| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-10-18 20:41 -0400 (Fri, 18 Oct 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4763 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4500 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4530 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4480 |
| 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 1320/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Moonlight2R 1.2.0 (landing page) Matteo Tiberti
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | TIMEOUT | OK | |||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
|
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. |
| Package: Moonlight2R |
| Version: 1.2.0 |
| 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_1.2.0.tar.gz |
| StartedAt: 2024-10-17 09:07:48 -0400 (Thu, 17 Oct 2024) |
| EndedAt: 2024-10-17 09:47:49 -0400 (Thu, 17 Oct 2024) |
| EllapsedTime: 2400.3 seconds |
| RetCode: None |
| Status: TIMEOUT |
| CheckDir: Moonlight2R.Rcheck |
| Warnings: NA |
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###
### 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_1.2.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/Moonlight2R.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 ‘Moonlight2R/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Moonlight2R’ version ‘1.2.0’
* 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 181.324 24.799 277.839
plotGMA 10.871 2.318 16.258
plotDMA 10.022 1.562 14.727
LiftMAF 6.486 1.878 12.374
getDataGEO 4.389 1.648 8.239
plotMoonlight 4.896 0.340 6.841
URA 4.862 0.349 7.422
plotMetExp 3.574 0.548 6.045
GLS 1.533 0.542 9.468
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
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-x86_64/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)
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: 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.
> # 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
Moonlight2R.Rcheck/Moonlight2R-Ex.timings
| name | user | system | elapsed | |
| DMA | 0.001 | 0.000 | 0.001 | |
| FEA | 0.835 | 0.039 | 1.323 | |
| GLS | 1.533 | 0.542 | 9.468 | |
| GMA | 181.324 | 24.799 | 277.839 | |
| GRN | 0.080 | 0.014 | 0.151 | |
| GSEA | 2.745 | 0.258 | 4.338 | |
| LPA | 0.372 | 0.013 | 0.537 | |
| LiftMAF | 6.486 | 1.878 | 12.374 | |
| MAFtoCscape | 0.081 | 0.007 | 0.127 | |
| PRA | 0.339 | 0.022 | 0.495 | |
| PRAtoTibble | 0.070 | 0.018 | 0.090 | |
| RunCscape_somatic | 0 | 0 | 0 | |
| URA | 4.862 | 0.349 | 7.422 | |
| confidence | 0.000 | 0.001 | 0.001 | |
| getDataGEO | 4.389 | 1.648 | 8.239 | |
| moonlight | 0 | 0 | 0 | |
| plotCircos | 1.807 | 0.255 | 2.572 | |
| plotDMA | 10.022 | 1.562 | 14.727 | |
| plotFEA | 0.651 | 0.043 | 0.982 | |
| plotGMA | 10.871 | 2.318 | 16.258 | |
| plotMetExp | 3.574 | 0.548 | 6.045 | |
| plotMoonlight | 4.896 | 0.340 | 6.841 | |
| plotMoonlightMet | 3.104 | 0.305 | 4.356 | |
| plotNetworkHive | 0.064 | 0.017 | 0.111 | |
| plotURA | 0.384 | 0.047 | 0.602 | |
| tabix_func | 0 | 0 | 0 | |