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CHECK report for MEAL on tokay1

This page was generated on 2019-04-13 11:25:59 -0400 (Sat, 13 Apr 2019).

Package 903/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MEAL 1.12.0
Carlos Ruiz-Arenas
Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019)
URL: https://git.bioconductor.org/packages/MEAL
Branch: RELEASE_3_8
Last Commit: e663698
Last Changed Date: 2018-10-30 11:41:59 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  TIMEOUT  skipped  skipped 

Summary

Package: MEAL
Version: 1.12.0
Command: C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MEAL.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings MEAL_1.12.0.tar.gz
StartedAt: 2019-04-13 03:35:48 -0400 (Sat, 13 Apr 2019)
EndedAt: 2019-04-13 03:46:41 -0400 (Sat, 13 Apr 2019)
EllapsedTime: 652.6 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: MEAL.Rcheck
Warnings: 3

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MEAL.install-out.txt --library=C:\Users\biocbuild\bbs-3.8-bioc\R\library --no-vignettes --timings MEAL_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.8-bioc/meat/MEAL.Rcheck'
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MEAL/DESCRIPTION' ... OK
* this is package 'MEAL' version '1.12.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 whether package 'MEAL' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp655KZP/R.INSTALL259c244b3c32/MEAL/man/runRDA.Rd:45: file link 'rda' in package 'vegan' does not exist and so has been treated as a topic
See 'C:/Users/biocbuild/bbs-3.8-bioc/meat/MEAL.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 ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... NOTE
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 colData data dmrcatedata mcols<- 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... WARNING
Found the following significant warnings:

  Warning: 'calculateRelevantSNPs' is deprecated.
  Warning: 'correlationMethSNPs' is deprecated.
  Warning: 'explainedVariance' is deprecated.
  Warning: 'normalSNP' is deprecated.
  Warning: 'plotLM' 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 15.89   2.25   18.14
** running examples for arch 'x64' ... WARNING
Found the following significant warnings:

  Warning: 'calculateRelevantSNPs' is deprecated.
  Warning: 'correlationMethSNPs' is deprecated.
  Warning: 'explainedVariance' is deprecated.
  Warning: 'normalSNP' is deprecated.
  Warning: 'plotLM' 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 23.39   0.89   24.28
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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: 3 WARNINGs, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.8-bioc/meat/MEAL.Rcheck/00check.log'
for details.



Installation output

MEAL.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/MEAL_1.12.0.tar.gz && rm -rf MEAL.buildbin-libdir && mkdir MEAL.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MEAL.buildbin-libdir MEAL_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL MEAL_1.12.0.zip && rm MEAL_1.12.0.tar.gz MEAL_1.12.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 51956  100 51956    0     0   935k      0 --:--:-- --:--:-- --:--:--  994k

install for i386

* installing *source* package 'MEAL' ...
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'MEAL'
    finding HTML links ... done
    MEAL-defunct                            html  
    MEAL                                    html  
    calculateRelevantSNPs                   html  
    computeRDAR2                            html  
    correlationMethExprs                    html  
    correlationMethSNPs                     html  
    explainedVariance                       html  
    exportResults                           html  
    filterResults                           html  
    getGeneVals                             html  
    getProbeResults                         html  
    getRDAresults                           html  
    normalSNP                               html  
    plotFeature                             html  
    plotLM                                  html  
    plotRDA                                 html  
    plotRegion                              html  
    runBlockFinder                          html  
    runBumphunter                           html  
    runDMRcate                              html  
    runDiffMeanAnalysis                     html  
    runDiffVarAnalysis                      html  
    runPipeline                             html  
    runRDA                                  html  
Rd warning: C:/Users/biocbuild/bbs-3.8-bioc/tmpdir/Rtmp655KZP/R.INSTALL259c244b3c32/MEAL/man/runRDA.Rd:45: file link 'rda' in package 'vegan' does not exist and so has been treated as a topic
    runRegionAnalysis                       html  
    topRDAhits                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'MEAL' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MEAL' as MEAL_1.12.0.zip
* DONE (MEAL)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'MEAL' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

MEAL.Rcheck/tests_i386/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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, basename, cbind, colMeans, colSums, colnames,
    dirname, 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: 48 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  50.46    6.75   57.56 

MEAL.Rcheck/tests_x64/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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, basename, cbind, colMeans, colSums, colnames,
    dirname, 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: 50 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  48.78    2.23   51.07 

Example timings

MEAL.Rcheck/examples_i386/MEAL-Ex.timings

nameusersystemelapsed
calculateRelevantSNPs000
correlationMethSNPs000
explainedVariance000
exportResults15.89 2.2518.14
getGeneVals000
normalSNP000
plotFeature1.140.701.84
plotLM000
plotRDA1.170.481.66
runDiffMeanAnalysis0.450.050.50
runDiffVarAnalysis0.720.060.78
runPipeline0.830.030.86
runRDA0.770.050.81
runRegionAnalysis0.840.060.91
topRDAhits0.530.000.54

MEAL.Rcheck/examples_x64/MEAL-Ex.timings

nameusersystemelapsed
calculateRelevantSNPs000
correlationMethSNPs000
explainedVariance000
exportResults23.39 0.8924.28
getGeneVals000
normalSNP000
plotFeature1.310.031.34
plotLM000
plotRDA1.020.081.09
runDiffMeanAnalysis0.940.131.07
runDiffVarAnalysis0.670.030.70
runPipeline1.810.141.95
runRDA1.030.051.08
runRegionAnalysis1.410.091.50
topRDAhits1.120.021.14