##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MAGAR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings MAGAR_1.3.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/MAGAR.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MAGAR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MAGAR' version '1.3.0'
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'MAGAR' 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 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
getOverlapUniverse: warning in overlapQTLs(meth.qtl.res = meth.qtl.res,
  type = type): partial argument match of 'meth.qtl.res' to
  'meth.qtl.result.list'
doGenoImport: no visible global function definition for
  'makeGRangesFromDataFrame'
doGenoImport: no visible global function definition for
  'seqlevelsStyle<-'
doGenoImport: no visible global function definition for 'findOverlaps'
doGenoImport: no visible global function definition for 'ggplot'
doGenoImport: no visible global function definition for 'aes'
doGenoImport: no visible binding for global variable 'PC1'
doGenoImport: no visible binding for global variable 'PC2'
doGenoImport: no visible global function definition for 'geom_point'
doGenoImport: no visible global function definition for 'xlab'
doGenoImport: no visible global function definition for 'ylab'
doGenoImport: no visible global function definition for 'theme_bw'
doGenoImport: no visible global function definition for 'theme'
doGenoImport: no visible global function definition for 'element_blank'
doGenoImport: no visible global function definition for 'element_text'
doGenoImport: no visible global function definition for 'element_line'
doGenoImport: no visible global function definition for 'ggsave'
doGenoImportIDAT: no visible global function definition for
  'featureData'
doGenoImportIDAT: no visible global function definition for
  'featureNames'
doGenoImportIDAT: no visible global function definition for
  'chromosome'
doGenoImportIDAT: no visible global function definition for 'calls'
doGenoImportIDAT: no visible global function definition for
  'makeGRangesFromDataFrame'
doGenoImportIDAT: no visible global function definition for 'GRanges'
doGenoImportIDAT: no visible global function definition for 'Rle'
doGenoImportIDAT: no visible global function definition for 'IRanges'
doGenoImportIDAT: no visible global function definition for
  'findOverlaps'
doGenoImportIDAT: no visible global function definition for 'queryHits'
doGenoImportIDAT: no visible global function definition for
  'subjectHits'
doGenoImportImputed: no visible global function definition for 'ggplot'
doGenoImportImputed: no visible global function definition for 'aes'
doGenoImportImputed: no visible binding for global variable 'PC1'
doGenoImportImputed: no visible binding for global variable 'PC2'
doGenoImportImputed: no visible global function definition for
  'geom_point'
doGenoImportImputed: no visible global function definition for 'xlab'
doGenoImportImputed: no visible global function definition for 'ylab'
doGenoImportImputed: no visible global function definition for
  'theme_bw'
doGenoImportImputed: no visible global function definition for 'theme'
doGenoImportImputed: no visible global function definition for
  'element_blank'
doGenoImportImputed: no visible global function definition for
  'element_text'
doGenoImportImputed: no visible global function definition for
  'element_line'
doGenoImportImputed: no visible global function definition for 'ggsave'
doImport: no visible binding for global variable 'anno'
doMethImport: no visible global function definition for 'GRanges'
doMethImport: no visible global function definition for 'Rle'
doMethImport: no visible global function definition for 'IRanges'
doMethImport: no visible global function definition for
  'makeGRangesFromDataFrame'
doMethImport: no visible global function definition for 'findOverlaps'
doMethImport: no visible global function definition for 'queryHits'
doMethQTLChromosome: no visible global function definition for 'ggplot'
doMethQTLChromosome: no visible global function definition for 'aes'
doMethQTLChromosome: no visible binding for global variable 'Size'
doMethQTLChromosome: no visible binding for global variable '..count..'
doMethQTLChromosome: no visible global function definition for
  'geom_histogram'
doMethQTLChromosome: no visible global function definition for
  'geom_vline'
doMethQTLChromosome: no visible global function definition for
  'theme_bw'
doMethQTLChromosome: no visible global function definition for 'theme'
doMethQTLChromosome: no visible global function definition for
  'element_blank'
doMethQTLChromosome: no visible global function definition for
  'element_text'
doMethQTLChromosome: no visible global function definition for
  'element_line'
doMethQTLChromosome: no visible global function definition for 'ggsave'
doMethQTLChromosome: no visible global function definition for
  'mclapply'
getOverlapUniverse: no visible global function definition for
  'makeGRangesFromDataFrame'
qtlAnnotationEnrichment: no visible global function definition for
  'findOverlaps'
qtlCorrelateCorBlockStat: no visible global function definition for
  'ggplot'
qtlCorrelateCorBlockStat: no visible global function definition for
  'aes_string'
qtlCorrelateCorBlockStat: no visible global function definition for
  'geom_point'
qtlCorrelateCorBlockStat: no visible global function definition for
  'geom_smooth'
qtlCorrelateCorBlockStat: no visible global function definition for
  'ggtitle'
qtlCorrelateCorBlockStat: no visible global function definition for
  'ylab'
qtlDistanceScatterplot: no visible global function definition for
  'ggplot'
qtlDistanceScatterplot: no visible global function definition for 'aes'
