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This page was generated on 2024-07-24 11:42 -0400 (Wed, 24 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4688
palomino8Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4284
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4455
kjohnson3macOS 13.6.5 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4404
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 1287/2248HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Moonlight2R 1.3.0  (landing page)
Matteo Tiberti
Snapshot Date: 2024-07-23 14:00 -0400 (Tue, 23 Jul 2024)
git_url: https://git.bioconductor.org/packages/Moonlight2R
git_branch: devel
git_last_commit: d5b0796
git_last_commit_date: 2024-04-30 11:51:36 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  
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 13.6.5 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for Moonlight2R on kjohnson3

To the developers/maintainers of the Moonlight2R package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Moonlight2R.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: Moonlight2R
Version: 1.3.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Moonlight2R.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Moonlight2R_1.3.0.tar.gz
StartedAt: 2024-07-23 23:15:57 -0400 (Tue, 23 Jul 2024)
EndedAt: 2024-07-23 23:20:20 -0400 (Tue, 23 Jul 2024)
EllapsedTime: 262.8 seconds
RetCode: 0
Status:   OK  
CheckDir: Moonlight2R.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Moonlight2R.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Moonlight2R_1.3.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/Moonlight2R.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-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 Ventura 13.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Moonlight2R/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Moonlight2R’ version ‘1.3.0’
* 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 ‘Moonlight2R’ 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
GMA 35.049  4.162  43.247
* 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

Moonlight2R.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Moonlight2R
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’
* installing *source* package ‘Moonlight2R’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (Moonlight2R)

Tests output

Moonlight2R.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-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.

> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/tests.html
> # * https://testthat.r-lib.org/reference/test_package.html#special-files
> 
> library(testthat)
> library(Moonlight2R)
Loading required package: doParallel
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel


Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
> 
> test_check("Moonlight2R")
[1] "Output folder already exists"
loading from cache
require("rtracklayer")
[1] "CScape_somatic files have been found in results-folder."
loading from cache

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Processing PubMed data ............. done!
Running Regular mode...
Fetching probe annotation...
see ?sesameData and browseVignettes('sesameData') for documentation
loading from cache
Found 13 samples with both methylation and gene expression data.
Modeling gene expression...

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Found 73 transcriptionally predictive probes.
Found 17 samples in group.1 and 6 samples in group.2

Starting Beta mixture modeling.
Running Beta mixture model on 73 probes and on 17 samples.

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Found 73 differentially methylated CpGs
Identifying functional CpG-gene pairs...

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Found 84 functional probe-gene pairs.
Saving the EpiMix results to the output directory...
Running Enhancer mode...
Fetching probe annotation...
see ?sesameData and browseVignettes('sesameData') for documentation
loading from cache
Found 17 samples in group.1 and 6 samples in group.2
Fetching enhancer CpGs from Roadmap Epigenomics...
Downloading chromatin states from the Roadmap Epigenomics...
trying URL 'https://egg2.wustl.edu/roadmap/data/byFileType/chromhmmSegmentations/ChmmModels/core_K27ac/jointModel/final/E096_18_core_K27ac_hg38lift_mnemonics.bed.gz'
Content type 'application/x-gzip' length 3835377 bytes (3.7 MB)
==================================================
downloaded 3.7 MB

	Identifed 65057 enhancer CpGs from the epigenome E096 
see ?sesameData and browseVignettes('sesameData') for documentation
loading from cache
Returning distal probes: 160862
Found 7 CpGs associated with distal enhancers in the methylation dataset

Starting Beta mixture modeling.
Running Beta mixture model on 7 probes and on 17 samples.

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Found 7 differentially methylated CpGs
Modeling the gene expression for enhancers...
Searching for the 20 near genes
Identifying gene position for each probe
Looking for differentially methylated enhancers associated with gene expression

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Found 2 functional probe-gene pairs.
Saving the EpiMix results to the output directory...
see ?sesameData and browseVignettes('sesameData') for documentation
loading from cache
[1] "3 oncogenic mediator(s) out of 3 were found in the None evidence category"

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[ FAIL 0 | WARN 2 | SKIP 0 | PASS 49 ]

[ FAIL 0 | WARN 2 | SKIP 0 | PASS 49 ]
> 
> proc.time()
   user  system elapsed 
 50.712   7.011  71.114 

Example timings

Moonlight2R.Rcheck/Moonlight2R-Ex.timings

nameusersystemelapsed
DMA000
FEA0.2230.0060.229
GLS0.4070.3971.511
GMA35.049 4.16243.247
GRN0.0260.0020.027
GSEA0.4660.0320.497
LPA0.0880.0030.091
LiftMAF1.2580.2372.111
MAFtoCscape0.0180.0020.019
PRA0.0750.0030.078
PRAtoTibble0.0100.0020.012
RunCscape_somatic000
URA0.8580.0750.933
confidence000
getDataGEO1.1180.1662.782
moonlight000
plotCircos0.2250.0310.257
plotDMA1.4300.1531.586
plotFEA0.1530.0070.159
plotGMA1.3520.2751.628
plotMetExp0.5330.0640.604
plotMoonlight0.7990.0330.831
plotMoonlightMet0.4350.0580.488
plotNetworkHive0.0110.0020.014
plotURA0.0890.0060.096
tabix_func000