| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-04-17 11:37:57 -0400 (Wed, 17 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4676 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4414 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4437 |
| 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 1304/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Moonlight2R 1.0.0 (landing page) Matteo Tiberti
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
|
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: 1.0.0 |
| 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_1.0.0.tar.gz |
| StartedAt: 2024-04-16 05:40:09 -0400 (Tue, 16 Apr 2024) |
| EndedAt: 2024-04-16 05:55:07 -0400 (Tue, 16 Apr 2024) |
| EllapsedTime: 897.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Moonlight2R.Rcheck |
| Warnings: 0 |
##############################################################################
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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_1.0.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/Moonlight2R.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-apple-darwin20 (64-bit)
* 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 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Moonlight2R/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Moonlight2R’ version ‘1.0.0’
* 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 ‘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 R 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
plotMoonlight 12.677 0.770 14.132
LiftMAF 6.904 1.080 9.214
plotDMA 7.298 0.478 8.387
getDataGEO 5.087 1.333 7.173
GLS 0.081 0.043 6.564
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
Moonlight2R.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Moonlight2R ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-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 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (64-bit)
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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[ FAIL 0 | WARN 1 | SKIP 0 | PASS 40 ]
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 40 ]
>
> proc.time()
user system elapsed
87.305 10.626 106.770
Moonlight2R.Rcheck/Moonlight2R-Ex.timings
| name | user | system | elapsed | |
| DMA | 0.000 | 0.001 | 0.001 | |
| FEA | 1.759 | 0.033 | 1.891 | |
| GLS | 0.081 | 0.043 | 6.564 | |
| GRN | 0.078 | 0.009 | 0.087 | |
| GSEA | 2.704 | 0.174 | 3.020 | |
| LPA | 0.361 | 0.011 | 0.392 | |
| LiftMAF | 6.904 | 1.080 | 9.214 | |
| MAFtoCscape | 0.086 | 0.011 | 0.101 | |
| PRA | 0.323 | 0.019 | 0.360 | |
| PRAtoTibble | 0.071 | 0.014 | 0.088 | |
| RunCscape_somatic | 0.000 | 0.001 | 0.000 | |
| URA | 4.372 | 0.168 | 4.710 | |
| confidence | 0.001 | 0.000 | 0.001 | |
| getDataGEO | 5.087 | 1.333 | 7.173 | |
| moonlight | 0.000 | 0.001 | 0.001 | |
| plotCircos | 1.664 | 0.095 | 1.844 | |
| plotDMA | 7.298 | 0.478 | 8.387 | |
| plotFEA | 0.667 | 0.026 | 0.703 | |
| plotMoonlight | 12.677 | 0.770 | 14.132 | |
| plotNetworkHive | 0.061 | 0.009 | 0.080 | |
| plotURA | 0.391 | 0.026 | 0.423 | |
| tabix_func | 0.001 | 0.000 | 0.000 | |