qtlDistanceScatterplot: no visible binding for global variable
  'Distance'
qtlDistanceScatterplot: no visible binding for global variable
  'P.value'
qtlDistanceScatterplot: no visible global function definition for
  'geom_point'
qtlDistanceScatterplot: no visible global function definition for
  'ggtitle'
qtlDistanceScatterplot: no visible global function definition for
  'xlab'
qtlDistanceScatterplot: no visible global function definition for
  'ylab'
qtlDistanceScatterplot: no visible binding for global variable 'Beta'
qtlDistanceScatterplot: no visible global function definition for
  'labs'
qtlDistanceScatterplot: no visible global function definition for
  'scale_color_gradient2'
qtlDistanceScatterplot: no visible global function definition for
  'scale_color_continuous'
qtlDistanceScatterplot: no visible global function definition for
  'annotate'
qtlDistanceScatterplot: no visible global function definition for
  'ggsave'
qtlLOLAEnrichment: no visible global function definition for
  'loadRegionDB'
qtlLOLAEnrichment: no visible global function definition for 'runLOLA'
qtlPlotAnnotationEnrichment: no visible global function definition for
  'ggplot'
qtlPlotAnnotationEnrichment: no visible global function definition for
  'aes'
qtlPlotAnnotationEnrichment: no visible binding for global variable
  'Type'
qtlPlotAnnotationEnrichment: no visible binding for global variable
  'Annotation'
qtlPlotAnnotationEnrichment: no visible binding for global variable
  'OddsRatio'
qtlPlotAnnotationEnrichment: no visible global function definition for
  'geom_tile'
qtlPlotAnnotationEnrichment: no visible global function definition for
  'scale_fill_gradient2'
qtlPlotBaseSubstitution: no visible global function definition for
  'ggplot'
qtlPlotBaseSubstitution: no visible global function definition for
  'aes'
qtlPlotBaseSubstitution: no visible binding for global variable
  'Substitution'
qtlPlotBaseSubstitution: no visible binding for global variable
  'OddsRatio'
qtlPlotBaseSubstitution: no visible global function definition for
  'geom_tile'
qtlPlotBaseSubstitution: no visible global function definition for
  'scale_fill_gradient2'
qtlPlotClusterSize: no visible global function definition for 'ggplot'
qtlPlotClusterSize: no visible global function definition for 'aes'
qtlPlotClusterSize: no visible binding for global variable 'Size'
qtlPlotClusterSize: no visible binding for global variable '..count..'
qtlPlotClusterSize: no visible global function definition for
  'geom_histogram'
qtlPlotSNPCorrelationBlock: no visible global function definition for
  'ggplot'
qtlPlotSNPCorrelationBlock: no visible global function definition for
  'aes'
qtlPlotSNPCorrelationBlock: no visible binding for global variable
  'SNP'
qtlPlotSNPCorrelationBlock: no visible binding for global variable
  'CpG'
qtlPlotSNPCorrelationBlock: no visible global function definition for
  'geom_point'
qtlPlotSNPCorrelationBlock: no visible binding for global variable
  'Representative'
qtlPlotSNPCorrelationBlock: no visible global function definition for
  'geom_smooth'
qtlPlotSNPCorrelationBlock: no visible global function definition for
  'facet_grid'
qtlPlotSNPCorrelationBlock: no visible global function definition for
  'theme'
qtlPlotSNPCorrelationBlock: no visible global function definition for
  'scale_color_manual'
qtlPlotSNPCpGInteraction: no visible global function definition for
  'ggplot'
qtlPlotSNPCpGInteraction: no visible global function definition for
  'aes'
qtlPlotSNPCpGInteraction: no visible binding for global variable 'SNP'
qtlPlotSNPCpGInteraction: no visible binding for global variable 'CpG'
qtlPlotSNPCpGInteraction: no visible global function definition for
  'geom_boxplot'
qtlPlotSNPCpGInteraction: no visible global function definition for
  'theme_bw'
qtlPlotSNPCpGInteraction: no visible global function definition for
  'ylab'
qtlPlotSNPCpGInteraction: no visible global function definition for
  'xlab'
qtlPlotSNPCpGInteraction: no visible global function definition for
  'ggsave'
qtlPlotSNPCpGInteraction: no visible binding for global variable
  'SNPDosage'
qtlPlotSNPCpGInteraction: no visible global function definition for
  'geom_point'
qtlPlotSNPCpGInteraction: no visible global function definition for
  'geom_smooth'
Undefined global functions or variables:
  ..count.. Annotation Beta CpG Distance GRanges IRanges OddsRatio
  P.value PC1 PC2 Representative Rle SNP SNPDosage Size Substitution
  Type aes aes_string anno annotate calls chromosome element_blank
  element_line element_text facet_grid featureData featureNames
  findOverlaps geom_boxplot geom_histogram geom_point geom_smooth
  geom_tile geom_vline ggplot ggsave ggtitle labs loadRegionDB
  makeGRangesFromDataFrame mclapply queryHits runLOLA
  scale_color_continuous scale_color_gradient2 scale_color_manual
  scale_fill_gradient2 seqlevelsStyle<- subjectHits theme theme_bw xlab
  ylab
* 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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
doMethQTLChromosome 9.29   0.16    9.68
doMethQTL           8.77   0.56    9.53
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'runTests.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: 2 NOTEs
See
  'D:/biocbuild/bbs-3.15-bioc/meat/MAGAR.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL MAGAR
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'MAGAR' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
No methods found in package 'oligoClasses' for request: 'mean' when loading 'crlmm'
** help
*** installing help indices
  converting help for package 'MAGAR'
    finding HTML links ... done
    MethQTLInput-class                      html  
    finding level-2 HTML links ... done

