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CHECK report for MEAL on malbec1

This page was generated on 2018-04-12 13:14:08 -0400 (Thu, 12 Apr 2018).

Package 805/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MEAL 1.8.0
Carlos Ruiz-Arenas
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/MEAL
Branch: RELEASE_3_6
Last Commit: 916313b
Last Changed Date: 2017-10-30 12:41:05 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  TIMEOUT  skipped  skipped 

Summary

Package: MEAL
Version: 1.8.0
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings MEAL_1.8.0.tar.gz
StartedAt: 2018-04-12 00:50:58 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 00:57:46 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 408.2 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: MEAL.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings MEAL_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/MEAL.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.8.0’
* 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 ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... NOTE
Missing or unexported object: 'Biobase::assays'
Missing object imported by a ':::' call: 'MultiDataSet:::nrows'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
calculateRelevantSNPs: no visible global function definition for
  'betas'
correlationMethSNPs: no visible binding for global variable 'num_cores'
plotRegion: no visible global function definition for 'data'
plotRegion: no visible binding for global variable 'dmrcatedata'
plotRegion: no visible binding for global variable 'tx.hg19'
plotRegion: no visible binding for global variable 'tx.hg38'
plotRegion: no visible binding for global variable 'tx.mm10'
plotRegion: no visible global function definition for
  'subsetByOverlaps'
plotRegion: no visible global function definition for 'mcols<-'
runBlockFinder: no visible global function definition for 'assays'
runBlockFinder: no visible global function definition for 'colData'
runRDA: no visible global function definition for 'rowData'
runSVA: no visible global function definition for 'resid'
Undefined global functions or variables:
  assays betas colData data dmrcatedata mcols<- num_cores resid rowData
  subsetByOverlaps tx.hg19 tx.hg38 tx.mm10
Consider adding
  importFrom("stats", "resid")
  importFrom("utils", "data")
to your NAMESPACE file.
* 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 ... WARNING
Found the following significant warnings:

  Warning: 'DAPipeline' is deprecated.
  Warning: 'DAProbe' is deprecated.
  Warning: 'DARegion' is deprecated.
  Warning: 'RDAset' is deprecated.
  Warning: 'filterSet' is deprecated.
  Warning: 'plotBestFeatures' is deprecated.
  Warning: 'preparePhenotype' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
                user system elapsed
exportResults 21.992  0.676  23.745
* 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, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/MEAL.Rcheck/00check.log’
for details.



Installation output

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)

Tests output

MEAL.Rcheck/tests/testthat.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(MEAL)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: MultiDataSet
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)


> 
> test_check("MEAL")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 62 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 47.156   1.176  49.485 

Example timings

MEAL.Rcheck/MEAL-Ex.timings

nameusersystemelapsed
DAPipeline0.0000.0000.001
DAProbe0.0040.0000.001
DARegion0.0000.0000.001
DARegionAnalysis0.0000.0000.001
RDAset000
analysisRegionResults000
analysisResults000
calculateRelevantSNPs0.0000.0000.001
createRanges000
explainedVariance0.0240.0040.041
exportResults21.992 0.67623.745
filterSet0.0000.0000.001
getGeneVals000
normalSNP0.0040.0000.001
plotBestFeatures000
plotFeature2.4760.0602.539
plotLM0.7160.0000.715
plotRDA1.2600.0081.271
prepareMethylationSet0.0000.0000.001
preparePhenotype0.0040.0000.001
runDiffMeanAnalysis0.6760.0000.675
runDiffVarAnalysis1.0120.0521.066
runPipeline2.2360.0202.257
runRDA1.4400.0281.468
runRegionAnalysis1.3040.0041.309
topRDAhits0.8360.0160.853