Michael Scherer
| Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/MAGAR |
| git_branch: RELEASE_3_17 |
| git_last_commit: 4db8511 |
| git_last_commit_date: 2023-04-25 11:26:54 -0400 (Tue, 25 Apr 2023) |
| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:38:05 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| 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 1103/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MAGAR 1.8.0 (landing page) Michael Scherer
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the MAGAR package: - 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. |
| Package: MAGAR |
| Version: 1.8.0 |
| 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_1.8.0.tar.gz |
| StartedAt: 2023-10-18 04:26:24 -0400 (Wed, 18 Oct 2023) |
| EndedAt: 2023-10-18 04:39:14 -0400 (Wed, 18 Oct 2023) |
| EllapsedTime: 770.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: MAGAR.Rcheck |
| Warnings: 0 |
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### Running command:
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### /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_1.8.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/MAGAR.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MAGAR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MAGAR’ version ‘1.8.0’
* 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 ... 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 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
doMethQTL 11.441 3.569 20.016
doMethQTLChromosome 9.868 2.658 18.550
computeCorrelationBlocks 4.725 1.662 9.258
* 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
‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/MAGAR.Rcheck/00check.log’
for details.
MAGAR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MAGAR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-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)
MAGAR.Rcheck/tests/runTests.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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, 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, 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 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/RtmpTYQPJ2/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 2.9-1 (2022-08-07) 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 1.5-9.8 2023-06-11
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
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rename
The following object is masked from 'package:matrixStats':
count
Welcome to oligoClasses version 1.62.0
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 1.58.0
Attaching package: 'MAGAR'
The following object is masked from 'package:foreach':
getResult
2023-10-18 04:38:27 1.0 STATUS STARTED Unit Testing
2023-10-18 04:38:27 1.0 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
2023-10-18 04:38:27 1.0 STATUS COMPLETED Testing constructors
2023-10-18 04:38:28 1.0 STATUS STARTED Testing options
2023-10-18 04:38:28 1.0 STATUS COMPLETED Testing options
2023-10-18 04:38:28 1.0 STATUS STARTED Testing cor blocks
2023-10-18 04:38:29 1.0 STATUS STARTED Compute correlation blocks
2023-10-18 04:38:29 1.0 STATUS STARTED Compute correlation matrix
2023-10-18 04:38:29 1.0 STATUS COMPLETED Compute correlation matrix
2023-10-18 04:38:30 1.0 STATUS STARTED Compute pairwise distances
2023-10-18 04:38:31 1.0 STATUS COMPLETED Compute pairwise distances
2023-10-18 04:38:33 1.0 STATUS STARTED Weight distances
2023-10-18 04:38:33 1.0 STATUS COMPLETED Weight distances
2023-10-18 04:38:35 1.0 STATUS STARTED Compute graph
2023-10-18 04:38:35 1.0 STATUS COMPLETED Compute graph
2023-10-18 04:38:35 1.0 STATUS STARTED Compute clustering
2023-10-18 04:38:37 1.0 STATUS COMPLETED Compute clustering
2023-10-18 04:38:37 1.0 STATUS COMPLETED Compute correlation blocks
2023-10-18 04:38:37 1.0 STATUS COMPLETED Testing cor blocks
2023-10-18 04:38:38 1.0 STATUS STARTED Test methQTL calling
2023-10-18 04:38:38 1.0 INFO Loading default option setting
2023-10-18 04:38:38 1.0 STATUS STARTED Imputation procedure knn
2023-10-18 04:38:39 1.0 STATUS COMPLETED Imputation procedure knn
2023-10-18 04:38:39 1.0 STATUS STARTED Computing methQTLs