    MethQTLResult-class                     html  
    QTL.OPTIONS                             html  
    computeCorrelationBlocks                html  
    doImport                                html  
    doMethQTL                               html  
    doMethQTLChromosome                     html  
    filterPval                              html  
    getAnno                                 html  
    getCorrelationBlocks                    html  
    getGeno                                 html  
    getMethData                             html  
    getOverlapUniverse                      html  
    getOverlappingQTL                       html  
    getPheno                                html  
    getResult                               html  
    getResultGWASMap                        html  
    getSamples                              html  
    getSpecificQTL                          html  
    imputeMeth                              html  
    joinMethQTLResult                       html  
    loadMethQTLInput                        html  
    loadMethQTLResult                       html  
    overlapInputs                           html  
    overlapQTLs                             html  
    qtlAnnotationEnrichment                 html  
    qtlBaseSubstitutionEnrichment           html  
    qtlDistanceScatterplot                  html  
    qtlGetOption                            html  
    qtlJSON2options                         html  
    qtlManhattanPlot                        html  
    qtlOptions2JSON                         html  
    qtlPlotBaseSubstitution                 html  
    qtlPlotClusterSize                      html  
    qtlPlotSNPCpGInteraction                html  
    qtlSetOption                            html  
    qtlTFBSMotifEnrichment                  html  
    qtlUpSetPlotCorBlocks                   html  
    qtlUpSetPlotTagCpGs                     html  
    qtlUpsetPlot                            html  
    qtlVennPlot                             html  
    saveMethQTLInput                        html  
    saveMethQTLResult                       html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
No methods found in package 'oligoClasses' for request: 'mean' when loading 'crlmm'
** testing if installed package can be loaded from final location
No methods found in package 'oligoClasses' for request: 'mean' when loading 'crlmm'
** testing if installed package keeps a record of temporary installation path
* DONE (MAGAR)
Making 'packages.html' ... done

