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CHECK report for MoonlightR on malbec2

This page was generated on 2020-10-17 11:55:12 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE MoonlightR PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1120/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MoonlightR 1.14.1
Antonio Colaprico
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/MoonlightR
Branch: RELEASE_3_11
Last Commit: 2e5f494
Last Changed Date: 2020-07-08 15:40:46 -0400 (Wed, 08 Jul 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: MoonlightR
Version: 1.14.1
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:MoonlightR.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings MoonlightR_1.14.1.tar.gz
StartedAt: 2020-10-17 03:22:58 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 03:29:45 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 406.7 seconds
RetCode: 0
Status:  OK 
CheckDir: MoonlightR.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:MoonlightR.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings MoonlightR_1.14.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/MoonlightR.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MoonlightR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MoonlightR’ version ‘1.14.1’
* 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 ‘MoonlightR’ 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
URA       18.884  0.642  14.998
FEA       17.037  0.431  17.380
plotFEA   11.117  0.439  11.485
DPA        7.044  0.078   7.120
moonlight  6.091  0.067   6.158
* 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


Installation output

MoonlightR.Rcheck/00install.out

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### Running command:
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###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL MoonlightR
###
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘MoonlightR’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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 (MoonlightR)

Tests output


Example timings

MoonlightR.Rcheck/MoonlightR-Ex.timings

nameusersystemelapsed
DPA7.0440.0787.120
FEA17.037 0.43117.380
GRN4.9410.0080.602
GSEA0.0010.0000.000
LPA0.0020.0000.002
PRA0.0020.0000.002
URA18.884 0.64214.998
getDataGEO000
getDataTCGA0.0000.0000.001
moonlight6.0910.0676.158
plotCircos0.9830.1291.093
plotFEA11.117 0.43911.485
plotNetworkHive0.0880.0000.087
plotURA0.0890.0040.092