Back to the "Multiple platform build/check report" A  B  C  D  E  F  G  H  I  J  K  L [M] N  O  P  Q  R  S  T  U  V  W  X  Y  Z 

BioC 3.5: CHECK report for MEAL on veracruz2

This page was generated on 2017-10-18 14:33:40 -0400 (Wed, 18 Oct 2017).

Package 773/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MEAL 1.6.0
Carlos Ruiz-Arenas
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/MEAL
Branch: RELEASE_3_5
Last Commit: f5ed6f3
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: MEAL
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MEAL_1.6.0.tar.gz
StartedAt: 2017-10-18 05:43:38 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 05:56:48 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 790.7 seconds
RetCode: 0
Status:  OK 
CheckDir: MEAL.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MEAL_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/MEAL.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MEAL/DESCRIPTION’ ... OK
* this is package ‘MEAL’ version ‘1.6.0’
* 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 ‘MEAL’ 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 loading without being on the library search path ... 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 ... NOTE
correlationMethSNPs: no visible binding for global variable 'num_cores'
prepareMethylationSet: no visible global function definition for
  'colData'
Undefined global functions or variables:
  colData num_cores
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
plotRDA-methods    57.302  1.406  62.155
plotRegion-methods 55.122  1.301  58.071
topRDAhits-methods 53.787  1.791  60.801
DAPipeline         21.365  1.406  23.454
DARegionAnalysis    6.551  0.492   7.257
DARegion            5.972  0.372   6.514
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/MEAL.Rcheck/00check.log’
for details.


MEAL.Rcheck/00install.out:

* installing *source* package ‘MEAL’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MEAL)

MEAL.Rcheck/MEAL-Ex.timings:

nameusersystemelapsed
AnalysisRegionResults-class0.0030.0010.004
AnalysisResults-class0.0020.0000.003
DAPipeline21.365 1.40623.454
DAProbe0.6700.0680.768
DARegion5.9720.3726.514
DARegionAnalysis6.5510.4927.257
RDAset1.6310.1601.844
calculateRelevantSNPs0.0010.0000.000
createRanges0.0250.0000.026
explainedVariance0.0280.0010.032
exportResults-methods4.0660.3914.581
filterSet-methods0.9940.0261.045
getGeneVals-methods2.9140.4013.407
normalSNP0.0010.0000.001
plotBestFeatures3.5730.1813.860
plotEWAS-methods4.2840.3624.779
plotFeature1.5440.1101.720
plotLM0.3310.0040.346
plotQQ-methods3.4440.4183.977
plotRDA-methods57.302 1.40662.155
plotRegion-methods55.122 1.30158.071
plotVolcano-methods3.0250.3963.510
prepareMethylationSet1.1050.1311.281
preparePhenotype0.0050.0000.006
topRDAhits-methods53.787 1.79160.801