R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 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.

> BiocGenerics:::testPackage("MAGAR")

Attaching package: 'BiocGenerics'

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, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min


Attaching package: 'MatrixGenerics'

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

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars


Attaching package: 'S4Vectors'

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

    expand, unname

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

    I, expand.grid, unname


Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows


Attaching package: 'DelayedArray'

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

    aperm, apply, rowsum, scale, sweep


Attaching package: 'HDF5Array'

The following object is masked from 'package:rhdf5':

    h5ls


Attaching package: 'bit'

The following object is masked from 'package:base':

    xor

Attaching package ff
- getOption("fftempdir")=="D:/biocbuild/bbs-3.15-bioc/tmpdir/RtmpAr4znb/ff"

- getOption("ffextension")=="ff"

- getOption("ffdrop")==TRUE

- getOption("fffinonexit")==TRUE

- getOption("ffpagesize")==65536

- getOption("ffcaching")=="mmnoflush"  -- consider "ffeachflush" if your system stalls on large writes

- getOption("ffbatchbytes")==16777216 -- consider a different value for tuning your system

- getOption("ffmaxbytes")==536870912 -- consider a different value for tuning your system


Attaching package: 'ff'

The following object is masked from 'package:DelayedArray':

    maxlength

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

    write.csv, write.csv2

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

    is.factor, is.ordered

Spam version 2.8-0 (2022-01-05) is loaded.
Type 'help( Spam)' or 'demo( spam)' for a short introduction 
and overview of this package.
Help for individual functions is also obtained by adding the
suffix '.spam' to the function name, e.g. 'help( chol.spam)'.

Attaching package: 'spam'

The following object is masked from 'package:Matrix':

    det

The following object is masked from 'package:stats4':

    mle

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

    backsolve, forwardsolve


Try help(fields) to get started.

Attaching package: 'gplots'

The following object is masked from 'package:IRanges':

    space

The following object is masked from 'package:S4Vectors':

    space

The following object is masked from 'package:stats':

    lowess


Attaching package: 'grid'

The following object is masked from 'package:ff':

    pattern


Attaching package: 'gridExtra'

The following object is masked from 'package:BiocGenerics':

    combine


Attaching package: 'limma'

The following object is masked from 'package:BiocGenerics':

    plotMA

Welcome to Bioconductor

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


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

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

    anyMissing, rowMedians


Attaching package: 'scales'

The following object is masked from 'package:viridis':

    viridis_pal


Attaching package: 'AnnotationDbi'

The following object is masked from 'package:MASS':

    select



Attaching package: 'Biostrings'

The following object is masked from 'package:grid':

    pattern

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

    mismatch, pattern

The following object is masked from 'package:base':

    strsplit

locfit 1.5-9.5 	 2022-03-01
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)

Attaching package: 'plyr'

The following object is masked from 'package:XVector':

    compact

The following object is masked from 'package:IRanges':

    desc

The following object is masked from 'package:S4Vectors':

    rename

The following object is masked from 'package:matrixStats':

    count

Welcome to oligoClasses version 1.57.0

Attaching package: 'oligoClasses'

The following object is masked from 'package:minfi':

    getM

No methods found in package 'oligoClasses' for request: 'mean' when loading 'crlmm'
Welcome to crlmm version 1.53.0

Attaching package: 'MAGAR'

The following object is masked from 'package:foreach':

    getResult

2022-03-17 19:34:15     Inf  STATUS STARTED Unit Testing
2022-03-17 19:34:15     Inf  STATUS     STARTED Testing constructors
Object of class MethQTLInput
	 Contains 3 samples
	 Methylation data for 5 CpGs
	 Genotyping data for 4 SNPs
	 Genome assembly: hg19 
Object of class MethQTLResult
	 Contains 10 methQTL
	 Contains 0 correlation blocks
	 methQTL called using classical.linear 
	 representative CpGs computed with row.medians 
2022-03-17 19:34:15     Inf  STATUS     COMPLETED Testing constructors
2022-03-17 19:34:15     Inf  STATUS     STARTED Testing options
2022-03-17 19:34:15     Inf  STATUS     COMPLETED Testing options
2022-03-17 19:34:15     Inf  STATUS     STARTED Testing cor blocks
2022-03-17 19:34:15     Inf  STATUS         STARTED Compute correlation blocks
2022-03-17 19:34:15     Inf  STATUS             STARTED Compute correlation matrix
2022-03-17 19:34:15     Inf  STATUS             COMPLETED Compute correlation matrix
2022-03-17 19:34:15     Inf  STATUS             STARTED Compute pairwise distances
2022-03-17 19:34:16     Inf  STATUS             COMPLETED Compute pairwise distances
2022-03-17 19:34:17     Inf  STATUS             STARTED Weight distances
2022-03-17 19:34:17     Inf  STATUS             COMPLETED Weight distances
2022-03-17 19:34:18     Inf  STATUS             STARTED Compute graph
2022-03-17 19:34:18     Inf  STATUS             COMPLETED Compute graph
2022-03-17 19:34:18     Inf  STATUS             STARTED Compute clustering
2022-03-17 19:34:18     Inf  STATUS             COMPLETED Compute clustering
2022-03-17 19:34:18     Inf  STATUS         COMPLETED Compute correlation blocks
2022-03-17 19:34:18     Inf  STATUS     COMPLETED Testing cor blocks
2022-03-17 19:34:18     Inf  STATUS     STARTED Test methQTL calling
2022-03-17 19:34:19     Inf    INFO         Loading default option setting
2022-03-17 19:34:19     Inf  STATUS         STARTED Imputation procedure knn 
2022-03-17 19:34:19     Inf  STATUS         COMPLETED Imputation procedure knn 
2022-03-17 19:34:19     Inf  STATUS         STARTED Computing methQTLs
2022-03-17 19:34:19     Inf  STATUS             STARTED Computing methQTL for chromosome chr18
2022-03-17 19:34:19     Inf  STATUS                 STARTED Compute methQTL per correlation block
2022-03-17 19:34:19     Inf  STATUS                     STARTED Setting up Multicore
2022-03-17 19:34:19     Inf    INFO                         Using 1 cores
2022-03-17 19:34:19     Inf  STATUS                     COMPLETED Setting up Multicore
2022-03-17 19:34:19     Inf  STATUS                 COMPLETED Compute methQTL per correlation block
2022-03-17 19:34:19     Inf  STATUS             COMPLETED Computing methQTL for chromosome chr18
2022-03-17 19:34:20     Inf  STATUS         COMPLETED Computing methQTLs
2022-03-17 19:34:20     Inf  STATUS     COMPLETED Test methQTL calling
2022-03-17 19:34:20     Inf  STATUS COMPLETED Unit Testing

