| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-04-17 11:37:00 -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: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Moonlight2R.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings Moonlight2R_1.0.0.tar.gz |
| StartedAt: 2024-04-16 02:50:52 -0400 (Tue, 16 Apr 2024) |
| EndedAt: 2024-04-16 02:58:51 -0400 (Tue, 16 Apr 2024) |
| EllapsedTime: 479.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Moonlight2R.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Moonlight2R.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings Moonlight2R_1.0.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/Moonlight2R.Rcheck'
* using R version 4.3.3 (2024-02-29 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 12.3.0
GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 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 6.28 0.09 6.37
LiftMAF 4.64 0.68 6.28
plotDMA 4.09 1.00 3.92
getDataGEO 4.35 0.70 6.83
URA 0.43 0.27 22.56
* 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: ### ### F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL Moonlight2R ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.18-bioc/R/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 ucrt) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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
|
| | 0%
|
|= | 1%
|
|= | 2%
|
|== | 3%
|
|=== | 4%
|
|=== | 5%
|
|==== | 6%
|
|===== | 7%
|
|====== | 8%
|
|====== | 9%
|
|======= | 10%
|
|======== | 11%
|
|======== | 12%
|
|========= | 13%
|
|========== | 14%
|
|========== | 15%
|
|=========== | 16%
|
|============ | 17%
|
|============ | 18%
|
|============= | 19%
|
|============== | 20%
|
|=============== | 21%
|
|=============== | 22%
|
|================ | 23%
|
|================= | 24%
|
|================= | 25%
|
|================== | 26%
|
|=================== | 27%
|
|=================== | 28%
|
|==================== | 29%
|
|===================== | 30%
|
|===================== | 31%
|
|====================== | 32%
|
|======================= | 33%
|
|======================== | 34%
|
|======================== | 35%
|
|========================= | 36%
|
|========================== | 37%
|
|========================== | 38%
|
|=========================== | 39%
|
|============================ | 40%
|
|============================ | 41%
|
|============================= | 42%
|
|============================== | 43%
|
|============================== | 44%
|
|=============================== | 45%
|
|================================ | 46%
|
|================================= | 47%
|
|================================= | 48%
|
|================================== | 49%
|
|=================================== | 50%
|
|==================================== | 51%
|
|===================================== | 52%
|
|===================================== | 53%
|
|====================================== | 54%
|
|======================================= | 55%
|
|======================================== | 56%
|
|======================================== | 57%
|
|========================================= | 58%
|
|========================================== | 59%
|
|========================================== | 60%
|
|=========================================== | 61%
|
|============================================ | 62%
|
|============================================ | 63%
|
|============================================= | 64%
|
|============================================== | 65%
|
|============================================== | 66%
|
|=============================================== | 67%
|
|================================================ | 68%
|
|================================================= | 69%
|
|================================================= | 70%
|
|================================================== | 71%
|
|=================================================== | 72%
|
|=================================================== | 73%
|
|==================================================== | 74%
|
|===================================================== | 75%
|
|===================================================== | 76%
|
|====================================================== | 77%
|
|======================================================= | 78%
|
|======================================================= | 79%
|
|======================================================== | 80%
|
|========================================================= | 81%
|
|========================================================== | 82%
|
|========================================================== | 83%
|
|=========================================================== | 84%
|
|============================================================ | 85%
|
|============================================================ | 86%
|
|============================================================= | 87%
|
|============================================================== | 88%
|
|============================================================== | 89%
|
|=============================================================== | 90%
|
|================================================================ | 91%
|
|================================================================ | 92%
|
|================================================================= | 93%
|
|================================================================== | 94%
|
|=================================================================== | 95%
|
|=================================================================== | 96%
|
|==================================================================== | 97%
|
|===================================================================== | 98%
|
|===================================================================== | 99%
|
|======================================================================| 100%
Processing PubMed data ............. done!
|
| | 0%
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 40 ]
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 40 ]
>
> proc.time()
user system elapsed
46.62 4.21 73.54
Moonlight2R.Rcheck/Moonlight2R-Ex.timings
| name | user | system | elapsed | |
| DMA | 0 | 0 | 0 | |
| FEA | 1.43 | 0.15 | 1.59 | |
| GLS | 0.02 | 0.02 | 0.31 | |
| GRN | 0.07 | 0.01 | 0.09 | |
| GSEA | 1.19 | 0.10 | 1.40 | |
| LPA | 0.14 | 0.04 | 0.19 | |
| LiftMAF | 4.64 | 0.68 | 6.28 | |
| MAFtoCscape | 0.04 | 0.01 | 0.07 | |
| PRA | 0.13 | 0.02 | 0.14 | |
| PRAtoTibble | 0.03 | 0.01 | 0.04 | |
| RunCscape_somatic | 0 | 0 | 0 | |
| URA | 0.43 | 0.27 | 22.56 | |
| confidence | 0 | 0 | 0 | |
| getDataGEO | 4.35 | 0.70 | 6.83 | |
| moonlight | 0 | 0 | 0 | |
| plotCircos | 0.70 | 0.06 | 0.78 | |
| plotDMA | 4.09 | 1.00 | 3.92 | |
| plotFEA | 0.38 | 0.10 | 0.47 | |
| plotMoonlight | 6.28 | 0.09 | 6.37 | |
| plotNetworkHive | 0.04 | 0.02 | 0.06 | |
| plotURA | 0.19 | 0.01 | 0.22 | |
| tabix_func | 0 | 0 | 0 | |