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CHECK report for MoonlightR on merida1

This page was generated on 2019-03-11 11:42:07 -0400 (Mon, 11 Mar 2019).

Package 990/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MoonlightR 1.8.0
Antonio Colaprico
Snapshot Date: 2019-03-10 17:02:16 -0400 (Sun, 10 Mar 2019)
URL: https://git.bioconductor.org/packages/MoonlightR
Branch: RELEASE_3_8
Last Commit: 5a26351
Last Changed Date: 2018-10-30 11:42:02 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  ERROR  OK  ERROR  ERROR 
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: MoonlightR
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MoonlightR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MoonlightR_1.8.0.tar.gz
StartedAt: 2019-03-11 01:31:11 -0400 (Mon, 11 Mar 2019)
EndedAt: 2019-03-11 01:39:02 -0400 (Mon, 11 Mar 2019)
EllapsedTime: 471.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: MoonlightR.Rcheck
Warnings: 1

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MoonlightR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MoonlightR_1.8.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/MoonlightR.Rcheck’
* using R version 3.5.2 Patched (2018-12-20 r75875)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.8.0’
* 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 ... WARNING
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Users/biocbuild/bbs-3.8-bioc/meat/MoonlightR.Rcheck/00install.out’ for details.
* 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 or elapsed time > 5s
      user system elapsed
URA 23.046  2.185  20.417
FEA  6.330  0.544   6.894
DPA  5.743  0.375   6.167
* 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: 1 WARNING
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/MoonlightR.Rcheck/00check.log’
for details.



Installation output

MoonlightR.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL MoonlightR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘MoonlightR’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in rgl.init(initValue, onlyNULL) :
  RGL: GLX extension missing on server
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
* DONE (MoonlightR)

Tests output


Example timings

MoonlightR.Rcheck/MoonlightR-Ex.timings

nameusersystemelapsed
DPA5.7430.3756.167
FEA6.3300.5446.894
GRN4.7370.1950.353
GSEA0.0010.0010.000
LPA0.3810.8601.053
PRA0.0030.0010.004
URA23.046 2.18520.417
getDataGEO000
getDataTCGA0.0000.0000.001
moonlight4.1150.3924.638
plotCircos0.9700.0781.042
plotFEA1.9180.1112.025
plotNetworkHive0.1780.0180.195
plotURA0.1180.0110.128