750.0843.890
multiOmicsTwoClassPathwayTest0.5950.0200.619
multiPathwayModuleReport9.7000.1069.933
multiPathwayReport1.3190.0311.374
plotFrequencies0.9970.0101.021
plotModuleHeat10.450 0.16311.000
plotModuleInGraph4.9670.0625.271
plotModuleKM7.8850.1038.196
plotModuleReport12.119 0.08212.286
plotMultiPathwayReport3.2040.0423.272
plotPathwayHeat4.3030.0624.400
plotPathwayKM3.9240.0353.982
resampling-Survival10.984 0.07111.162
resampling-TwoClass10.976 0.08111.777
runSupertest0.2640.0040.281
showMOSpalette0.0320.0010.035
showModule3.8540.0644.131
showOmics0.0770.0080.087
showPathway0.6010.0120.640
stripModulesFromPathways0.0010.0010.002
summarizeOmicsResByMinPvalue0.0000.0000.001