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BioC 3.5: CHECK report for MEAL on malbec2

This page was generated on 2017-08-16 13:17:00 -0400 (Wed, 16 Aug 2017).

Package 773/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MEAL 1.6.0
Carlos Ruiz-Arenas
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/MEAL
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -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: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings MEAL_1.6.0.tar.gz
StartedAt: 2017-08-16 00:23:46 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 00:34:14 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 628.2 seconds
RetCode: 0
Status:  OK 
CheckDir: MEAL.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings MEAL_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/MEAL.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (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
topRDAhits-methods 44.208  0.244  44.484
plotRegion-methods 42.168  0.144  42.344
plotRDA-methods    41.168  0.132  41.358
DAPipeline         19.480  3.132  24.303
DARegion            5.748  0.376   6.179
* 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
  ‘/home/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-class0.0040.0000.003
AnalysisResults-class0.0000.0000.002
DAPipeline19.480 3.13224.303
DAProbe0.9040.1681.075
DARegion5.7480.3766.179
DARegionAnalysis3.1680.3483.666
RDAset1.3360.1841.520
calculateRelevantSNPs000
createRanges0.0160.0000.019
explainedVariance0.0240.0000.024
exportResults-methods2.1640.0082.173
filterSet-methods0.8400.0000.839
getGeneVals-methods2.4440.1042.550
normalSNP0.0040.0000.001
plotBestFeatures2.6360.0002.639
plotEWAS-methods2.2240.0082.235
plotFeature1.4640.0601.525
plotLM0.2480.0000.249
plotQQ-methods2.7600.0002.757
plotRDA-methods41.168 0.13241.358
plotRegion-methods42.168 0.14442.344
plotVolcano-methods2.4960.0042.501
prepareMethylationSet1.1840.0001.184
preparePhenotype0.0000.0000.003
topRDAhits-methods44.208 0.24444.484