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BioC 3.5: CHECK report for MEAL on oaxaca

This page was generated on 2016-11-20 16:27:58 -0500 (Sun, 20 Nov 2016).

Package 725/1294HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MEAL 1.5.0
Carlos Ruiz
Snapshot Date: 2016-11-19 17:15:22 -0500 (Sat, 19 Nov 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MEAL
Last Changed Rev: 122712 / Revision: 124290
Last Changed Date: 2016-10-17 15:10:43 -0400 (Mon, 17 Oct 2016)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: MEAL
Version: 1.5.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MEAL_1.5.0.tar.gz
StartedAt: 2016-11-20 03:21:16 -0800 (Sun, 20 Nov 2016)
EndedAt: 2016-11-20 03:32:31 -0800 (Sun, 20 Nov 2016)
EllapsedTime: 675.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: MEAL.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MEAL_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/MEAL.Rcheck’
* using R Under development (unstable) (2016-10-21 r71549)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MEAL/DESCRIPTION’ ... OK
* this is package ‘MEAL’ version ‘1.5.0’
* 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 ‘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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'multiCorrMethExprs'
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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
plotRegion-methods 61.085  0.916  62.053
plotRDA-methods    56.371  0.889  57.290
topRDAhits-methods 54.811  0.943  55.788
DAPipeline         16.484  0.878  17.890
DARegionAnalysis    4.896  0.210   5.227
* 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 WARNING
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-class0.0030.0010.002
AnalysisResults-class0.0010.0000.001
DAPipeline16.484 0.87817.890
DAProbe0.9820.0391.023
DARegion4.0140.1194.137
DARegionAnalysis4.8960.2105.227
RDAset3.3850.0813.468
calculateRelevantSNPs0.0010.0000.001
createRanges0.0150.0000.016
explainedVariance0.0310.0020.032
exportResults-methods3.2500.0553.306
filterSet-methods2.4110.0452.456
getGeneVals-methods3.3020.0983.401
normalSNP0.0010.0000.001
plotBestFeatures3.2790.0523.332
plotEWAS-methods3.8320.0503.884
plotFeature3.1680.0583.238
plotLM0.2500.0060.261
plotQQ-methods3.8270.0673.896
plotRDA-methods56.371 0.88957.290
plotRegion-methods61.085 0.91662.053
plotVolcano-methods3.9940.2124.209
preparePhenotype0.0030.0000.004
topRDAhits-methods54.811 0.94355.788