Object of class MethQTLInput
	 Contains 3 samples
	 Methylation data for 5 CpGs
	 Genotyping data for 4 SNPs
	 Genome assembly: hg19 
Object of class MethQTLResult
	 Contains 10 methQTL
	 Contains 0 correlation blocks
	 methQTL called using classical.linear 
	 representative CpGs computed with row.medians 
2022-03-17 19:34:20     Inf    INFO Loading default option setting
2022-03-17 19:34:20     Inf  STATUS STARTED Imputation procedure knn 
2022-03-17 19:34:20     Inf  STATUS COMPLETED Imputation procedure knn 

2022-03-17 19:34:21     Inf  STATUS STARTED Computing methQTLs
2022-03-17 19:34:21     Inf  STATUS     STARTED Computing methQTL for chromosome chr18
2022-03-17 19:34:21     Inf  STATUS         STARTED Compute methQTL per correlation block
2022-03-17 19:34:21     Inf  STATUS             STARTED Setting up Multicore
2022-03-17 19:34:21     Inf    INFO                 Using 1 cores
2022-03-17 19:34:21     Inf  STATUS             COMPLETED Setting up Multicore
2022-03-17 19:34:21     Inf  STATUS         COMPLETED Compute methQTL per correlation block
2022-03-17 19:34:21     Inf  STATUS     COMPLETED Computing methQTL for chromosome chr18
2022-03-17 19:34:22     Inf  STATUS COMPLETED Computing methQTLs

2022-03-17 19:34:22     Inf  STATUS STARTED Compute correlation blocks
2022-03-17 19:34:22     Inf  STATUS     STARTED Compute correlation matrix
2022-03-17 19:34:22     Inf  STATUS     COMPLETED Compute correlation matrix
2022-03-17 19:34:22     Inf  STATUS     STARTED Compute pairwise distances
2022-03-17 19:34:23     Inf  STATUS     COMPLETED Compute pairwise distances
2022-03-17 19:34:24     Inf  STATUS     STARTED Weight distances
2022-03-17 19:34:24     Inf  STATUS     COMPLETED Weight distances
2022-03-17 19:34:25     Inf  STATUS     STARTED Compute graph
2022-03-17 19:34:25     Inf  STATUS     COMPLETED Compute graph
2022-03-17 19:34:25     Inf  STATUS     STARTED Compute clustering
2022-03-17 19:34:26     Inf  STATUS     COMPLETED Compute clustering
2022-03-17 19:34:26     Inf  STATUS COMPLETED Compute correlation blocks



RUNIT TEST PROTOCOL -- Thu Mar 17 19:34:26 2022 
*********************************************** 
Number of test functions: 4 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
MAGAR RUnit Tests - 4 test functions, 0 errors, 0 failures
Number of test functions: 4 
Number of errors: 0 
Number of failures: 0 
There were 50 or more warnings (use warnings() to see the first 50)
> 
> proc.time()
   user  system elapsed 
  24.28    1.21   26.03