2023-10-18 04:38:39 1.0 STATUS STARTED Computing methQTL for chromosome chr18
2023-10-18 04:38:39 1.0 STATUS STARTED Compute methQTL per correlation block
2023-10-18 04:38:40 1.0 STATUS STARTED Setting up Multicore
2023-10-18 04:38:40 1.0 INFO Using 1 cores
2023-10-18 04:38:40 1.0 STATUS COMPLETED Setting up Multicore
2023-10-18 04:38:41 1.0 STATUS COMPLETED Compute methQTL per correlation block
2023-10-18 04:38:41 1.0 STATUS COMPLETED Computing methQTL for chromosome chr18
2023-10-18 04:38:43 1.0 STATUS COMPLETED Computing methQTLs
2023-10-18 04:38:43 1.0 STATUS COMPLETED Test methQTL calling
2023-10-18 04:38:43 1.0 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
2023-10-18 04:38:44 1.0 INFO Loading default option setting
2023-10-18 04:38:44 1.0 STATUS STARTED Imputation procedure knn
2023-10-18 04:38:44 1.0 STATUS COMPLETED Imputation procedure knn
2023-10-18 04:38:45 1.0 STATUS STARTED Computing methQTLs
2023-10-18 04:38:45 1.0 STATUS STARTED Computing methQTL for chromosome chr18
2023-10-18 04:38:45 1.0 STATUS STARTED Compute methQTL per correlation block
2023-10-18 04:38:45 1.0 STATUS STARTED Setting up Multicore
2023-10-18 04:38:46 1.0 INFO Using 1 cores
2023-10-18 04:38:46 1.0 STATUS COMPLETED Setting up Multicore
2023-10-18 04:38:47 1.1 STATUS COMPLETED Compute methQTL per correlation block
2023-10-18 04:38:47 1.1 STATUS COMPLETED Computing methQTL for chromosome chr18
2023-10-18 04:38:49 1.1 STATUS COMPLETED Computing methQTLs
2023-10-18 04:38:49 1.1 STATUS STARTED Compute correlation blocks
2023-10-18 04:38:49 1.1 STATUS STARTED Compute correlation matrix
2023-10-18 04:38:50 1.1 STATUS COMPLETED Compute correlation matrix
2023-10-18 04:38:50 1.1 STATUS STARTED Compute pairwise distances
2023-10-18 04:38:52 1.1 STATUS COMPLETED Compute pairwise distances
2023-10-18 04:38:53 1.1 STATUS STARTED Weight distances
2023-10-18 04:38:54 1.1 STATUS COMPLETED Weight distances
2023-10-18 04:38:55 1.1 STATUS STARTED Compute graph
2023-10-18 04:38:56 1.1 STATUS COMPLETED Compute graph
2023-10-18 04:38:56 1.1 STATUS STARTED Compute clustering
2023-10-18 04:38:58 1.1 STATUS COMPLETED Compute clustering
2023-10-18 04:38:58 1.1 STATUS COMPLETED Compute correlation blocks
RUNIT TEST PROTOCOL -- Wed Oct 18 04:38:58 2023
***********************************************
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
35.200 9.048 66.386
MAGAR.Rcheck/MAGAR-Ex.timings
| name | user | system | elapsed | |
| computeCorrelationBlocks | 4.725 | 1.662 | 9.258 | |
| doImport | 0.060 | 0.008 | 0.095 | |
| doMethQTL | 11.441 | 3.569 | 20.016 | |
| doMethQTLChromosome | 9.868 | 2.658 | 18.550 | |
| filterPval | 0.022 | 0.003 | 0.043 | |
| getAnno | 0.092 | 0.015 | 0.167 | |
| getCorrelationBlocks | 0.029 | 0.002 | 0.048 | |
| getGeno | 0.115 | 0.015 | 0.202 | |
| getMethData | 0.089 | 0.014 | 0.159 | |
| getOverlapUniverse | 0.131 | 0.003 | 0.206 | |
| getOverlappingQTL | 0.022 | 0.002 | 0.035 | |
| getPheno | 0.058 | 0.009 | 0.093 | |
| getResult | 0.021 | 0.003 | 0.032 | |
| getResultGWASMap | 0.080 | 0.011 | 0.136 | |
| getSamples | 0.057 | 0.009 | 0.099 | |
| getSpecificQTL | 0.020 | 0.002 | 0.036 | |
| imputeMeth | 0.219 | 0.286 | 0.761 | |
| joinMethQTLResult | 0.066 | 0.004 | 0.109 | |
| loadMethQTLInput | 0.058 | 0.008 | 0.100 | |
| loadMethQTLResult | 0.019 | 0.002 | 0.028 | |
| overlapInputs | 0.060 | 0.008 | 0.099 | |
| overlapQTLs | 0.019 | 0.001 | 0.032 | |
| qtlAnnotationEnrichment | 1.113 | 0.048 | 1.759 | |
| qtlBaseSubstitutionEnrichment | 0.068 | 0.004 | 0.111 | |
| qtlDistanceScatterplot | 0.577 | 0.014 | 0.894 | |
| qtlGetOption | 0.000 | 0.000 | 0.001 | |
| qtlJSON2options | 0.002 | 0.001 | 0.004 | |
| qtlManhattanPlot | 0.038 | 0.006 | 0.067 | |
| qtlOptions2JSON | 0.002 | 0.001 | 0.006 | |
| qtlPlotBaseSubstitution | 0.073 | 0.002 | 0.117 | |
| qtlPlotClusterSize | 0.251 | 0.006 | 0.395 | |
| qtlPlotSNPCpGInteraction | 0.263 | 0.020 | 0.439 | |
| qtlSetOption | 0 | 0 | 0 | |
| qtlTFBSMotifEnrichment | 0.035 | 0.130 | 0.243 | |
| qtlUpSetPlotCorBlocks | 1.460 | 0.020 | 2.196 | |
| qtlUpSetPlotTagCpGs | 0.523 | 0.009 | 0.786 | |
| qtlUpsetPlot | 0.533 | 0.010 | 0.821 | |
| qtlVennPlot | 0.133 | 0.174 | 0.499 | |
| saveMethQTLInput | 0.218 | 0.030 | 0.352 | |
| saveMethQTLResult | 0.117 | 0.007 | 0.195 | |