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This page was generated on 2025-08-04 12:09 -0400 (Mon, 04 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4796
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4536
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4578
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4519
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (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 1328/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MOSClip 1.3.2  (landing page)
Paolo Martini
Snapshot Date: 2025-08-03 13:25 -0400 (Sun, 03 Aug 2025)
git_url: https://git.bioconductor.org/packages/MOSClip
git_branch: devel
git_last_commit: d29262d
git_last_commit_date: 2025-05-19 04:42:27 -0400 (Mon, 19 May 2025)
nebbiolo2Linux (Ubuntu 24.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for MOSClip on lconway

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: 1.3.2
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: 2025-08-03 22:30:24 -0400 (Sun, 03 Aug 2025)
EndedAt: 2025-08-03 22:39:08 -0400 (Sun, 03 Aug 2025)
EllapsedTime: 523.5 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_1.3.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/MOSClip.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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    6.517  0.195   6.732
annotePathwayToFather 6.064  0.229   6.317
plotModuleReport      5.297  0.061   5.388
resampling-Survival   4.937  0.045   5.010
* 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-3.22-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 ‘1.3.2’
** 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)

Tests output

MOSClip.Rcheck/tests/testthat.Rout


R version 4.5.1 (2025-06-13) -- "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 0 | SKIP 0 | PASS 198 ]
> 
> proc.time()
   user  system elapsed 
 86.500   2.688  93.337 

Example timings

MOSClip.Rcheck/MOSClip-Ex.timings

nameusersystemelapsed
annotePathwayToFather6.0640.2296.317
availableOmicMethods000
computeFreqs0.0020.0000.003
computeOmicsIntersections0.0030.0000.004
downloadPathwayRelationFromReactome0.0690.0390.108
evaluateResampling6.5170.1956.732
makeOmics0.2250.0040.229
minOrNA0.0000.0010.000
multiOmicsSurvivalModuleTest1.5580.0341.597
multiOmicsSurvivalPathwayTest0.3470.0150.365
multiOmicsTwoClassModuleTest1.5920.0341.633
multiOmicsTwoClassPathwayTest0.3410.0160.358
multiPathwayModuleReport3.8810.0503.953
multiPathwayReport0.5810.0180.601
plotFrequencies0.3100.0120.323
plotModuleHeat4.5160.1024.665
plotModuleInGraph2.0220.0502.078
plotModuleKM3.0620.0753.153
plotModuleReport5.2970.0615.388
plotMultiPathwayReport1.5450.0281.586
plotPathwayHeat2.2240.0432.279
plotPathwayKM1.3970.0271.434
resampling-Survival4.9370.0455.010
resampling-TwoClass4.7480.0474.818
runSupertest0.1120.0020.115
showMOSpalette0.0110.0010.012
showModule1.6240.0271.659
showOmics0.0410.0010.043
showPathway0.3590.0130.374
stripModulesFromPathways000
summarizeOmicsResByMinPvalue0.0000.0010.001