Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-07-12 17:42 -0400 (Fri, 12 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4741
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4483
merida1macOS 12.7.4 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4512
kjohnson1macOS 13.6.6 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4461
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 1146/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MAGAR 1.12.0  (landing page)
Michael Scherer
Snapshot Date: 2024-07-10 14:00 -0400 (Wed, 10 Jul 2024)
git_url: https://git.bioconductor.org/packages/MAGAR
git_branch: RELEASE_3_19
git_last_commit: b5601fa
git_last_commit_date: 2024-04-30 11:31:25 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for MAGAR on kjohnson1

To the developers/maintainers of the MAGAR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MAGAR.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: MAGAR
Version: 1.12.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MAGAR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MAGAR_1.12.0.tar.gz
StartedAt: 2024-07-12 00:05:31 -0400 (Fri, 12 Jul 2024)
EndedAt: 2024-07-12 00:14:35 -0400 (Fri, 12 Jul 2024)
EllapsedTime: 544.8 seconds
RetCode: 0
Status:   OK  
CheckDir: MAGAR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MAGAR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MAGAR_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/MAGAR.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MAGAR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MAGAR’ version ‘1.12.0’
* 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 for sufficient/correct file permissions ... 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 code 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 ... NOTE
Namespace in Imports field not imported from: ‘RnBeads.hg38’
  All declared Imports should be used.
* 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 global function definition for
  ‘after_stat’
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 global function definition for
  ‘after_stat’
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:
  Annotation Beta CpG Distance GRanges IRanges OddsRatio P.value PC1
  PC2 Representative Rle SNP SNPDosage Size Substitution Type aes
  aes_string after_stat 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
doMethQTL                12.668  6.693  19.475
doMethQTLChromosome      10.663  5.014  15.749
computeCorrelationBlocks  6.908  3.141  10.115
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/MAGAR.Rcheck/00check.log’
for details.


Installation output

MAGAR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MAGAR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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
** 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)

Tests output

MAGAR.Rcheck/tests/runTests.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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, aperm, 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, 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 object is masked from 'package:utils':

    findMatches

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

    I, expand.grid, unname


Attaching package: 'S4Arrays'

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

    abind

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

    rowsum


Attaching package: 'DelayedArray'

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

    apply, 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")=="/tmp/RtmprrR0Um/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:S4Arrays':

    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 2.10-0 (2023-10-23) 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:SparseArray':

    rowMedians

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

    rowMedians

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

    anyMissing, rowMedians


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 1.5-9.10 	 2024-06-24
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 1.66.0

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 1.62.0

Attaching package: 'MAGAR'

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

    getResult

2024-07-12 00:13:51     1.1  STATUS STARTED Unit Testing
2024-07-12 00:13:51     1.1  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 
2024-07-12 00:13:52     1.1  STATUS     COMPLETED Testing constructors
2024-07-12 00:13:52     1.1  STATUS     STARTED Testing options
2024-07-12 00:13:52     1.1  STATUS     COMPLETED Testing options
2024-07-12 00:13:53     1.1  STATUS     STARTED Testing cor blocks
2024-07-12 00:13:53     1.1  STATUS         STARTED Compute correlation blocks
2024-07-12 00:13:53     1.1  STATUS             STARTED Compute correlation matrix
2024-07-12 00:13:54     1.1  STATUS             COMPLETED Compute correlation matrix
2024-07-12 00:13:54     1.1  STATUS             STARTED Compute pairwise distances
2024-07-12 00:13:56     1.1  STATUS             COMPLETED Compute pairwise distances
2024-07-12 00:13:58     1.1  STATUS             STARTED Weight distances
2024-07-12 00:13:58     1.1  STATUS             COMPLETED Weight distances
2024-07-12 00:14:00     1.1  STATUS             STARTED Compute graph
2024-07-12 00:14:00     1.1  STATUS             COMPLETED Compute graph
2024-07-12 00:14:00     1.1  STATUS             STARTED Compute clustering
2024-07-12 00:14:02     1.1  STATUS             COMPLETED Compute clustering
2024-07-12 00:14:02     1.1  STATUS         COMPLETED Compute correlation blocks
2024-07-12 00:14:03     1.1  STATUS     COMPLETED Testing cor blocks
2024-07-12 00:14:03     1.1  STATUS     STARTED Test methQTL calling
2024-07-12 00:14:03     1.1    INFO         Loading default option setting
2024-07-12 00:14:04     1.1  STATUS         STARTED Imputation procedure knn 
2024-07-12 00:14:04     1.1  STATUS         COMPLETED Imputation procedure knn 
2024-07-12 00:14:04     1.1  STATUS         STARTED Computing methQTLs
2024-07-12 00:14:05     1.1  STATUS             STARTED Computing methQTL for chromosome chr18
2024-07-12 00:14:05     1.1  STATUS                 STARTED Compute methQTL per correlation block
2024-07-12 00:14:05     1.1  STATUS                     STARTED Setting up Multicore
2024-07-12 00:14:06     1.1    INFO                         Using 1 cores
2024-07-12 00:14:06     1.1  STATUS                     COMPLETED Setting up Multicore
2024-07-12 00:14:07     1.1  STATUS                 COMPLETED Compute methQTL per correlation block
2024-07-12 00:14:07     1.1  STATUS             COMPLETED Computing methQTL for chromosome chr18
2024-07-12 00:14:09     1.1  STATUS         COMPLETED Computing methQTLs
2024-07-12 00:14:09     1.1  STATUS     COMPLETED Test methQTL calling
2024-07-12 00:14:09     1.1  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 
2024-07-12 00:14:10     1.1    INFO Loading default option setting
2024-07-12 00:14:10     1.1  STATUS STARTED Imputation procedure knn 
2024-07-12 00:14:10     1.1  STATUS COMPLETED Imputation procedure knn 

