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This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 1311/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MOSClip 1.0.0  (landing page)
Paolo Martini
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/MOSClip
git_branch: RELEASE_3_20
git_last_commit: 3324c1e
git_last_commit_date: 2024-10-29 11:35:08 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 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
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


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: 1.0.0
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_1.0.0.tar.gz
StartedAt: 2024-12-20 06:19:09 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 06:35:11 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 962.1 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_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/MOSClip.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* 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 ‘1.0.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ... OK
* 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       14.488  0.285  15.144
annotePathwayToFather    12.828  0.502  14.022
plotModuleReport         12.225  0.093  12.605
resampling-Survival      11.142  0.071  11.529
resampling-TwoClass      11.000  0.081  11.369
plotModuleHeat           10.314  0.153  10.791
multiPathwayModuleReport  9.871  0.082  10.327
plotModuleKM              6.519  0.116   6.840
* 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: OK


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/4.4-x86_64/Resources/library’
* installing *source* package ‘MOSClip’ ...
** 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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 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 
172.021   4.245 186.701 

Example timings

MOSClip.Rcheck/MOSClip-Ex.timings

nameusersystemelapsed
annotePathwayToFather12.828 0.50214.022
availableOmicMethods0.0010.0010.001
computeFreqs0.0040.0000.005
computeOmicsIntersections0.0080.0010.008
downloadPathwayRelationFromReactome0.1520.1150.296
evaluateResampling14.488 0.28515.144
makeOmics0.4710.0080.496
minOrNA0.0010.0010.001
multiOmicsSurvivalModuleTest3.7990.0743.920
multiOmicsSurvivalPathwayTest0.6490.0220.775
multiOmicsTwoClassModuleTest3.8190.0644.154
multiOmicsTwoClassPathwayTest0.6610.0210.690
multiPathwayModuleReport 9.871 0.08210.327
multiPathwayReport1.3200.0211.412
plotFrequencies0.5810.0110.612
plotModuleHeat10.314 0.15310.791
plotModuleInGraph4.6270.0874.804
plotModuleKM6.5190.1166.840
plotModuleReport12.225 0.09312.605
plotMultiPathwayReport3.2110.0353.319
plotPathwayHeat4.2250.0584.362
plotPathwayKM2.8170.0272.887
resampling-Survival11.142 0.07111.529
resampling-TwoClass11.000 0.08111.369
runSupertest0.2700.0040.284
showMOSpalette0.0330.0030.046
showModule3.9330.0454.089
showOmics0.0760.0040.084
showPathway0.6720.0130.704
stripModulesFromPathways0.0010.0010.001
summarizeOmicsResByMinPvalue0.0010.0000.001