2024-07-12 00:14:11     1.1  STATUS STARTED Computing methQTLs
2024-07-12 00:14:11     1.1  STATUS     STARTED Computing methQTL for chromosome chr18
2024-07-12 00:14:11     1.1  STATUS         STARTED Compute methQTL per correlation block
2024-07-12 00:14:12     1.1  STATUS             STARTED Setting up Multicore
2024-07-12 00:14:12     1.1    INFO                 Using 1 cores
2024-07-12 00:14:12     1.1  STATUS             COMPLETED Setting up Multicore
2024-07-12 00:14:13     1.1  STATUS         COMPLETED Compute methQTL per correlation block
2024-07-12 00:14:13     1.1  STATUS     COMPLETED Computing methQTL for chromosome chr18
2024-07-12 00:14:15     1.1  STATUS COMPLETED Computing methQTLs

2024-07-12 00:14:15     1.1  STATUS STARTED Compute correlation blocks
2024-07-12 00:14:16     1.1  STATUS     STARTED Compute correlation matrix
2024-07-12 00:14:16     1.1  STATUS     COMPLETED Compute correlation matrix
2024-07-12 00:14:16     1.1  STATUS     STARTED Compute pairwise distances
2024-07-12 00:14:18     1.1  STATUS     COMPLETED Compute pairwise distances
2024-07-12 00:14:20     1.1  STATUS     STARTED Weight distances
2024-07-12 00:14:20     1.1  STATUS     COMPLETED Weight distances
2024-07-12 00:14:22     1.1  STATUS     STARTED Compute graph
2024-07-12 00:14:22     1.1  STATUS     COMPLETED Compute graph
2024-07-12 00:14:23     1.1  STATUS     STARTED Compute clustering
2024-07-12 00:14:24     1.1  STATUS     COMPLETED Compute clustering
2024-07-12 00:14:25     1.1  STATUS COMPLETED Compute correlation blocks



RUNIT TEST PROTOCOL -- Fri Jul 12 00:14:25 2024 
*********************************************** 
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 
> 
> proc.time()
   user  system elapsed 
 41.371  15.866  57.473 

Example timings

MAGAR.Rcheck/MAGAR-Ex.timings

nameusersystemelapsed
computeCorrelationBlocks 6.908 3.14110.115
doImport0.0460.0070.053
doMethQTL12.668 6.69319.475
doMethQTLChromosome10.663 5.01415.749
filterPval0.0340.0020.037
getAnno0.0820.0150.112
getCorrelationBlocks0.0360.0020.037
getGeno0.1060.0110.118
getMethData0.0680.0110.079
getOverlapUniverse0.0990.0020.101
getOverlappingQTL0.0290.0030.033
getPheno0.0480.0080.054
getResult0.0280.0020.029
getResultGWASMap0.0730.0090.084
getSamples0.0490.0080.057
getSpecificQTL0.0270.0020.029
imputeMeth0.2150.5060.728
joinMethQTLResult0.0820.0070.090
loadMethQTLInput0.0580.0080.066
loadMethQTLResult0.0270.0020.029
overlapInputs0.0480.0070.055
overlapQTLs0.0260.0020.028
qtlAnnotationEnrichment1.4690.0311.501
qtlBaseSubstitutionEnrichment0.0620.0010.063
qtlDistanceScatterplot0.5090.0050.513
qtlGetOption0.0000.0000.001
qtlJSON2options0.0010.0000.003
qtlManhattanPlot0.0460.0060.052
qtlOptions2JSON0.0020.0010.004
qtlPlotBaseSubstitution0.0700.0020.072
qtlPlotClusterSize0.2140.0060.221
qtlPlotSNPCpGInteraction0.2290.0180.248
qtlSetOption0.0010.0000.001
qtlTFBSMotifEnrichment0.0680.2440.315
qtlUpSetPlotCorBlocks1.3060.0141.322
qtlUpSetPlotTagCpGs0.4390.0040.443
qtlUpsetPlot0.6130.0060.619
qtlVennPlot0.1770.0480.228
saveMethQTLInput0.1430.0230.165
saveMethQTLResult0.1490.0040.153